Interferon Antagonism of SARS-CoV-2

It has become clear that the type 1 interferon responses to SARS-CoV-2 have a great deal to do with the outcome of infection. Patients with benign courses of infection yield high levels of expression of interferon-α (IFNα), while critical cases of COVID-19 show low levels of its expression. Paradoxically, in severe disease, expression of INF receptors is elevated, while expression of INF sensitive genes is depressed, suggesting that things are awry downstream from the receptors. It is not clear if this is because of the activity of virally encoded gene products or the lack of adequate INF-α or both. Variants of genes involved in INF activity have been identified in severe cases of Covid-19 patients. And the virus seems to have multiple proteins that are able to antagonize aspects of INF signaling. We will consider these points separately.

Coronavirus infections in general appear to involve perturbations in INF activities. A good overview of the role of INF in coronavirus infections shows some of the involved signaling pathways(1). Innate immunity is abnormal in severe disease. Early expression of INF-α appears to correlate with a favorable outcome in controlling SARS-CoV-2 infection, whereas INF-β expression appears to be negligible(2). While mild infections are correlated with continued high levels of expression of INF-α, severe disease is marked by low levels of INF-α expression(2). In contrast, inflammatory cytokine expression, as evidenced by IL-6 and TNFα, is high. Although INF-α and inflammatory cytokines are both part of innate immunity, the former is regulated by the transcription factors IRF3 and 7, while the latter are regulated by NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells), a protein complex controlling transcription of DNA, cytokine production and cell survival. This suggests that NF-κB signaling is relatively unperturbed by the virus. Thus, its IFN perturbation could be important for antagonizing host defense system.

Some clues as to which factors involved in regulating INF activities may be affected in Covid-19 have been learned by whole exome sequencing of patients with severe disease genomes, particularly those that lack obvious risk factors. In light of this, it is instructive to look at a study of two pairs of young adult brothers, one pair from the Netherlands and the other from West Africa, who had severe Covid-19 (one died)(3). The pairs each had different loss-of-function mutations in TLR7, an intracellular receptor for viral RNA. Primary mononuclear cells showed downregulation of downstream INF signaling, including that of IRF7. The genes are X-linked; this means that men who inherit the defective gene are at greater risk than females, who would need to be homozygous for risk. While loss of function mutations in TLR7 are rare, so is severe Covid-19 in young people, and the congruency of these two rare phenomena is telling. Another study showed loss of function variants in 3.5% (out of 659) of severely ill patients of 13 genes involved in TLR3 and IRF7-dependent INF activities(4). Cells with IRF7 variants produced no type 1 IFN when infected in vitro with SARS-CoV-2.

There is also a report that some patients with severe Covid-19 have neutralizing autoantibodies to IFN-α, -ω, or both(5). These were present in 101 of 987 patients with life threatening disease but in none of the 663 patients with mild or asymptomatic infection. The autoantibodies existed prior to infection.  Oddly, most of the patients with autoantibodies were male, whereas generally women have a higher incidence of autoimmunity. This suggests an X-linked genetic basis.

The above studies (and others for which space constraints preclude detailed consideration) point to a failure of INF-related activities as a critical risk factor for the development of severe Covid-19 and suggest that INF represents a potentially serious block to replication of SARS-CoV-2. We might then ask how the virus deals with this problem.

It appears that the virus encodes a number proteins that potentially antagonize cellular signaling pathways involved in INF activity. As a convenient reference to the proteins encoded by SARS-CoV2, we commend you to a website maintained by the Zhang lab at the University of Michigan (https://zhanglab.ccmb.med.umich.edu/COVID-19/).  Several studies have shown an effect on IFN activity in vitro(6-10), but these should be interpreted with caution as they use artificially high levels of viral gene expression. In fact, it is not clear at what levels these proteins are expressed in vivo. Moreover, these studies do not completely agree on which are the most relevant viral proteins.

Yuen et al.(10) transfected expression constructs for 27 different genes for their ability to inhibit RIG-I-dependent induction of an IFN-β promoter. RIG-I (retinoic acid-inducible gene I) is a cytosolic pattern recognition receptor (PRR) responsible for the type 1 interferon (IFN1) response. They found that four viral proteins (nsp13, 14 and 15 and orf6) were strongly inhibitory. However,  the papain-like protease (PLpro) of SARS-CoV-2 was not an inhibitor, even though the SARS-CoV-1 PLpro is known to inhibit type I IFN by inhibiting IRF3 phosphorylation, thus blocking downstream Interferon induction. This suggests interference with activities downstream from RIG-I. Orf6 also inhibited IFN α-2, β, and λ secretion induced by Sendai virus infection. Using similar methodology, Lei et al.(7) found similar activities with nsp1, 3, 12, 13 and 14, ORFs 3 and 6, and the membrane (M) protein leading to RIG I or MDA5 activation. In contrast, ORF6 overexpression inhibited nuclear translocation of STAT1, which is required for IFN-stimulated gene expression. Li et al.(8) looked at the ability of selected viral proteins to inhibit Sendai virus-induced IFN activity. ORF 6 strongly inhibited the activity of IFN-β, interferon-sensitive response element (ISRE), and NF-κB promoters, as assessed by reporter gene activity. ORF8 and the nucleocapsid protein (N) showed less dramatic inhibitory activity. ISRE related activity was inhibited less markedly by ORF6 when cells were stimulated by IFN-β. From the above studies, there appears to be general agreement that ORF6 is a critical component of IFN antagonism by SARS-CoV-2 infection, with the caveat that the studies all involve overexpression.

Liu et al.(9) show that PLpro has IFN antagonistic activity, but by a different mechanism than those reported above. ISG15 is a multi-function protein that serves as a cytokine but also as a ubiquitin-like intracellular protein conjugate. ISGylation activates the viral RNA sensor MDA5, which is involved in IFN activity. MDA5 activity is antagonized by removal of ISG moieties by PLpro, thus inhibiting IFN expression.

Konno et al.(6) reported that ORF3b, a 22 amino acid protein that is truncated by introduction of a stop codon, antagonizes IFN activity. This is contradictory to SARS-COV-1 homolog. In spite of its small size, ORF3b suppressed Sendai virus-mediated stimulation of the IFNβ1 promoter more strongly than did the larger size of SARS-CoV-1 protein. Interestingly, there are naturally occurring SARS-CoV2 variants in which the full length ORF3b is restored; these are even more strongly inhibitory than is the truncated version.

The above presents a complicated picture that nonetheless points to the importance of type 1 INF in the outcome of Covid-19. A wide variety of data point to defects in the host IFN response that are correlative with severe disease. According to in vitro studies of the viral proteins (with the caveats inherent from the use of overexpression systems), the virus mounts multifactorial defenses against IFN antiviral activities, with ORF6 and PLpro (and perhaps ORF3b) being prime candidates. Hopefully, future in vivo studies will bring more clarity. Overall these studies point to type 1 IFN-signaling as a potential important therapeutic target.

 

References

 

  1. A. Park, A. Iwasaki, Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19. Cell Host Microbe 27, 870-878 (2020).
  2. J. Hadjadj et al., Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients. Science 369, 718-724 (2020).
  3. C. I. van der Made et al., Presence of Genetic Variants Among Young Men With Severe COVID-19. JAMA 324, 663-673 (2020).
  4. Q. Zhang et al., Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science, (2020).
  5. P. Bastard et al., Auto-antibodies against type I IFNs in patients with life-threatening COVID-19. Science, (2020).
  6. Y. Konno et al., SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant. Cell Rep 32, 108185 (2020).
  7. X. Lei et al., Activation and evasion of type I interferon responses by SARS-CoV-2. Nat Commun 11, 3810 (2020).
  8. J. Y. Li et al., The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res 286, 198074 (2020).
  9. G. Liu et al., ISG15-dependent Activation of the RNA Sensor MDA5 and its Antagonism by the SARS-CoV-2 papain-like protease. bioRxiv, (2020).
  10. C. K. Yuen et al., SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerg Microbes Infect 9, 1418-1428 (2020).

Progress in the Treatments of COVID-19

Since the beginning of the COVID-19 pandemic, extensive research has focused on therapeutics. A combinational approach of traditional drug development and drug repurposing is necessary to make progress in treating and preventing COVID-19 in a timely manner. While developing new drugs is critical, repurposing existing molecules has been a major strategy. In the early stages of the COVID-19 pandemic, Remdesivir has been identified as a promising repurposing drug to treat COVID-19 patients (1). Indeed, it became the first treatment for COVID-19 to receive the U.S. Food and Drug Administration (FDA)’s Emergency Use Authorization (EUA) (2). Recently, the FDA issued an EUA for three more treatments. In this perspective, we will review these available treatments based on the findings of clinical trials. In addition, we are updating other COVID-19 therapeutics according to recent publications.

