New Study Warns That Rapidly Evolving SARS-CoV-2 Strains Are Giving Rise To More Escape Variants

Researchers from UCLA School of Public Health-USA, the Institute of Genetics at the University of Cologne- Germany, the Department of Medicine at the University of California, Davis-USA and the Institute for Clinical and Molecular Virology, Friedrich-Alexander University-Germany have in a new study found that the various SARS-Cov-2 strains are evolving rapidly and are giving rise to more escape variants.


 
The study team warns that the scale and scope of mutation may pose a threat to the continuing successful use of the current vaccines and therapies.
 
The team has followed the time course of emerging viral mutants and variants during the SARS-CoV-2 pandemic in ten countries on four continents. They examined > 383,500 complete SARS-CoV-2 nucleotide sequences in GISAID (Global Initiative of Sharing All Influenza Data) with sampling dates extending until April 05, 2021.
 
These sequences originated from ten different countries: United Kingdom, South Africa, Brazil, United States, India, Russia, France, Spain, Germany, and China. Among the 77 to 100 novel mutations, some previously reported mutations waned and some of them increased in prevalence over time. VUI2012/01 (B.1.1.7) and 501Y.V2 (B.1.351), the so-called UK and South Africa variants, respectively, and two variants from Brazil, 484K.V2, now called P.1 and P.2, increased in prevalence.
 
Despite lockdowns, worldwide active replication in genetically and socio-economically diverse populations facilitated selection of new mutations. The data on mutant and variant SARS-CoV-2 strains provided here comprise a global resource for easy access to the myriad mutations and variants detected to date globally. Rapidly evolving new variant and mutant strains might give rise to escape variants, capable of limiting the efficacy of vaccines, therapies, and diagnostic tests.
 
The study findings were published in the peer reviewed journal: EMBO Molecular Medicine.
 https://www.embopress.org/doi/full/10.15252/emmm.202114062
 
Dr Christina Ramirez, UCLA Fielding School of Public Health professor of biostatistics and a co-lead author of the study, which examined mutations in SARS-CoV-2 RNA sequences isolated between January, 2020, and March, 2021 told Thailand Medical News, "While there were only about 10 dominant mutations of the virus worldwide in April, 2020, their number had risen to roughly 100 mutations by spring, 2021. Throughout 2020 and into the first quarter of 2021, more mutations in combination were found and propagated rapidly, despite lockdowns and other efforts to contain the spread. The speed by which the virus travelled, even during lockdowns, emphasizes the difficulty in suppressing transmission of highly contagious respiratory viruses."
 
The study team defines variants as viruses with a specific set of mutations, and by that measure, while up to April, 2020, only about 10 mutations were prevalent, at least 77 and possibly as many as 100 new mutations were found up to January, 2021.
 
Co-author Dr. Stefanie Weber, Friedrich-Alexander University added,  "At the end of April of this year, we followed the SARS-CoV-2 infection explosion in India with more than 353,000 cases and 2,812 deaths per day - the highest number of cases ever recorded worldwide. The virus variants known to date could be more contagiou s and potentially more disease-causing than the original virus from Wuhan."
 
One example cited in the study analysis is the so-called UK variant, also known as B.1.1.7 or alternatively VOC202012/01 now known as Alpha, was first identified in England in September, 2020.
 
In early December, it was reported as a rapidly spreading variant of concern that had 14 mutations in total. This variant has been associated with higher transmissibility and at least one confirmed case of reinfection. On December 23, 2020, the time of the lockdown, the variant was found in three countries. As of April 5, it was found in 108.
 
Dr Walter Doerfler, with the Institute for Virology, Friedrich-Alexander University Erlangen-Nürnberg and Institute of Genetics, University of Cologne added, "This process continues and, despite the vaccine campaign, could develop further if it is not possible to stem the spread quickly enough. However, it is still unknown whether the infection with certain coronavirus mutants are specifically related to the type and severity of COVID-19 disease. Another aspect of interest we have pursued was the finding that between 40 and 70% of the new SARS-CoV-2 mutations occurring in the 10 countries investigated were cytidine (C) to uridine (U) transitions. Apparently, this loss of C residues in the viral genome seemed to be counteracted by about 20% of guanosine (G) or C mutations to adenosine (A) or U residues. We are still puzzled by the intricate interactions of mutagenesis and selection of SARS-CoV-2 mutants."
 
Considering how much remains unknown about COVID-19, and the risks of further mutations and variants, the study team said public health agencies must commit resources for in-depth and on-going research; especially important is tracking the potential for mutations across the entirety of the SARS-CoV-2 viral genome, including replication functions, all the virus's various proteins, and the viral genome.
 
Co-author Dr Barbara Weiser, an infectious disease specialist at UC Davis further added, "Our work documents the speed and power of SARS-CoV-2 mutant selection, which in turn may reduce the efficacy of COVID therapies and vaccines. Molecular sequencing of Covid-19 to detect new mutants and variants must continue in order to optimize treatment and prevention of SARS-CoV-2."
 
Another co-author Dr Harold Burger, also and infectious disease physician from UC Davis added that "ideally, the molecular sequencing should include viruses from asymptomatic and mildly ill people with a spectrum of ages in addition to specimens obtained from sicker patients. Asymptomatic individuals can and do transmit the virus to others. The degree of illness is a consequence of the condition of the patient, not only a function of the virus. This approach will provide valuable information on the evolution and spread of the epidemic."
 
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