The Evolution and Biology of SARS-CoV-2 Variants

Telenti, Amalio; Hodcroft, Emma B.; Robertson, David L.

doi:10.1101/cshperspect.a041390

Cited by 137 publications

(127 citation statements)

References 121 publications

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“…The successive waves and replacement of variants in Venezuela are also consistent with the relative fitness evaluated for them [32]. According to this review, the relative average fitness of the Omicron BA.1 has been estimated around 60% higher than that of the Delta VOC, which in turn is around 50% higher than that of the Gamma VOC.…”

Section: Discussionsupporting

confidence: 75%

“…The Mu VOI displayed on average a slightly higher fitness compared to the Gamma VOC, which might explain that this VOI was able to circulate in the whole country despite the presence of the Gamma VOC. In contrast, the founder effect of the Gamma VOC did not allow the dissemination of the Alpha VOC or the Lambda VOI, which exhibit lower or similar fitness, respectively, compared to the Gamma one [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

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Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela

Jaspe

Loureiro

Sulbarán

et al. 2022

Viruses

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Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody-mediated neutralization and were designated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela from March 2021 to February 2022. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of the Delta VOC in June 2021, it became the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela

Jaspe

Loureiro

Sulbarán

et al. 2022

Viruses

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“…While Paxlovid is already proving useful in blunting SARS-CoV-2 disease pathogenesis, the long-term consequences of its wide-spread prescription are unknown. Resistance is a major concern given the relatively rapid rates at which SARS-CoV-2 is changing (Alpha, Beta, Delta, Omicron, etc) and the fact that the potency of nirmatrelvir and ensitrelvir varies widely against other coronavirus species (14) . For instance, the main proteases of the human α-coronaviruses NL63 and 229E are less susceptible to these drugs suggesting that natural mechanisms of resistance are indeed possible and may already exist in nature (12, 15) .…”

Section: Introductionmentioning

confidence: 99%

Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors

Moghadasi

Heilmann

Khalil³

et al. 2022

Preprint

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First-generation vaccines and drugs have helped reduce disease severity and blunt the spread of SARS-CoV-2. However, ongoing virus transmission and evolution and increasing selective pressures have the potential to yield viral variants capable of resisting these interventions. Here, we investigate the susceptibility of natural variants of the main protease (Mpro/3CLpro) of SARS-CoV-2 to protease inhibitors. Multiple single amino acid changes in Mpro confer resistance to nirmatrelvir (the active component of Paxlovid). An additional inhibitor in clinical development, ensitrelvir, shows a different resistance mutation profile. Importantly, phylogenetic analyses indicate that nirmatrelvir-resisting variants have pre-existed the introduction of this drug into the human population and are capable of spreading. A similarly strong argument can be made for ensitrelvir. These results caution against broad administration of protease inhibitors as stand-alone therapies and encourage the development of additional protease inhibitors and other antiviral drugs with different mechanisms of action and resistance profiles.

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“…4 While Omicron (lineage B.1.1.529) appears to cause less severe disease than Delta on a per-infection basis—likely due to a combination of lower intrinsic severity and the high observed concentration of cases among the previously vaccinated or infected 5 —its elevated transmissibility, including among the seropositive, resulted in the largest wave of SARS-CoV-2 transmission in the U.S. to date. 6, 7 Vaccines developed against the non-variant SARS-CoV-2 are less effective at protecting against infection with Delta and Omicron, but remain highly effective against severe disease. 8–10…”

Section: Introductionmentioning

confidence: 99%

One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants

Walker

Grubaugh

Gonsalves

et al. 2022

Preprint

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Background: Over one million COVID-19 deaths have been recorded in the United States. Sustained global SARS-CoV-2 transmission has led to the emergence of new variants with increased transmissibility, virulence, and/or immune evasion. The specific burden of mortality from each variant over the course of the U.S. COVID-19 epidemic remains unclear. Methods: We constructed an epidemiologic model using data reported by the CDC on COVID-19 mortality and circulating variant proportions to estimate the number of recorded COVID-19 deaths attributable to each SARS-CoV-2 variant in the U.S. We conducted sensitivity analysis to account for parameter uncertainty. Findings: Of the 1,003,419 COVID-19 deaths recorded as of May 12, 2022, we estimate that 460,124 (46%) were attributable to WHO-designated variants. By U.S. Census Region, the South recorded the most variant deaths per capita (median estimate 158 per 100,000), while the Northeast recorded the fewest (111 per 100,000). Over 40 percent of national COVID-19 deaths were estimated to be caused by the combination of Alpha (median estimate 39,548 deaths), Delta (273,801), and Omicron (117,560). Interpretation: SARS-CoV-2 variants that have emerged around the world have imposed a significant mortality burden in the U.S. In addition to national public health strategies, greater efforts are needed to lower the risk of new variants emerging, including through global COVID-19 vaccination, treatment, and outbreak mitigation.

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The Evolution and Biology of SARS-CoV-2 Variants

Cited by 137 publications

References 121 publications

Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela

Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela

Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors

One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants

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