Remdesivir is an intravenous nucleotide prodrug of an adenosine analog and is recognized as an antiviral drug against various RNA viruses (3). It binds to the viral RNA-dependent RNA polymerase and incorporates into nascent viral RNA chains. This results in pre-mature termination of RNA transcription and inhibiting viral replication. The FDA approved remdesivir (Veklury) for use in adult and pediatric patients 12 years of age and older and weighing at least 40 kilograms (about 88 pounds) for the treatment of COVID-19 requiring hospitalization (2). In a recently published report, a double-blind, randomized, placebo-controlled trial of intravenous remdesivir was conducted with hospitalized adults having lower respiratory tract infection (4). A total of 1062 patients underwent randomization (with 541 assigned to remdesivir and 521 to placebo). The reported clinical effect of intravenous remdesivir was very modest. The recovery time was significantly shorter among patients who received remdesivir than among those who received placebo (10 days vs. 15 days). A trend toward lower mortality was observed among patients who received remdesivir than among those who received placebo, both at day 15 (6.7% vs. 11.9%) and at day 29 (11.4% vs. 15.2%), but the differences were not statistically significant. Therefore, the primary outcome was the time to recovery. In fact, WHO has issued a conditional recommendation against the use of remdesivir in hospitalized patients, regardless of disease severity (5). Consistent with this, in a huge WHO sponsored clinical study, remdesivir treatment did not improve mortality for hospitalized COVID-19 patients (6). This trial was conducted in 405 hospitals in 30 countries. A total of 11,266 adults were randomized, with 2750 allocated remdesivir, 954 hydroxychloroquine, 1411 lopinavir, 651 interferon plus lopinavir, 1412 interferon only, and 4088 no study drug. Interestingly, this study concluded that remdesivir, hydroxychloroquine, lopinavir and interferon regimens appeared to have little or no effect on hospitalized COVID-19, as indicated by overall mortality, initiation of ventilation and duration of hospital stay.

The pathogenesis of SARS-CoV-2 involves not only viral replication, but also immunomodulation and inflammation (7). Therefore, a combination therapy of remdesivir with other antivirals or antiinflammatory agents could enhance its efficacy. On November 19, 2020, the FDA authorized a combination of remdesivir (Veklury) and the JAK (Janus kinase) inhibitor, baricitinib (Olumiant) for the treatment of suspected or laboratory confirmed COVID-19 in hospitalized adults and pediatric patients 2 years of age or older requiring supplemental oxygen, invasive mechanical ventilation. This approval is based on data from the Adaptive COVID-19 Treatment Trial (ACTT-2), a randomized double-blind, placebo-controlled study to evaluate the efficacy and safety of baricitinib in combination with remdesivir versus placebo with remdesivir in hospitalized patients with or without oxygen requirements (8). The recommended dose for this approval is baricitinib 4-mg once daily for 14 days or until hospital discharge. Baricitinib has been already approved to treat moderate to severe rheumatoid arthritis. Baricitinib, taken orally, inhibits cytokine signaling in the body that play roles in causing inflammatory responses. Rational of this clinical study is that adding an anti-inflammatory agent to the remdesivir treatment can provide additional benefit for patients, including improving mortality outcomes (8). The putative benefit of baricitinib for COVID-19 has been described in a case series of critically ill patients who recovered from COVID-19. The data from this clinical study have not been published yet. It has been suggested that patients treated with baricitinib in combination with remdesivir had a significant reduction in median time to recovery from 8 to 7 days (12.5% improvement) compared to remdesivir (9). The proportion of patients who progressed to ventilation (non-invasive or invasive) or died by Day 29 was lower in baricitinib in combination with remdesivir (23%) compared to remdesivir (28%). The proportion of patients who died by Day 29 was 4.7% for baricitinib in combination with remdesivir vs. 7.1% for remdesivir. However, the safety of this treatment needs to be validated.

In November 9, 2020, the FDA approved investigational monoclonal antibody therapy bamlanivimab for the treatment of mild-to-moderate COVID-19 in adult and pediatric patients (10). Bamlanivimab is authorized for the treatment of nonhospitalized patients with mild to moderate COVID-19 who are at high risk for progressing to severe disease and/or hospitalization This includes those who are 65 years of age or older, or who have certain chronic medical conditions. The approval is based on data from BLAZE-1, a randomized, double-blind, placebo-controlled Phase 2 study in patients with recently diagnosed mild to moderate COVID-19 in the outpatient setting (11). It is not authorized for patients who are hospitalized due to COVID-19 or require oxygen therapy due to COVID-19. Bamlanivimab (Lily)also known as LY-CoV555 and LY3819253) is a neutralizing monoclonal antibody that targets the receptor-binding domain of the spike protein of SARS-CoV-2. Because this drug may block SARS-CoV-2 entry into host cells, it is being evaluated for the treatment of COVID-19. This trial randomly assigned 452 patients to receive a single intravenous infusion of neutralizing antibody LY-CoV555 in one of three doses (700 mg, 2800 mg, or 7000 mg) or placebo (12). After undergoing randomization, patients received an infusion of LY-CoV555 or placebo within a median of 4 days after the onset of symptoms. The viral load at day 11 (the primary outcome) was lower than that in the placebo group only among those who received the 2800-mg dose. However, the evaluation of the effect of LY-CoV555 therapy on patients’ symptoms at earlier time points during treatment (e.g., on day 3) showed a possible treatment effect, with no substantial differences observed among the three doses. While the safety and effectiveness of this investigational therapy continues to be evaluated, bamlanivimab was shown in this trial to reduce COVID-19-related hospitalization or emergency room visits in patients at high risk for disease progression within 28 days after treatment when compared to placebo. For patients at high risk for disease progression, hospitalizations and emergency room visits occurred in 3% of bamlanivimab-treated patients on average compared to 10% in placebo-treated patients. However, a benefit of bamlanivimab treatment has not been shown in patients hospitalized due to COVID-19. Monoclonal antibodies, such as bamlanivimab, may be associated with worse clinical outcomes when administered to hospitalized patients with COVID-19 requiring high flow oxygen or mechanical ventilation (10).

In November 21, 2020, the FDA approved monoclonal antibodies, casirivimab and imdevimab (Regeneron) to be administered together by intravenous infusion for the treatment of mild to moderate COVID-19 in adults and pediatric patients (12 years of age or older weighing at least 40 kilograms) with positive results of direct SARS-CoV-2 viral testing and who are at high risk for progressing to severe COVID-19 (13). This includes those who are 65 years of age or older or who have certain chronic medical conditions. However, this treatment is not authorized for patients who are hospitalized due to COVID-19 or require oxygen therapy due to COVID-19. These monoclonal antibodies are specifically directed against the spike protein of SARS-CoV-2, designed to block the virus’ attachment and entry into human cells. This approval is based on a randomized, double-blind, placebo-controlled clinical trial in 799 non-hospitalized adults with mild to moderate COVID-19 symptoms. Of these patients, 266 received a cocktail of casirivimab and imdevimab (1,200 mg each), 267 received a cocktail of casirivimab and imdevimab (4,000 mg each), and 266 received a placebo intravenously, within three days of obtaining a positive SARS-CoV-2 test. Viral load reduction in patients treated with casirivimab and imdevimab was larger than in patients treated with placebo at day seven. Further, for patients at high risk for disease progression, hospitalizations and emergency room visits occurred in 3% of casirivimab and imdevimab-treated patients on average compared to 9% in placebo-treated patients. The findings of this study have not been published in a peer-reviewed journal yet. The safety and effectiveness of this investigational therapy for use in the treatment of COVID-19 continues to be evaluated.

As an experimental monoclonal antibody treatment, two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) were isolated and characterized for their potential use as a prophylaxis or therapy (14). Cryo–electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment. Furthermore, S2M11 is a distinct class of potent neutralizers of SARS-CoV-2 by additionally locking the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Combinations of monoclonal antibodies leveraging multiple distinct mechanisms of action with additive or synergistic effects could provide additional benefits for clinical application. Indeed, using cocktail of these antibodies enhanced antibody responses to SARS-CoV-2 S and conferred significant protection in hamster models. The mAb cocktails are also expected to take advantage of both ultrapotent neutralization, different mechanisms of action, and Fc-mediated effector functions to protect from a broad spectrum of circulating SARSCoV-2 isolates. The findings of this study also has important implication in implementing antibody cocktails for circumventing or limiting the emergence of viral escape mutants.

