Abstract
The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.
Highlights
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is a member of the Coronaviridae family, a diverse group of virus species, seven of which are known to infect humans
As many vaccine programs initiated at that time, it is likely that this severe acute respiratory syndrome (SARS)-CoV-2 sequence, sampled in December
Focusing on the receptor binding domain (RBD), we found no evidence that mutations could affect binding to the angiotensin-converting enzyme 2 (ACE2) receptor, as only two shared mutations were identified at contact sites with the ACE2 receptor: a non-synonymous mutation (G476S) found in 8 sequences (0.15% of sequences) and a synonymous mutation found in 2 sequences at position 489 (0.04% of sequences)
Summary
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is a member of the Coronaviridae family, a diverse group of virus species, seven of which are known to infect humans. As many vaccine programs initiated at that time, it is likely that this SARS-CoV-2 sequence, sampled in December We can obtain insights about the transmission pathways and temporal spread of a virus by analyzing viral sequences sampled from individuals who became infected.
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