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A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants.
Dearlove, Bethany; Lewitus, Eric; Bai, Hongjun; Li, Yifan; Reeves, Daniel B; Joyce, M Gordon; Scott, Paul T; Amare, Mihret F; Vasan, Sandhya; Michael, Nelson L; Modjarrad, Kayvon; Rolland, Morgane.
  • Dearlove B; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Lewitus E; US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Bai H; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817.
  • Li Y; Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Reeves DB; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Joyce MG; US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Scott PT; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817.
  • Amare MF; Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Vasan S; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Michael NL; US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
  • Modjarrad K; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817.
  • Rolland M; Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910.
Proc Natl Acad Sci U S A ; 117(38): 23652-23662, 2020 09 22.
Article in English | MEDLINE | ID: covidwho-737878
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Vaccines / Genome, Viral / Betacoronavirus Topics: Vaccines / Variants Limits: Humans Language: English Journal: Proc Natl Acad Sci U S A Year: 2020 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Vaccines / Genome, Viral / Betacoronavirus Topics: Vaccines / Variants Limits: Humans Language: English Journal: Proc Natl Acad Sci U S A Year: 2020 Document Type: Article