Ivermectin is an FDA-approved broad-spectrum antiparasitic agent with demonstrated antiviral activity against a number of DNA and RNA viruses, including SARS-CoV-2 (15). The inhibition of importin α/β1-mediated nuclear import of viral proteins is suggested as the probable mechanism underlying its antiviral activity. In addition, ivermectin could ultimately induce an ionic imbalance that disrupts the potential of the viral membrane, thereby threatening its integrity and functionality.  A recent study showed that a single dose of ivermectin was able to reduce the replication of an Australian isolate of SARS-CoV-2 in Vero/hSLAM cells by 5000-fold (16). In addition to the indication for antiviral therapy, anti-inflammatory intervention may also be necessary to prevent acute lung injury in SARS-CoV-2 infection. With regard to its anti-inflammatory properties, ivermectin have been shown to mitigate skin inflammation. A study evaluating the ability of ivermectin to inhibit lipopolysaccharide (LPS)-induced inflammation revealed significantly decreased production of TNF-alpha, IL-1ss and IL-6 in vivo and in vitro. Further studies may establish the role of ivermectin in inflammatory response caused by SARS-CoV-2. A number of clinical studies are being conducted in various countries. The data from these studies are not available yet. However, it has been suggested that the necessary inhibitory concentration may only be achieved via high dosage regimes in humans. Further, safety of using high-dose antiviral therapy needs to be evaluated. Currently, no commercially available injectable forms of ivermectin are available for human use. The development of ivermectin formulations presents challenges, primarily due to its property of poor water solubility. Novel delivery strategies are needed to optimize ivermectin bioavailability. Furthermore, efficacy of ivermectin for COVID-19 treatment needs to be defined with extensive in vivo study and clinical trials.

Lastly, antiparasitic drug nitazoxanide is widely available and exerts broad-spectrum antiviral activity in vitro. For its use for treatment of mild COVID-19 patients, randomized, double-blind, placebo-controlled was conducted in a multicenter (17). In patients with mild Covid-19, symptom resolution did not differ between the nitazoxanide and placebo groups after 5 days of therapy. However, at the 1-week follow-up, 78% in the nitazoxanide group and 57% in the placebo group reported complete resolution of symptoms. Further, viral load was also reduced after nitazoxanide treatment compared to placebo. This study showed only partially analyzed data from the clinical trials. Complete analysis of this study will be required to clearly assess the efficacy of nitazoxanide for the treatment.

Reinforcing the efficacy of drug repurposing can provide much shorter and less costly development process than developing a new drug. Yet, we have to recognize that beside the very modest activity of remdesivir nothing has so far emerged from these efforts. In fact, patients with respiratory symptoms due to COVID-19 are still best treated by combining the vintage steroids combined with oxygen and anticoagulants.  On the other hand, the monoclonal antibody-based treatments have now become available for people in high-risk groups and seem to be effective early in the course of the disease; yet there is a limitation in the production capacity of such therapies and their cost must not be a barrier to get them widely available in low- and middle-income countries. In general, a combination of two to three different therapeutic agents for the treatment has become a common approach. Finally, treatment which might potentially prevent infection (such as Nitazoxanide, Romark LLC) are being evaluated. Overall, despite many difficulties, there is now hope that innovative and cost-effective therapeutic agents can be effectively developed.

 

References

  1. Wang M, Cao R, Zhang L, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30(3):269-271. Available at: https://www.ncbi.nlm.nih.gov/pubmed/32020029.
  2. Food and Drug Administration. FDA Approves First Treatment for COVID-19. 2020. Available at: https://www.fda.gov/news-events/press-announcements/fda-approves-first-treatment-covid-19.
  3. Warren TK, et al. Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature. 2016;531:381–385. doi: 10.1038/nature17180.
  4. Beigel JH, Tomashek KM, Dodd LE, et al. Remdesivir for the treatment of Covid-19 — final report. N Engl J Med 2020;383:1813-1826.
  5. World Health Organization. WHO recommends against the use of remdesivir in COVID-19 patients. Available at: https://www.who.int/news-room/feature-stories/detail/who-recommends-against-the-use-of-remdesivir-in-covid-19-patients.
  6. WHO Solidarity Trial Consortium. Repurposed antiviral drugs for covid-19—interim WHO Solidarity trial results. 15 Oct 2020. doi:10.1101/2020.10.15.20209817.
  7. Mehta P, McAuley DF, Brown M, Sanchez E, Tattersall RS, Manson JJ. COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet 2020;395:1033-1034.
  8. National Institute of Health. NIH clinical trial testing antiviral remdesivir plus anti-inflammatory drug baricitinib for COVID-19 begins. Available at: https://www.nih.gov/news-events/news-releases/nih-clinical-trial-testing-antiviral-remdesivir-plus-anti-inflammatory-drug-baricitinib-covid-19-begins.
  9. Lilly. Baricitinib Receives Emergency Use Authorization from the FDA for the Treatment of Hospitalized Patients with COVID-19. Available at: https://investor.lilly.com/news-releases/news-release-details/baricitinib-receives-emergency-use-authorization-fda-treatment
  10. Food and Drug Administration. Fact sheet for healthcare providers: emergency use authorization (EUA) of bamlanivimab. 2020. Available at: https://www.fda.gov/media/143603/download.
  11. Lilly. Lilly’s neutralizing antibody bamlanivimab (LY-CoV555) receives FDA emergency use authorization for the treatment of recently diagnosed COVID-19. Available at: https://investor.lilly.com/news-releases/news-release-details/lillys-neutralizing-antibody-bamlanivimab-ly-cov555-receives-fda.
  12. Chen P, Nirula A, Heller B, et al. SARS-CoV-2 neutralizing antibody LY-CoV555 in outpatients with COVID-19. N Engl J Med. 2020; Available at: https://www.ncbi.nlm.nih.gov/pubmed/33113295.
  13. Food and Drug Administration Coronavirus (COVID-19) Update: FDA Authorizes Monoclonal Antibodies for Treatment of COVID-19. Available at: https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-monoclonal-antibodies-treatment-covid-19.
  14. M. ALEJANDRA TORTORICI et al., A potent antibody cocktail blocks attachment of SARS-CoV-2 to the host receptor and activates a protective immune response. SCIENCE20 NOV 2020 : 950-957.
  15. Fabio Rocha Formiga, Roger Leblanc, Juliana de Souza Rebouças, Leonardo Paiva Farias, Ronaldo Nascimento de Oliveira, Lindomar Pena, Ivermectin: an award-winning drug with expected antiviral activity against COVID-19, Journal of Controlled Release, 2020, https://doi.org/10.1016/j.jconrel.2020.10.009.
  16. L. Caly, J.D. Druce, M.G. Catton, D.A. Jans, K.M. Wagstaff. The FDA-approved drug Ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antivir. Res., 178 (2020), p. 104787, 10.1016/j.antiviral.2020.104787.
  17. Patricia R. M. Rocco et al. Early use of nitazoxanide in mild Covid-19 disease: randomized, placebocontrolled trial. medRxiv preprint doi: https://doi.org/10.1101/2020.10.21.20217208.

Rapid and Frequent Testing for COVID-19

The cases of new SARS-CoV-2 infections are currently increasing at an alarming rate, suggesting that winter might bring a large healthcare crisis. Diagnostics have become a critical tool in curbing COVID-19. It is important that accurate results be obtained rapidly and that collection of samples be as fast, simple, and convenient as possible.

What tests are becoming available, which promise better accuracy and greater speed and ease of use?  Thus far, testing has been based on a real-time reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 RNA detection and serology on enzyme-linked immunosorbent assay (ELISA) for antibody tests. Yet, PCR can show false positives due to detection of fragmented RNA of virus. This has been an obstacle in determining the presence of infectious virus particles in COVID-19 patients. A recent study showed that the presence of infectious virus may be predictable by evaluating the threshold cycle (Ct value, the number of cycles of PCR amplification) (1).  Now, there are also a variety of novel tests for SARS-CoV-2 RNA detection in development that rely on CRISPR12 or 13 cleavage of SARS-CoV-2 amplified RNA, which releases a visually readable fluorescent chromophore. These rely on isothermal amplification, either LAMP(7) or recombinase polymerase amplification (RPA)(8-10), which does not require a thermal cycler. These test all have rapid turnaround times (on the order of an hour) and sensitivities that can be well comparable with other tests. One of these tests can use a cheap chemical hand warmer as the thermal source(9). Another similar CRISPR based assay can simultaneously detect and identify 169 different human viruses(11), illustrating the potential utility and efficiency of this system. These tests all have advantages of speedy detection and user-friendly application over RT-PCR.

Serological testing is also necessary. The presence of antibodies marks an ongoing or past infection, and anti-spike protein and neutralizing antibodies are considered a possible indication of immunity, although T cell activities are also contributing to protective immunity. Antibody tests can indicate past infections but are prone to be false positive in low frequency settings and have provided a difficulty with uneven results because of wide variations in test kit quality. What serological tests are likely to be most useful? As with RNA tests, this requires sensitivity, specificity, speed, and user-friendly application.

One consideration for serological tests is that there is some degree of serologic cross-reactivity of SARS-CoV-2 proteins with those of the other coronaviruses, especially SARS-CoV-1(12). It is also possible that the S2 spike domain of SARS-CoV-2  may also have some degree of cross-reactivity with that of other human coronavirus (13). Interestingly, some of these cross-reactive antibodies also appear to cross-neutralize, suggesting that there may exist conserved epitopes for the development of a broadly effective vaccine.

