MYTH: There are multiple strains of SARS-CoV-2
FACT: There are not multiple strains of SARS-CoV-2
By: Joseph Osmundson
Last updated: January 13, 2021
Some research pre-prints claim that there are multiple SARS-CoV-2 strains circulating in different geographical regions. One study appeared to show that various mutations in the SARS-CoV-2 genome caused a 270-fold decrease in viral replication. These studies were widely reported in the media, stoking fears about COVID-19 in New York differing substantially from more virulent or benign strains in Singapore, China, Europe, and the West Coast. This would make vaccine development more difficult and raises the horrifying spectre of SARS-CoV-2 evolving to become more pathogenic and deadly or more transmissible.
To our best scientific understanding, there is currently only one SARS-CoV-2 strain circulating worldwide, and there is no good evidence for differences in COVID-19 disease pathology along geographical lines or due to changes in viral RNA sequence.
Coronaviruses have a slow rate of mutation due to an exonuclease (error checking) domain in the viral RNA polymerase. There are currently thousands of SARS-CoV-2 viruses that have been sequenced from patient samples worldwide. Across the 30,000 base genome, these viruses differ by 25 individual mutations at most. This is likely not sufficient genetic variation to create separate strains of the virus. Further, there is no evidence that different viruses – by sequence or geography – have different disease outcomes. Because SARS-CoV-2 evolves so slowly and has only been transmitting in the human population for months, it is entirely inaccurate to denote separate strains of the virus without in vivo data showing varying disease severity.
In late 2020, a novel variant (termed B.1.1.7) was identified by sequencing full SARS-CoV-2 viruses in the UK. This variant spread rapidly through various regions of that country, leading epidemiologists to estimate it was indeed more infectious. Initial analyses and subsequent work estimate that B.1.1.7 transmits 50-70% more effectively than the original (wild type) virus. These conclusions are based upon noisy epidemiological data of only viruses that were fully sequenced. Subsequent work in vitro, to determine if the virus binds better to host cells, and in animal models, to determine the levels of viral shedding in various tissues, are urgently needed to determine whether B.1.1.7 is indeed phenotypically different, and therefore a novel SARS-CoV-2 strain.
In their recent application for an Emergency Use Authorization for their COVID-19 vaccine, Pfizer tested clinical trial participant antibodies against various mutants of SARS-CoV-2. Antibodies against the SARS-CoV-2 Spike protein from all patients effectively neutralized all the tested variants of SARS-CoV-2. The Moderna and AstraZeneca vaccines also use the wild type (unmutated) Spike protein as the antigen to develop antibodies, and these vaccines will therefore likely neutralize all currently circulating mutants of SARS-CoV-2 as well. Early indications support the conclusion that this variant will be effectively neutralized by current COVID-19 vaccines.