Large-scale population analysis of SARS-CoV-2 whole genome sequences reveals host-mediated viral evolution with emergence of mutations in the viral Spike protein associated with elevated mortality rates

Abstract

Background We aimed to further characterize and analyze in depth intra-host variation and founder variants of SARS-CoV-2 worldwide up until August 2020, by examining in excess of 94,000 SARS-CoV-2 viral sequences in order to understand SARS-CoV-2 variant evolution, how these variants arose and identify any increased mortality associated with these variants. Methods and Findings We combined worldwide sequencing data from GISAID and Sequence Read Archive (SRA) repositories and discovered SARS-CoV-2 hypermutation occurring in less than 2% of COVID19 patients, likely caused by host mechanisms involved APOBEC3G complexes and intra-host microdiversity. Most of this intra-host variation occurring in SARS-CoV-2 are predicted to change viral proteins with defined variant signatures, demonstrating that SARS-CoV-2 can be actively shaped by the host immune system to varying degrees. At the global population level, several SARS-CoV-2 proteins such as Nsp2, 3C-like proteinase, ORF3a and ORF8 are under active evolution, as evidenced by their increased πN/πS ratios per geographical region. Importantly, two emergent variants: V1176F in co-occurrence with D614G mutation in the viral Spike protein, and S477N, located in the Receptor Binding Domain (RBD) of the Spike protein, are associated with high fatality rates and are increasingly spreading throughout the world. The S477N variant arose quickly in Australia and experimental data support that this variant increases Spike protein fitness and its binding to ACE2. Conclusions SARS-CoV-2 is evolving non-randomly, and human hosts shape emergent variants with positive fitness that can easily spread into the population. We propose that V1776F and S477N variants occurring in the Spike protein are two novel mutations occurring in SARS-CoV-2 and may pose significant public health concerns in the future.

Epidemic trends of SARS-CoV-2 associated with immunity, race, and viral mutations

“…The Spike: S477N mutation has been shown to enhance folding and binding to the angiotensin-converting enzyme 2 (ACE2) receptor. 25,26 Consistent with our results, Spike: S477N has been correlated with higher CFR. 25 Spike: V1176F mutation has been predicted to increase stability of the protein and flexibility of the trimeric stalk.…”

“…25,26 Consistent with our results, Spike: S477N has been correlated with higher CFR. 25 Spike: V1176F mutation has been predicted to increase stability of the protein and flexibility of the trimeric stalk. 25 It is also reported that the Spike: V1176F, ORF6: I33T, and ORF1a: L3930F mutations are correlated with increased CFR in Brazil.…”

“…In contrast to our results, Clade GV has been reported to increase CFR. 25 However, because Clade GV is widespread in Europe, where CFR is high, regional differences become confounding factors and apparently increase the Clade's CFR. Our ecological analysis conducted exclusively in Spain to eliminate confounding factors is expected to more accurately reflect the nature of the virus.…”

“…25 It is also reported that the Spike: V1176F, ORF6: I33T, and ORF1a: L3930F mutations are correlated with increased CFR in Brazil. 25 Overall, the mutations may improve the fitness of SARS-CoV-2 in the cell and promote the spread of the virus.…”

“…25 Spike: V1176F mutation has been predicted to increase stability of the protein and flexibility of the trimeric stalk. 25 It is also reported that the Spike: V1176F, ORF6: I33T, and ORF1a: L3930F mutations are correlated with increased CFR in Brazil. 25 Overall, the mutations may improve the fitness of SARS-CoV-2 in the cell and promote the spread of the virus.…”