Most point-of care serologic assays rely in lateral flow-type assays, in which the results are read as bands on a strip and indicate the presence of IgG and/or IgM antibodies. The regulatory processes for these tests has perhaps lacked some of the usual rigor, and their accuracy tends to vary. This can be a problem in low incidence settings, where false positives are an issue. Fortunately, a recently published  study carefully compared five different test kits to ELISA and viral neutralization tests(14). As might be expected, antibodies were more readily detected when sera were collected more than 14 days after symptom onset. Using samples collected from this time period, three lateral flow tests for IgG were comparable to ELISA, but the other two kits were inferior. Prior to 14 days post symptoms, sensitivity was only on the order of 50-60% by any test. It is clear that serological tests are mostly retrospective in nature. They are useful for diagnosing past infections and viral prevalence in populations, and will be very important in evaluating vaccine durability.

In this last aspect, it would be extremely convenient to have a neutralization assay that does not involve live virus, with its attendant requirement for biosafety level 3 containment. One of the studies is based upon inhibition of binding of the receptor binding domain (RBD) of the S protein to immobilized ACE2 protein (15). The results are read colorimetrically and are near 100% sensitive and specific. An advantage of this test is that it would measure neutralization by IgA, IgM, and IgG all at the same time, increase sensitivity. This type of test will obviously be highly useful as vaccines begin to be widely deployed.

Regarding the sampling procedures, we are still using taking nasal swabs; this is a sensitive method but is prone to be false negatives due to poor sampling. Saliva is clearly far simpler to collect than nasal swabs or blood. How do tests of saliva compare with those of nasal swabs and blood?  For RNA detection by RT-PCR, tests of saliva appear to have at least comparable sensitivity to those of nasal swabs(2-4), representing a considerable simplification of testing. Potentially better is RNA detection in saliva using loop-mediated isothermal amplification (LAMP), which avoids the necessity for thermal cycler instrumentation and for RNA purification. Results appear to be equally sensitive and specific to those from RT-PCR(5). Another isothermal method that is fully automated with less sensitivity, delivers results on a dipstick in 90 minutes(6). What about antibodies in saliva? Saliva is much easier to collect. It appears that antibodies are as detectable in saliva as in serum. It’s been shown that viral antibodies persist in saliva for months(16). Another study showed persistent IgG activity against both N protein and the RBD of the S protein(17). The anti-N antibody showed 100% of sensitivity and the RBD antibody 100% specificity. Thus, a multiplexed assay should be 100% accurate.

We are heading into a period of perhaps explosive increases in rates of infection. Widespread and frequent testing with contact tracing can be a practical way to actively prevent transmission of virus, particularly, in big groups of people (i.e., school settings). The tests described above are playing a role in curbing the pandemic.

 

  1. J. Bullard et al., Predicting infectious SARS-CoV-2 from diagnostic samples. Clin Infect Dis, (2020).
  2. L. Azzi et al., Saliva is a reliable tool to detect SARS-CoV-2. J Infect 81, e45-e50 (2020).
  3. M. Baghizadeh Fini, Oral saliva and COVID-19. Oral Oncol 108, 104821 (2020).
  4. K. K. To et al., Consistent detection of 2019 novel coronavirus in saliva. Clin Infect Dis, (2020).
  5. S. Wei et al., Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2. medRxiv, (2020).
  6. D. A. Collier et al., Point of Care Nucleic Acid Testing for SARS-CoV-2 in Hospitalized Patients: A Clinical Validation Trial and Implementation Study. Cell Rep Med 1, 100062 (2020).
  7. Z. Ali et al., iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Res 288, 198129 (2020).
  8. J. Arizti-Sanz et al., Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2. bioRxiv, (2020).
  9. X. Ding et al., Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun 11, 4711 (2020).
  10. T. Hou et al., Development and evaluation of a rapid CRISPR-based diagnostic for COVID-19. PLoS Pathog 16, e1008705 (2020).
  11. C. M. Ackerman et al., Massively multiplexed nucleic acid detection with Cas13. Nature 582, 277-282 (2020).
  12. W. N. Chia et al., Serological differentiation between COVID-19 and SARS infections. Emerg Microbes Infect 9, 1497-1505 (2020).
  13. K. W. Ng et al., Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science, (2020).
  14. K. Bond et al., Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting. J Infect Dis 222, 1280-1288 (2020).
  15. C. W. Tan et al., A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2-spike protein-protein interaction. Nat Biotechnol 38, 1073-1078 (2020).
  16. B. Isho et al., Persistence of serum and saliva antibody responses to SARS-CoV-2 spike antigens in COVID-19 patients. Sci Immunol 5, (2020).
  17. N. Pisanic et al., COVID-19 serology at population scale: SARS-CoV-2-specific antibody responses in saliva. J Clin Microbiol, (2020).

Herd Immunity – Can We Get There?

The concept of herd immunity is frequently brought up as an alternative to lockdown and intervention-based strategies for curbing the COVID-19 pandemic, this sensitive issue being much influenced by policy makers. In this context it is important to first define herd immunity. This is obtained when enough of the population has immunity to an infectious pathogen, thus resulting in prevention of its transmission. The clearest examples of achieving herd immunity are provided by successful vaccination programs (i.e., polio, smallpox and measles). The question of whether acquisition of herd immunity to SARS-CoV-2 is possible depends upon important questions. How long will it take to get such herd immunity? What will be the cost in human deaths? Will there be a successful vaccine program? And does infection provide a lasting immunity for further prevention of reinfection?

Let’s first consider the possibility of obtaining herd immunity by vaccination. Ideally, strong herd immunity can be achieved if a vaccine provides a very significant (say around 80-90%) protection (sterilizing immunity) for extended periods, and if most of the population has been vaccinated. However, it is currently uncertain that these conditions will be met. A recent survey conducted in 19 countries showed that approximately, 70% of participants were likely to take a SARS-CoV-2 vaccine(1), indicating that public acceptance will by no means be universal. Assuming such a vaccine were 70% effective, this would leave 50% of the population able to be infected. Interestingly, if a vaccine were government mandated, acceptance dropped to 50 to 60%. Obviously if we are trying to reach herd immunity by vaccination, vaccine efficacy and acceptance will be critical.

Is it possible that natural infection of a large percentage of the population would result in widespread immunity? This could in theory lead to a reduction in further viral spread to the point where it would become relatively insignificant. This depends, however, upon several factors. First, is that a large proportion of the population would need to be infected. Given an estimated infection mortality rate of 0.3 to 0.5%, this would likely result in an unacceptably high number of deaths. Second, how long would it take? Indeed we know that beside some areas such as New York or Paris for example the percentage of infected individuals has apparently remained quite low (10-15%). Third, infection would need to lead to reasonably durable immunity, and we will consider this in more detail.

As to whether infection confers immunity, this is complicated by not knowing the levels of protective immunity to SARS-CoV-2. Inducing neutralizing antibodies have been a major target for development of many vaccines based on the evaluation of immunity to other coronaviruses. Importantly, evaluation of the rate of reinfection can predict a potential acquisition of protective immunity by natural infection. Reinfection is not necessarily proven by the second positive diagnostic to SARS-CoV-2; there is a question of whether the patient has truly become reinfected or the original infecting virus has simply rebounded.

The answer seems to be that reinfection does occur but is quite rare. Indeed, there are only a handful of well documented cases showing reinfection with SARS-CoV-2. In one well characterized instance, a patient was asymptomatically reinfected 4-5 months after a first symptomatic infection(2). Viruses from the first and second infections were phylogenetically distinct, indicating that they were independent infections. Interestingly, although neutralizing and IgG antibodies were not detectable at the onset of the second infection, they rapidly and robustly appeared (3). A handful of other cases have been reported.  However, their relative rarity suggests that reinfection is the exception rather than the rule. What, then, are the potential protective mechanisms and how long do they last?

The short answer is that we don’t have exact answers yet. Much attention has focused on antibody response and durability, particularly on antibodies to the spike protein and neutralizing antibodies (NA), which are a subset of the anti-spike antibodies. Both anti-spike and neutralizing IgG (but not IgM and IgA) antibodies decrease but persist at measurable levels for at least three to six months after the resolution of the infection. Indeed, anti-spike and NA correlate reasonably well with protective immunity ((4, 5) and these two studies). and. Moreover, as mentioned above, priming by memory cells can result in rapid and robust expression of antibodies. One study showed that a better correlation between NAs and spike antibodies could be obtained by measuring NAs and both anti-receptor binding domain (RBD) and S2 domain antibodies(5). However, it is unclear what level of NAs would be protective against SARS-CoV-2 infection.

