Update on SARS-CoV-2 Variants
Efficient Vaccine Distribution is Critical to Mitigate the Continuing Evolution of SARS-CoV-2
February 5, 2021
We’ve recently reported on SARS-CoV-2 variants, and described some of the reasons for concern. These include increased transmissibility, the possibility of false negative tests for viral RNA, resistance to immune protection from vaccine or prior infection, and pathogenicity. Rapid spread of variants makes it difficult to mitigate an ongoing pandemic.
Sequences containing MHC-I restricted CTL epitopes are similarly affected. Sequencing of 233 samples identified 197 non-synonymous changes in 27 CTL epitopes that are presented by two HLA subtypes, HLA-A*02:01 (a relatively common MHC subtype) and HLA-B*40:01(5). Identical mutations were often found in multiple samples. A survey of available SARS-CoV-2 sequences showed mutation prevalence in these epitopes ranging from ~0 to 7%. Serial samples showed that these variants tended to arise later in infection, suggesting that CTL activity was exerting evolutionary pressure on the virus, which implies that CTL activity is protective. Analyses of a subset of the mutant peptides showed reduced affinity for the HLA proteins mentioned above, suggesting that the mutations reflect an escape from CTL activity.
It is critical to extend our effort to genetic surveillance for monitoring the emergence of immune escape mutants against currently available COVID-19 vaccines. If necessary, currently available vaccine platforms (i.e., mRNA-based and viral vectored vaccines) can also facilitate to update COVID-19 vaccines against emerging immune escape mutants. No matter what, we need to keep in mind that vaccination can be the most efficient and effective measures in controlling the pandemics. Now, our public health strategy to fight the ongoing pandemic should be a combination of vaccination and continuation of wearing masks and maintaining physical distances.
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