Published 31 January
Variants
With viruses, some mutations emerge while others recede. Rarely does one or more mutations confer a “selective advantage” to a new variant, for example enhanced transmissibility. Such variants can then become the new dominant virus.
Introduction
Over the last two months, several new SARS-CoV-2 variants have been described that are more transmissible, may escape both natural and vaccine-induced immunity and could impact COVID-19 morbidity and mortality. It is too early to assert that these variants will create a new pandemic within the pandemic, however, in countries like England, South Africa, Brazil, Ireland, Portugal and Israel, they may have modified the dynamic of the latest outbreaks for the worse. More transmissible SARS-CoV-2 variants will replace older variants – everywhere! Countries where the prevalence of these new variants is still low should anticipate rapid spread within the next weeks and months and plan ahead accordingly, ie closing/restricting borders, etc.
The current trio infernale:
- B117 (first described in England; Rambaut 2020)
- B1351 (first described in South Africa; Tegally 2020)
- P1 (first described in Brazil; Faria 2021)
Paper of the Day
Vogels CBF, Breban M, Alpert T, et al. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern. medRxiv 2021, posted 1 February. Full-text: https://doi.org/10.1101/2021.01.28.21250486
Nathan Grubaugh, Chantal Vogels and colleagues identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in the new trio infernale variants B117, B1351, and P1 which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, they designed and validated an open source PCR assay to detect the new variants. The authors assure that their assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B117, B1351, P1.
Figure 1. Identification of genome targets to differentiate between B.1.1.7, B.1.351, P.1, and other SARS-CoV-2 lineages. (A) Location on the SARS-CoV-2 genome where the targeted deletions in the ORF1a gene at amino acid positions 3675-3677 (Δ3675-3677) and the spike gene at amino acid positions 69-70 (Δ69-70) occur. (B) The Nextstrain ‘global build’ (nextstrain.org/ncov/global) accessed… | Continue reading at https://doi.org/10.1101/2021.01.28.21250486.
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Copy-editor: Rob Camp