It is likely that T cell activity will be necessary for significantly durable immunity. T cell activity is more difficult to assess than antibody response, and correspondingly less is known for its role in lasting protective immunity. We should point out that some patients who have recovered from mild COVID-19 and are PCR negative for SARS-CoV-2, show T cell activity against viral peptides even though they were antibody negative(6), suggesting the involvement of cell-mediated immunity. A strong T cell cytotoxic response is evident during disease, and in the convalescent phase, a memory T cell response is common even in the absence of antibodies(7). This suggests that immune responses will be durable, although this is not yet known for SARS-CoV-2.

Many immunologists are still evaluating a lasting immunity to SARS-CoV-2.  No matter what, infecting a substantial majority of the population to reach herd immunity would likely result in a massive death toll. For example, in the U.S., probably one to two million people would die. In addition, we need to consider serious medical and financial consequences for ill individuals with COVID-19. Further, many people who have recovered from the virus report lingering health effects. Earlier in the pandemic, Sweden was pursuing a herd immunity strategy by essentially relaxed containment; yet that strategy has led in June and July 2020 to the highest rate of death in Northern Europe.

Overall containing the pandemics will not be the result of a single intervention; it will combine efficient prevention measures, novel preventive and curative treatments as well as sufficiently effective and safe vaccine. In any case, waiting for spontaneous herd immunity does not appear as a reasonable option for the population.

  1. J. V. Lazarus et al., A global survey of potential acceptance of a COVID-19 vaccine. Nature Medicine, (2020).
  2. K. K. To et al., COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing. Clin Infect Dis, (2020).
  3. K. K. To et al., Serum antibody profile of a patient with COVID-19 reinfection. Clin Infect Dis, (2020).
  4. A. S. Iyer et al., Persistence and decay of human antibody responses to the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 patients. Sci Immunol 5, (2020).
  5. T. J. Ripperger et al., Detection, prevalence, and duration of humoral responses to SARS-CoV-2 under conditions of limited population exposure. medRxiv, (2020).
  6. S. Schwarzkopf et al., Cellular Immunity in COVID-19 Convalescents with PCR-Confirmed Infection but with Undetectable SARS-CoV-2-Specific IgG. Emerg Infect Dis 27, (2020).
  7. T. Sekine et al., Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19. Cell, (2020).
  8. N. Le Bert et al., SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 584, 457-462 (2020).

How Long Is A SARS-CoV-2 Infected Person Contagious?

As the COVID-19 pandemic rages on, the global community has become accustomed to comprehensive, interventional strategies such as wearing a mask, social distancing, hand hygiene, and surface cleaning and disinfection. It is well known that transmission of SARS-CoV-2 occurs through direct, indirect, or close contact with infected people through infectious secretions, such as saliva and respiratory secretions or their respiratory droplets. In addition, the scientific community has confirmed that the airborne transmission of SARS-CoV-2 viruses in aerosols (smaller than 100 μm) can remain suspended in air for many seconds to hours and are highly concentrated near an infected person, thus infecting people most easily in close proximity (1). Furthermore, aerosols containing infectious virus can also travel more than 2 m and accumulate in poorly ventilated indoor air, leading to superspreading events. World Health Organization and Centers for Disease Control and Prevention have also acknowledged this under certain circumstances, such as enclosed spaces, prolonged exposure to respiratory particles (i.e., shouting, singing, and exercising), and inadequate ventilation or air (2, 3). Thus, effective control strategies and standardized guidance to the public are integral in mitigating COVID-19. In particular, understanding the duration of infectiousness in infected persons with SARS-CoV-2 is critical for developing evidence-based public health policies on isolation, contact tracing and returning to work. In general, the levels of viral RNA were determined by using quantitative reverse transcription-polymerase chain reaction. However, detection of viral RNA does not necessarily indicate that a person is infectious and able to transmit the virus to another person. Although it is critical to determine the levels of infectious virus particles in infected COVID-19 patients, requirement of Biosafety Level-3 laboratory for the virus titration has hindered this approach. In this perspective section, we will discuss currently available scientific data regarding the levels of infectious virus particles in asymptomatic individuals, in mild and severe COVID-19 patients and in children and young adults.

Asymptomatic and presymptomatic individuals represent a source of potentially transmissible virus (4). Asymptomatic infections have no specific incubation period due to no clinical signs. However, the viral loads detected in asymptomatic populations have been reported in several studies to be similar to those in symptomatic patients. In a nursing facility, quantitative SARS-CoV-2 viral loads detected in residents were similarly high in the four symptom groups (residents with typical symptoms, those with atypical symptoms, those who were presymptomatic, and those who remained asymptomatic). Notably, 17 of 24 specimens (71%) from presymptomatic persons had viable virus by culture 1 to 6 days before the development of symptoms. In a surveillance study, asymptomatic cases of samples were collected through swabbing of contacts or facility/family/household testing in the context of outbreak investigations. Despite the uncertainty of their date of exposure or start of infection, cultivable virus was isolated from samples collected from asymptomatic individuals (41% of tested samples).

Detection of infectious SARS-CoV-2 from upper respiratory tract of mild-to-moderate COVID-19 patients showed that infectious virus can persist for more than a week after symptom onset, declining over time (5). At 10 days after symptom onset, probability of culturing virus declines to 6%. This is in line with current WHO guidance on release from isolation. Similarly, shedding of the virus in mild COVID-19 patients was determined by measuring the levels of transcribed subgenomic mRNA and isolation of infectious viruses (6). Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.1 × 108 RNA copies per throat swab on day 4. In addition, infectious viruses were successfully isolated from these samples, confirming active virus replication in the upper respiratory tract. No viruses were isolated after day 7 onset. These findings suggest efficient transmission of SARS-CoV-2, through active pharyngeal viral shedding at a time at which symptoms are still mild and typical of infections of the upper respiratory tract. In a surveillance study in Manitoba, Canada, the presence of infectious viruses was determined by evaluating samples from day of symptom onset (day 0) up to 21 days after symptom onset (7). Within this range of samples, positive cultures were observed up to day 8 after symptom onset with the probability of obtaining peak titers on day 3. Similarly, in Hong Kong, virus was isolated from the samples of mild patients collected within the first 8 days of illness with median viral RNA load of 7.54 log10 genome copies/mL (8). From severe COVID patients, prolonged duration of cultivable virus was detected for up to 20 days after symptom onset, suggesting that prolonged excretion of infectious virus is associated to the severity of the disease (9).

Severity in most children is limited, and children do not seem to be major drivers of transmission. However, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects children of all ages. In South Korea, large-scale testing, aggressive contact tracing and testing, and isolation/direct observation of asymptomatic or mildly symptomatic children have identified the presence of asymptomatic (20 of 91 [22%]), presymptomatic (18 of 91 [20%]), and symptomatic children (53 of 91 [58%]) (10). Presymptomatic children remained symptom free for a median (range) of 2.5 (1-25) days before exhibiting any symptoms. A minority of children (6 [7%]) were identified as infected; this highlights the concept that infected children may be more likely to go unnoticed either with or without symptoms and continue on with their usual activities, which may contribute to viral circulation in the community. In a separate study with 12 symptomatic children, infectious viruses were detected at a median of 2 days after symptom onset (11). Median viral RNA load at diagnosis was 3.0 × 106 copies/mL (mean 4.4 × 108 ranging from 6.9 × 103 to 4.4 × 108 copies/mL. A limitation of this study is the small number of children assessed. However, viral load at diagnosis is comparable to that of adults and symptomatic children of all ages shed infectious virus in early acute illness, a prerequisite for further transmission. Considering the relatively low frequency of infected children, even in severely affected areas, biological or other unknown factors could lead to the lower transmission in this population. Large serologic investigations and systematic surveillance for acute respiratory diseases and asymptomatic presentations are still needed to assess the role of children in this pandemic.

Although the spectrum of COVID-19 ranges from asymptomatic to severe infections, most patients experience mild disease (80%). Scientific data indicate that infectious virus in mild patients can persist for a week after symptom onset. Furthermore, infectious virus can be isolated from asymptomatic individuals. This clearly enforces the importance of wearing a mask, quarantine, and contact tracing to mitigate the transmission of SARS-CoV-2. Recent studies support that wearing masks can save lives not only by cutting down the chances of both transmitting and catching the coronavirus (12) but also by reducing the severity of infection in contracted individuals (13). It is well demonstrated that self-quarantine of close contacts exposed to COVID-19 prevents transmission to others. Contact tracing must be conducted for close contacts (any individual within 6 feet of an infected person for at least 15 minutes) of laboratory-confirmed or probable COVID-19 patients. However, relaxed social distancing and opposition of wearing masks are hindering the mitigation of SARS-CoV-2, resulting in continuous increase of COVID-19 cases. Even when the vaccine will be available, we would not immediately stop social distancing, wearing masks, and other interventional measures until reaching efficient levels of viral mitigation. The message is clear that a simple practice of wearing masks can protect ourselves and save other lives from circulating SARS-CoV-2.

