Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease (COVID-19), continues to spread globally.
With this spread, new variants and strains have emerged, posing a threat to the newly developed and distributed SARS-CoV-2 vaccine. efficacy.
Researchers at the Department of Integrative Biomedical Sciences, University of Cape Town, South Africa, found evidence of significant changes in the selective power acting on immunologically important SARS-CoV-2 genes, such as N and S. This likely coincided with their appearance. of the 501Y lineage.
In the study, published on a pre-print server medRxiv*, the team examined patterns of mutations that appeared in the SARS-CoV-2 genome during the pandemic.
Between December 2019 and October 2020, worldwide viral evolution involved new, highly vulnerable host populations. D614G (Asp614-to-Gly) mutation in viruses spike protein accelerate the spread of the virus.
From there, only a few mutations were epidemiologically significant without affecting the pathogenesis of SARS-CoV-2. However, these mutations are characterized by a mutation pattern of slow and selectively neutral random genetic drift.
Since October 2020, SARS-CoV-2 has mutated several times. Currently, three variants are actively spreading – the British variant is called B.1.1.7 with multiple mutations in fall 2020, the South African variant is called B.1.351, and the Brazilian variant is called P.1.
SARS-CoV-2 genome map showing location and amino acid changes encoding of what we consider here to be the signature mutations of the V1, V2 and V3 sequences. Genes represented with light blue blocks encode non-structural proteins and genes in orange encode structural proteins: S encode spike protein, E envelope protein, M matrix protein, and N nucleocapsid protein. Within the S-gene, the receptor-binding domain (RBD) is shown in darker color and the site where the S protein is cleaved into two subunits during priming for receptor binding and cell entry is indicated by a dotted vertical line.
The British variant spreads faster and easier than the other variants. In January 2021, scientists said that the variant may be associated with an increased risk of death compared to other variants of the virus. It has spread to many countries around the world.
Variant B.1.351 is known to be resistant to the effects of vaccines and therapy against COVID-19. Meanwhile, the P.1 variant appeared on travelers from Brazil in early January. This variant contains an additional set of mutations that can affect their ability to be recognized by antibodies.
In the study, variants B.1.17 or 501Y.V1 were referred to as V1, B.1.351 or 501Y.V2 variants were V2, and variants P.1 or 501Y.V3 were referred to as V3.
To date, research has shown that antibodies produced by vaccination with approved vaccines recognize this variant, but further investigations are ongoing.
Amino acid locations encoded by codons evolved under positive selection and / or encoding convergent amino acid changes between lineages mapped to the 3D Spike structure (PDB 7DF4 structure; 47). Human ACE2 receptors are shown in light blue color. Signature mutations are not represented unless concluded to be under positive selection. Site pairs detected coexisting in different lineages are connected by purple lines.
This study aims to determine the evolutionary capacity of SARS-CoV-2 to adapt to increased population immunity and infection control measures such as social distancing and vaccinations.
The researchers examined the mutation patterns that appeared in the SARS-CoV-2 genome during the pandemic.
The team used a series of phylogenetic-based natural selection analysis techniques to examine positive selection patterns in the protein-coding sequences of the three lineages.
The study findings suggest the emergence of the 501Y lineage is consistent with substantial global changes in positive selection signals. This implies a general change in the selective environment in which SARS-CoV-2 thrives.
They also found significant changes in the selective power acting on the SARS-CoV-2 gene. Furthermore, the team revealed that the adaptive evolution of the 501Y lineage unites between lineages. This study highlights the essence of surveillance on how members of the 501Y lineage develop similar stages to ensure their survival and persistence.
The sudden appearance of the 501Y lineage
The team explained that in the first months of the pandemic no mutations had appeared. This is the sluggish pace of virus evolution. The start of the pandemic was like the pinnacle of a virus’ fitness in its ability to infect and transmit between people.
However, since October 2020, the sudden appearance of the 501Y lineage has caused cases to skyrocket around the world. V1, V2, and V3 caused faster virus transmission, which has now reached 192 countries and regions.
“Given the number of infections that occurred in October, all of these individual mutations, and even all pairs of mutations that could potentially interact epistatically, would have emerged independently,” the investigators explain.
To date, the number of cases has reached more than 117 million and 2.59 million deaths. The United States reports the highest number of infections, exceeding 29 million. Other countries whose cases have skyrocketed include India with 11.22 million cases; Brazil 11 million cases, Russia 4.28 million cases, and Britain 4.23 million cases.
* Important Notice
medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.