Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Nov 23;78(Suppl 2):ii25-ii36.
doi: 10.1093/jac/dkad309.

SARS-CoV-2 genomics and impact on clinical care for COVID-19

Ramon Lorenzo-Redondo  1   2 , Alexandre Machado de Sant'Anna Carvalho  1   2 , Judd F Hultquist  1   2 , Egon A Ozer  1   2
Affiliations

SARS-CoV-2 genomics and impact on clinical care for COVID-19

Ramon Lorenzo-Redondo et al. J Antimicrob Chemother. .

Abstract

The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Viral genetic diversity is the basis of natural selection and viral evolution. All viruses mutate over time. Mutations that are disadvantageous or that come at a cost to viral fitness are selected against. Mutations that confer a fitness advantage, especially in the presence of a selective pressure (represented by the horizontal dotted line), will be more likely to persist in future generations. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.
Figure 2.
Figure 2.
Different SARS-CoV-2 ORFs have accumulated different amounts of variability. (a) Schematic of the SARS-CoV-2 genome and encoded proteins, separated broadly in the figure by function. (b) Entropy (a measure of genetic variability) in each SARS-CoV-2 ORF. Dot size and colour reflect the degree of entropy accumulated in the viral population since its emergence. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.
Figure 3.
Figure 3.
Workflow diagram comparing metagenomic, amplicon-based and target capture strategies for pathogen genomics. The pie charts at the end depict the theoretical yield of pathogen sequence versus host or non-specific background. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.
Figure 4.
Figure 4.
The ongoing evolution of SARS-CoV-2. (a) Phylogenetic tree of representative consensus sequences for globally prominent SARS-CoV-2 clades and variants of concern (Alpha, Beta, Gamma, Delta, and Omicron). (b) Cumulative frequency plot of globally prominent SARS-CoV-2 clades and variants of concern from December 2019 to February 2023. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

  • Lessons identified for a future pandemic.
    Cunningham N, Hopkins S. Cunningham N, et al. J Antimicrob Chemother. 2023 Nov 23;78(Suppl 2):ii43-ii49. doi: 10.1093/jac/dkad310. J Antimicrob Chemother. 2023. PMID: 37995355 Free PMC article.

References

    1. Dolan PT, Whitfield ZJ, Andino R. Mapping the evolutionary potential of RNA viruses. Cell Host Microbe 2018; 23: 435–46. 10.1016/j.chom.2018.03.012 - DOI - PMC - PubMed
    1. Dolan PT, Whitfield ZJ, Andino R. Mechanisms and concepts in RNA virus population dynamics and evolution. Annu Rev Virol 2018; 5: 69–92. 10.1146/annurev-virology-101416-041718 - DOI - PubMed
    1. Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biol 2018; 16: e3000003. 10.1371/journal.pbio.3000003 - DOI - PMC - PubMed
    1. Lauring AS, Frydman J, Andino R. The role of mutational robustness in RNA virus evolution. Nat Rev Microbiol 2013; 11: 327–36. 10.1038/nrmicro3003 - DOI - PMC - PubMed
    1. Sanjuan R. From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses. PLoS Pathog 2012; 8: e1002685. 10.1371/journal.ppat.1002685 - DOI - PMC - PubMed

Publication types

Substances

-