 

References

  1. PRATHER, K.A., MARR, L.C., SCHOOLEY, R.T. MCDIARMID, M.A., WILSON, M.E., MILTON, D.K. 2020. Airborne transmission of SARS-CoV-2. DOI: 10.1126/science.abf0521
  2. 2020. Transmission of SARS-CoV-2: implications for infection prevention precautions. https://www.who.int/news-room/commentaries/detail/transmission-of-sars-cov-2-implications-for-infection-prevention-precautions
  3. 2020. Scientific Brief: SARS-CoV-2 and Potential Airborne Transmission. https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-sars-cov-2.html
  4. Arons MM, Hatfield KM, Reddy SC, et al. 2020. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med 382:2081-2090.
  5. Singanayagam Anika, Patel Monika , Charlett Andre , Lopez Bernal Jamie , Saliba Vanessa , Ellis Joanna , Ladhani Shamez , Zambon Maria , Gopal Robin. 2020. Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020. Euro Surveill. 25.
  6. Wölfel R, Corman  VM, Guggemos  W, Seilmaier  M, Zange  S, Müller  MA, et al. 2020. Virological assessment of hospitalized patients with COVID-2019. Nature. 581:465–469.
  7. Bullard J, Dust K, Funk D, Strong JE, Alexander D, Garnett L, et al. 2020. Predicting infectious SARS-CoV-2 from diagnostic samples. Clin Infect Dis. ciaa638.
  8. Perera RAPM, Tso E, Tsang OTY, Tsang DNC, Fung K, Leung YWY, et al. SARS-CoV-2 virus culture and subgenomic RNA for respiratory specimens from patients with mild coronavirus disease. Emerg Infect Dis. 2020;26(11).
  9. van Kampen JJA, van de Vijver DAMC, Fraaij PLA, Haagmans BL, Lamers MM, Okba N, et al. Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants. medRxiv. 2020.06.08.20125310.
  10. Han MS, Choi EH, Chang  SH,  et al.  Clinical characteristics and viral RNA detection in children with coronavirus disease 2019 in the Republic of Korea. JAMA Pediatr. doi:10.1001/jamapediatrics.2020.3988.
  11. L’Huillier AG, Torriani G, Pigny F, Kaiser L, Eckerle I. Culture-Competent SARS-CoV-2 in Nasopharynx of Symptomatic Neonates, Children, and Adolescents. Emerg Infect Dis. 2020 Oct;26(10):2494-2497. doi: 10.3201/eid2610.202403. Epub 2020 Jun 30. PMID: 32603290; PMCID: PMC7510703.
  12. Leffler, C. T. et al.Preprint at medRxiv https://doi.org/10.1101/2020.05.22.20109231 (2020).
  13. Gandhi, M., Beyrer, C. & Goosby, E. Gen. Intern. Med. https://doi.org/10.1007/s11606-020-06067-8 (2020).

Effect of Suppressed Innate Immunity on Covid-19 Severity

One of the important determinants of severe Covid-19 appears to be an inappropriate response by the innate immune system. Specifically, this involves, on the one hand, insufficient or delayed expression and signaling by type 1 interferons (IFNs), which induce innate cell-mediated immunity. The interferon (IFN) response constitutes the major first line of defense against viruses. On the other hand, this involves an overly active inflammatory cytokine response, with its attendant tissue damage (this “cytokine storm” was explored in our previous Perspective at https://gvn.org/category/sars-cov-2/gvn-sars-cov-2-perspectives/). Let’s look at some of the lines of evidence for these contradictory events.

One way in which an aberrant immune response to SARS-CoV-2 is reflected at the cellular level is by a greatly increased ratio of neutrophils to lymphocytes(1). This is correlated with low expression of type I and III interferons and high expression of pro-inflammatory factors including IL-6 and a variety of chemokines(2) that act as attractants for neutrophils and monocyte/macrophages. These activities are the outcome of interactions between host factors that recognize pathogen associated molecular patterns (PAMPs), such as viral RNA in endosomes, and viral proteins that are antagonistic to these factors and their signaling pathways. Genetic differences in host factors can result in profound differences in host responses to pathogens (recent findings are described below). Different viruses also tend to have different or unique antagonists to host immune factors that can greatly influence the outcome of infection.

What are some of the molecular studies that point to defects in interferon activity in severe Covid-19? Recently, interest has been increasing in toll-like receptors (TLRs), especially TLR3 and TLR7, which recognize viral RNA and are important in interferon type I and inflammatory cytokine expression. TLRs play a key role in the recognition of PAMPs and trigger the activation of specific signaling pathways, thereby inducing the transcription of inflammatory and/or anti-inflammatory cytokine. One interesting report looked at two sets of two brothers(3) who, although young and otherwise healthy, had severe Covid-19 (one died). Whole exome sequencing revealed that both sets of brothers had mutations in TLR7, which serves as a sensor for viral RNA. One set had a missense mutation predicted to result in an inactive TLR7, while the other set had a frame shifting 4 nucleotide deletion, resulting in a nonsense protein. Stimulation of primary immune cells in vitro with the TLR agonist imiquimod resulted in defective expression of type I interferon-related genes normally regulated by TLR7. While the limited nature of the study does not permit a conclusion of causality, several factors make it likely that these loss of function mutations are significant. Exhibition of severe disease in young men is rare. Despite rare cases of loss of function mutations in TLR7, two different loss of function mutations in two young brother pairs with severe disease indicate its potential role in Covid-19 severity. It should be pointed out that TLR7 is located on the X chromosome, so a single mutant copy would cause loss of function. One of the mothers was heterozygous for wild type TLR7, making her a carrier. Thus, if problems with the TLR7 pathway exacerbate Covid-19, males might be likelier to have an insufficiency.

Another study analyzed the complete genomes or exomes of 659 patients with life threatening Covid-19 and compared them with those of 534 people with asymptomatic or benign infections(4). They characterized 13 genetic loci encoding factors in the TLR3-interferon regulatory factor 7 (IRF7) pathway, which also regulates type I interferon production and immunity to influenza virus. They found that 3.5% of the people with life threatening Covid-19 had loss of function variants at these loci. Moreover, when immune cells from patients with these variants were tested in vitro, they were found to be defective in type-I interferon immune activities, and further in vivo study confirmed impaired production of type I IFN during the course of SARS-CoV-2 infection. About half of these patients also had extremely low levels of serum interferon α, a type I interferon.

Yet, another study further implicates lack of appropriate interferon activity in severe Covid-19(5). In this study, 101 of 987 patients with life threatening Covid-19 had auto-antibodies against interferon α, interferon ω or both. These were not present in 663 patients with mild disease. The auto-antibodies were able to neutralize the antiviral effects of interferon in vitro (and likely in vivo). Interestingly, the auto-antibodies were about 5-fold more prevalent in men than in women.

None of these studies by themselves show a specific defect in interferon activity in a majority of cases. However, taken together, they certainly suggest that a great variety of different defects related to the antiviral activities of type 1 interferons may be surprisingly common. Probably, one of the factors explains why some people resist serious disease while, for others, it is life-threatening. Further, investigations in this area will be most interesting.

One other study identified a 3p21.31 gene cluster that conferred a risk of severe Covid-19. This region contains three chemokine receptor genes, all involved in innate immunity(6). It turns out to be a region derived from Neanderthals, and is present at variable incidence worldwide except in Africa. This provides yet another clue that the innate immune response to SARS-CoV-2 may be an important determinant of whether an infected individual will, or will not, develop critical Covid-19.

In this light, it has been proposed that some cross-protection could be afforded by administering live attenuated vaccines, such as measles-mumps-rubella, and oral polio vaccine(7) (non-specific effect of vaccination against SARS-CoV-2). The stimulation of innate immunity by these vaccines could provide temporary protection against Covid-19. If proven to be effective against Covid-19, emergency immunization with these vaccines could be used for protection against other unrelated emerging pathogens.

 

References

  1. Y. Liu et al., Neutrophil-to-lymphocyte ratio as an independent risk factor for mortality in hospitalized patients with COVID-19. J Infect 81, e6-e12 (2020).
  2. D. Blanco-Melo et al., Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell 181, 1036-1045 e1039 (2020).
  3. C. I. van der Made et al., Presence of Genetic Variants Among Young Men With Severe COVID-19. JAMA 324, 663-673 (2020).
  4. Q. Zhang et al., Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science, (2020).
  5. P. Bastard et al., Auto-antibodies against type I IFNs in patients with life-threatening COVID-19. Science, (2020).
  6. D. Ellinghaus et al., Genomewide Association Study of Severe Covid-19 with Respiratory Failure. N Engl J Med, (2020).
  7. K. Chumakov, C. S. Benn, P. Aaby, S. Kottilil, R. Gallo, Can existing live vaccines prevent COVID-19? Science 368, 1187-1188 (2020).

Transmission Dynamics of SARS-CoV-2: Superspreaders and Superspreading Events

The concept of Superspreaders and Superspreading events has recently attracted a lot of attention. In fact it is important to understand that most of SARS-CoV-2 infected persons are in fact not contagious! Thus, transmission is really dependent on a handful of individuals we call Superspreaders who nurture Superspreading events. Let’s distinguish between Superspreaders and Superspreading events. Superspreaders are individuals who infect a high number of persons; why?  This is not clear, and this is a most important issue to clarify in the future.  We know they yield high viral load and that they are generally, but not always, young people.  But, this cannot fully explain their massive contamination impact.  Moreover, they are frequently asymptomatic, thereby significantly increasing risk of dissemination. Superspreading events, which involve at least one Superspreader, are events which favor large scale transmission, such as close contacts in indoor situations. Secondary transmissions from infected people then result in a large number of further infections, and so on. Thus, by some estimations  only 20% of infected individuals cause 80% of infections(1).  Identification of Superspreading events depends upon contact tracing.  Furthermore, DNA sequencing of viral genomes adds a great deal to a clearer understanding of these phenomena, thus, confirming the substantial role of Superspreaders in the pandemic. Let’s look at some well-characterized superspreader events to try to better understand how the majority of SARS-CoV-2 infections occur, enabling us to gain an understanding of what might be done to prevent them.

One of the early recognized superspreading events occurred in mid-March in Skagit County, Washington(2) at a 2.5 hr-long choir practice in which 61 people sang in close proximity. Probable or confirmed infections occurred in 87% of the attendees. Given the low incidence of COVID-19 at the time of this event, it is likely that all the infections originated with a single individual, and that the act of singing vigorously launched many viral laden particles into the air. People were relatively closely positioned. Thus, it is likely that superspreading occurs in an unusually favorable environment. Looking at it another way, the virus got “lucky.”  Another study, unrelated to the choir event, analyzed the sequences of 453 viral genomes collected between February and March in Washington(3).  It is possible to infer the likelihood of how many people have been infected by a single person using viral genomic epidemiology, especially given the relative genetic stability of SARS-CoV-2. A phylogenetic analysis strongly suggested that 84% of the 453 viral genomes derived from a single introduction sometime in early February.  In the choir study, it is clear how virus was transmitted. In the genomic study, it is only clear that a single infected individual somehow infected a great number of people through primary, secondary, and other less direct routes.

Another well-studied superspreader event began with a single infected individual in a meat packing plant is Postville, Iowa. In this case, viral spread could be ascertained by both contact tracing and by genomic epidemiology. Fourteen independent viral introductions were identified in the region, but the only virus to spread widely was the one from the meat packing plant. The virus from this individual passed first to numerous other workers, then to family members, then to the community in Postville (87 cases), and finally to other locations in an area of 185 square miles in Iowa, Wisconsin and Minnesota. These conclusions were supported by genomic sequences from 27 different infected individuals. Again, it appears that prolonged close contact indoors facilitated transmission and suggests that this is a critical feature of superspreading events.

Perhaps, the best characterized superspreading event, originating from an international business meeting of Biogen in Boston(4) in which more than 90 individuals became infected.  This event recently received considerable attention. The large number of infections was indicative of a possible superspreading event. A recent study looked at this event and its consequences in detail, using genomic epidemiology(5). They were able to identify and track the virus in question by a single nucleotide polymorphism (SNP), C2416T. Among 80 separate introductions from four continents into the Boston area early in the pandemic, which they inferred from phylogenetic analyses, the C2416 SNP was unique to one virus. Comparing other viral genomes from various parts of the world with C2416T, the parental origin appears to be in Europe, perhaps France, with an estimated most recent common ancestor existing about two weeks prior to the conference aroundFebruary 26-27. Of all samples collected prior to March 10, the only instances of C2416T were from people who had attended the conference, indicating that a superspreading event had indeed occurred there.

Subsequent samples (744) from infected individuals in Boston and surrounding areas were collected over a period from February to June and genomes were sequenced. Remarkably, 35% of the samples had the C2416 SNP. Since no sample prior the March 10 had this SNP, it suggests that the superspreading event at the Biogen meeting February 26-27 resulted in virus from a single individual infecting more than a third of all infected people in the Boston area. Percentages of the C2416T SNP in regions around Boston ranged from 30-46% in four adjacent counties. In addition, a second SNP, G26233T, appears to have emerged during the event, enabling further tracking. Data from this SNP shows a likely export to other states and countries, with further community spread in Virginia, Michigan and Australia. Some caution is warranted, however, since genomic sampling is not generally done on a randomized basis.

The same report looked at infection clusters at homeless shelters, nursing facilities, and a hospital to gain a better understanding of transmission dynamics. They analyzed 193 viral genomes collected from the Boston Health Care for the Homeless Program and identified 4 clusters of 20 or more highly similar genomes, including two clusters containing the C2416T SNP. They also investigated a superspreading event at a skilled nursing facility, in which 82/97 (84%) residents and 36/97 (37%) of staff were infected. In fact, 75% of viral genomes from different individuals had highly similar genomes, suggesting that they arose from a single recent introduction. This took place even though strict interventional measures were in place. Interestingly, two other clusters of three closely related genomes were detected. This represents independent introductions, but these failed to massively spread. In the case of two clusters of infection at Massachusetts General Hospital, highly similar genomes were not found, suggesting a lack of significant in-hospital spread.

What is our conclusion? First, it is now clear that a majority of transmissions result from superspreading events, facilitated by conducive conditions. These include indoor location, close contact, lengthy contact, indoor activity such as singing or talking, poor air ventilation, and lack of mitigation procedures (i.e., wearing masks and physical distancing). Tracing Superspreading events in Hong Kong also confirmed that the largest cluster (106 cases) was traced to four bars followed by a wedding (22 cases) and attendance at a temple (19 cases) (1). This study suggests that disease control efforts should focus on avoiding gathering events and mitigating their impact.  The rapid tracing and quarantine of confirmed contacts, along with the implementation of physical distancing policies including either closures or reduced capacity measures targeting high-risk social settings such as bars, weddings, religious sites and restaurants, should be efficient to prevent the occurrence of superspreading events. Overall, the issue of Superspreaders and Superspreading events illustrates the impact of molecular epidemiology for deciphering the patterns of COVID-19 dissemination. What we still clearly lack, however, is the understanding of the very early phases of the pandemics in China. This would be very useful for the whole appraisal of transmission dynamics.

  1. D. C. Adam et al., Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong. Nat Med, (2020).
  2. L. Hamner et al., High SARS-CoV-2 Attack Rate Following Exposure at a Choir Practice – Skagit County, Washington, March 2020. MMWR Morb Mortal Wkly Rep 69, 606-610 (2020).
  3. T. Bedford et al., Cryptic transmission of SARS-CoV-2 in Washington state. Science, (2020).
  4. A. Schuchat, C. C.-R. Team, Public Health Response to the Initiation and Spread of Pandemic COVID-19 in the United States, February 24-April 21, 2020. MMWR Morb Mortal Wkly Rep 69, 551-556 (2020).
  5. J. Lemieux et al., Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv, (2020).

Current Status of COVID-19 Vaccine Development

As the COVID-19 pandemic expands, interests in the progress of vaccine development are intensifying. Despite an unprecedented rate of progress, it is still uncertain when a safe, effective vaccine will be available for wide distribution to the public. Successful vaccine development goes through a series of stages, from animal studies for the evaluation of its protective immunogenicity to phase 1 (safety and antibody production), phase 2 (safety and immunogenicity by including a placebo group), and phase 3 (verification of safety, and efficacy in, a large population group) clinical trials. This is obviously a long, drawn out process, yet it is necessary to ensure the efficacy and safety of vaccines. In addition, it takes very high numbers of participants to generate meaningful and significant statistics to prove vaccine protection. This makes these trials expensive and their enrollment process lengthy, but phase 3 trials are clearly necessary, and are the most important step for its approval.

Immunogenicity studies are especially critical because there is not yet a clear understanding of what constitutes a protective immune response. Neutralizing or IgG antibody titers against the spike (S) protein do not seem to correlate inversely with disease severity, although it may be that rapid expression of such antibodies would be protective. Another issue is that neutralizing antibodies may only last a few months. However, immune memory cells may facilitate rapid production of such antibodies after infection. Even less is known about the role or relevance of T cell responses in protection. With all these caveats in mind, we will discuss nine candidate vaccines that are in the most advanced stages of development.  Most, but not all, are focused exclusively on the S protein, in large part because it is the target of neutralizing antibodies.

There are currently two vaccines in the late stage of development that depend upon injection of mRNA encoding the spike protein or portions including the receptor binding domain (RBD) of the S protein. These have an advantage of being easy to produce but have the disadvantage of needing to be stored at 4°C, requiring a cold chain supply, thus presenting difficulties for use in low-income countries. These two vaccines are produced by Moderna and Pfizer/BioNTech. Its limitations associated with the intracellular instability and inefficient delivery of mRNA have been addressed by chemically modifying the RNA and encapsulating it in lipid nanoparticles.

The Moderna vaccine (mRNA-1273) and one of the two Pfizer vaccines (BNT162b2) encode prefusion conformation of the S proteins. The other Pfizer vaccine (BNT162b1) encodes trimerized soluble S protein receptor binding domains on a peptide linker scaffold. The Moderna vaccine was protective in rhesus macaques. Human phase 1 trial results were reported in June by demonstrating its safety and immunogenicity with induction of binding and neutralizing antibodies equivalent to the levels that are seen in natural infection. The antibody levels persisted until at least day 43 post-vaccination. A phase 2 trial with 600 participants was begun in June. Phase 3 trials to determine efficacy and safety were initiated in August and will have 30,000 participants.

Pfizer decided to concentrate on BNT162b2, as it is equally immunogenic to BNT162b1 but generates fewer side effects. There do not appear to be any reports of trials with non-human primates. Three phase 1 trials showed that both vaccines elicited binding and neutralizing antibodies, but lesser side effects led to the selection of BNT162b2 for phase 3 trials (Publication 1, Publication 2). Trials began in August and, as with the Moderna trials, aim to enroll 30,000 participants.

The other nucleic acid-based vaccine, developed by Inovio (INO-4800), is comprised of DNA encoding the S protein. The DNA vaccine, unlike the mRNA vaccines, is stable at room temperature. The DNA is injected intramuscularly and then electroporated into cells by a hand-held device delivering a brief electric pulse.  The vaccine was partially protective in rhesus monkeys against a viral challenge three months after vaccination as judged by a reduction in viral titers. Inovio claims that antibody and/or T cell responses were induced after two doses of the vaccine in 94% of the 40 participants in Phase 1 trials, but they have not yet published the results. They are scheduling Phase 3 trials for September.

The Novavax vaccine candidate, NVX-CoV2373, is a full-length stabilized spike protein produced in insect cells and formulated into a lipid nanoparticle. Reports from a phase 1-2 trial showed that binding and neutralizing antibodies were elicited(1). Antibody levels were greatly increased, and T cell activities (especially Th1) were induced when NVX-CoV2373 was combined with a saponin-based adjuvant. Phase 3 trials are planned for late 2020.

There are currently three late stage vaccines that use adenoviral vectors to deliver their payloads to express the S protein. These include AstraZeneca/University of Oxford, which uses a chimpanzee adenovirus originally isolated from a chimp stool sample, Johnson and Johnson/Janssen (adeno26) and Cansino/Beijing Institute of Biotechnology (adeno5), the two latter of which are human adenoviruses. All three adenoviral vectors have been genetically modified to render them incapable of self-replication. The reasoning behind the use of a chimp adenovirus was to avoid the possibility that vaccinees previously infected by human adenoviruses would mount in an immune response against the vector, thus diminishing the efficacy of the vaccine.

The AstraZeneca vaccine, ChAdOx1 nCoV-19, was shown to partially protect rhesus macaques from viral challenge(2). Out of 6 vaccinated animals, none showed signs of pneumonia or lung pathology, while 3 of 6 controls developed interstitial pneumonia. The vaccine elicited binding and neutralizing antibodies against the S protein as well as Th1 and Th2 responses. Protection was not, however, sterilizing. Vaccinated animals had reduced viral loads in their lower respiratory tracts compared to controls, but viral loads in the nasopharynx were equivalent in both groups. A randomized phase1/2 trial with >1,000 subjects was injected with either ChAdOx1 nCoV-19 or the same vector with an unrelated antigen(3). The vaccine elicited binding and neutralizing anti-S antibodies as well as a T cell response without exhibiting serious adverse events. ChAdOx1 nCoV-19, currently in phase 3 trials, has recently been in the news because of a potential serious adverse reaction that temporarily halted the trials. A vaccinated women developed a severe spinal inflammation (transverse myelitis), which can occasionally develop following viral infections. She has since recovered, and it is not clear whether this is related to the vaccine. Trials have since resumed in Britain, but the Food and Drug Administration (FDA) has not yet approved resumption in the US. There are two ways to view this event. It could be considered to reflect the speed with which these vaccines are being developed and might be a cause for apprehension.

The Johnson and Johnson vaccine, Ad26.COV2.S, expresses a prefusion conformation of S protein (proline-stabilized S protein) in a human adeno 26 vector. In rhesus macaques, vaccinated animals developed high levels of binding and neutralizing anti-S protein antibodies and a Th1 biased T cell response(4). The authors suggested that neutralizing antibodies, but not cell-mediated immune activities, were correlative on protection. All 20 controls were infected and developed minimal disease after intratracheal and intranasal challenge. Five of six vaccinated animals were protected from detectable infection, and the sixth had a 3-4 log reduction in virus loads. Ad26.COV2.S is currently in phase 1/2 trials with 11,000 subjects that was started in June. Phase three trials are scheduled for September with 30,000 participants.

The CanSino vaccine, Ad5-S-nb2, contains a codon-optimized gene expressing the S protein. In rhesus macaques, a single dose elicited neutralizing and S protein binding antibodies and activated cell mediated immune responses after intramuscular inoculation(5). Intranasal inoculation induced antibody production but only weak cellular immunity. In an open label non-randomized trial, the vaccine was immunogenic in humans and generally well tolerated with the main adverse effect of being pain(6).  A phase 2 trial with ~600 participants confirmed immunogenicity and safety(7).

There are three vaccines, developed by Sinovac, Beijing Institute of Biological Products, and Sinopharm, that are based upon chemically inactivated whole SARS-CoV-2. These vaccines, unlike the others, contain all the viral structural proteins, and thus, might be expected to induce a wider T cell response than the other vaccines, which contain only the S protein. The Sinovac candidate, Coronavac, elicited neutralizing and binding antibodies against the S protein(8). The highest vaccine dose protected animals completely against an intratracheal challenge, and lower doses prevented severe interstitial pneumonia and resulted in greatly reduced vial loads. In a phase 1/2 trial, Sinovac claimed that 90% of the volunteers developed neutralizing antibodies and had no serious adverse effects. There was no sign of antibody-dependent enhancement within the time frame reported. Sinovac initiated phase 3 trials in Indonesia and Brazil in August and is planning another trial in Bangladesh. Another inactivated virus vaccine (BBIBP-CorV), developed by the Beijing Institute of Biological Products, induced anti-S protein binding and neutralizing antibodies in rhesus macaques and cynomolgus monkeys and protected rhesus macaques from intratracheal challenge(9). BBIBP-CorV will soon be entering human trials. Two other similarly inactivated whole vaccines, produced by Sinopharm, induced neutralizing antibodies in phase 1 trials and had no serious adverse effects(10). Phase 3 trials with this vaccine were started in July in the UAE. 

The speed of vaccine development with which this has happened is remarkable. The general take home message gleaned from an overview of these vaccines is that they induce neutralizing antibodies, stimulate T cell-mediated activity, and partially or completely protect non-human primates from infection and/or serious disease. None appear to cause an undue level of adverse events. The most pressing question is of course when one or more will be available. However, many uncertainties remain given the lack of robust clinical data. We still need to wait for finalization of phase III trials to confirm the safety and efficacy of the vaccine candidates. In particular, potential induction of antibody-dependent enhancement could be a concern. Immunogenicity of vaccine candidates are focused on the induction of neutralizing antibodies. Furthermore, they are mostly administrated by using the intramuscular route, thus limiting the induction of mucosal immunity. Intranasal immunization approach also needs to be considered. In addition, most vaccine candidates might require two doses (prime and boost vaccinations) to enhance their protective efficacy. For a global vaccination, this poses challenges financially and logistically. Therefore, we also need to consider the non-specific protective effects of live vaccines based on stimulation of innate immunity and trained innate immunity (i.e. epigenetic changes induced by live vaccines).

References

 

  1. C. Keech et al., Phase 1-2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine. N Engl J Med, (2020).
  2. N. van Doremalen et al., ChAdOx1 nCoV-19 vaccine prevents SARS-CoV-2 pneumonia in rhesus macaques. Nature, (2020).
  3. P. M. Folegatti et al., Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet 396, 467-478 (2020).
  4. N. B. Mercado et al., Single-shot Ad26 vaccine protects against SARS-CoV-2 in rhesus macaques. Nature, (2020).
  5. L. Feng et al., An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques. Nat Commun 11, 4207 (2020).
  6. F. C. Zhu et al., Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. Lancet 395, 1845-1854 (2020).
  7. F. C. Zhu et al., Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial. Lancet 396, 479-488 (2020).
  8. Q. Gao et al., Development of an inactivated vaccine candidate for SARS-CoV-2. Science 369, 77-81 (2020).
  9. H. Wang et al., Development of an Inactivated Vaccine Candidate, BBIBP-CorV, with Potent Protection against SARS-CoV-2. Cell 182, 713-721 e719 (2020).
  10. S. Xia et al., Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes: Interim Analysis of 2 Randomized Clinical Trials. JAMA, (2020).