No detectable signal for ongoing genetic recombination in SARS-CoV-2

Richard, Damien; Owen, Christopher J.; Dorp, Lucy van; Balloux, François

doi:10.1101/2020.12.15.422866

Cited by 19 publications

(17 citation statements)

References 61 publications

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“…Another potential source of novel variants within individual infections is recombination. There is debate about the extent of recombination in SARS-CoV-2 20,21 , in part because detecting recombination is challenging when there is relatively little genomic variation 22 . All circulating SARS-CoV-2 viruses are similar and closely related by descent from the virus that first infected humans in late 2019.…”

Section: Factors At Play In the Emergence And Spread Of Vocsmentioning

confidence: 99%

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

et al. 2021

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One year into the global COVID-19 pandemic, the focus of attention has shifted to the emergence and spread of SARS-CoV-2 variants of concern (VOCs). After nearly a year of the pandemic with little evolutionary change affecting human health, several variants have now been shown to have substantial detrimental effects on transmission and severity of the virus. Public health officials, medical practitioners, scientists, and the broader community have since been scrambling to understand what these variants mean for diagnosis, treatment, and the control of the pandemic through nonpharmaceutical interventions and vaccines. Here we explore the evolutionary processes that are involved in the emergence of new variants, what we can expect in terms of the future emergence of VOCs, and what we can do to minimise their impact.

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Section: Factors At Play In the Emergence And Spread Of Vocsmentioning

confidence: 99%

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

et al. 2021

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“…The beta-binomial method adopts several important assumptions. It assumes viral genetic diversity is neutral and variant frequencies are not impacted by selection; it also assumes variant sites are independent, which may not be true given that SARS-CoV-2 contains a continuous genome thought to undergo limited recombination (55). In addition, the betabinomial method assumes that identical variants found in the index and contact are shared as a result of transmission, though it is possible that identical variants occurring in a donor and a .…”

Section: Transmission Bottleneck Calculationmentioning

confidence: 99%

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

Braun

Moreno

Wagner

et al. 2021

Preprint

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The recent emergence of divergent SARS-CoV-2 lineages has raised concerns about the role of selection within individual hosts in propagating novel variants. Of particular concern are variants associated with immune escape and/or enhanced transmissibility. Though growing evidence suggests that novel variants can arise during prolonged infections, most infections are acute. Understanding the extent to which variants emerge and transmit among acutely infected hosts is therefore critical for predicting the pace at which variants resistant to vaccines or conferring increased transmissibility might emerge in the majority of SARS-CoV-2 infections. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely infected individuals. We find that within-host diversity during acute infection is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household. Accordingly, we also find that within-host variants are rarely detected along phylogenetically linked infections in the broader community. Together, these findings suggest that efficient selection and transmission of novel SARS-CoV-2 variants is unlikely during typical, acute infection.

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“…Two more recent pre-prints have also identified recombinant SARS-CoV-2 genomes, but used substantially different methods 7,8 . Although these analyses identified recombinant SARS-CoV-2 genomes, four studies have reported evidence of strong linkage disequilibrium among polymorphic sites and no disruption of the clonal pattern of inheritance, suggesting recombinant SARS-CoV-2 strains are not widespread 9–12 .…”

Section: Introductionmentioning

confidence: 96%

Recombinant SARS-CoV-2 genomes are currently circulating at low levels

VanInsberghe

Neish

Lowen

et al. 2020

Preprint

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Viral recombination has the potential to bring about viral genotypes with modified phenotypic characteristics, including transmissibility and virulence. Although the capacity for recombination among Betacoronaviruses is well documented, SARS-CoV-2 has only been circulating in humans for approximately 8 months and thus has had a relatively short window of opportunity for the occurrence of recombination. The ability to detect recombination has further been limited by the relatively low levels of genetic diversity in SARS-CoV-2. Despite this, two studies have reported recombinants among SARS-CoV-2 strains. Here we first revisit these findings with a new analysis approach, arguing that neither presents a clear case of within-SARS-CoV-2 recombination. Applying this same approach to available SARS-CoV-2 sequences, we then identify five recombinant genomes. Each of these genomes contain phylogenetic markers of two distinct SARS-CoV-2 clades. Further, the predicted parent clades of these recombinant genomes were, with one exception, documented to be co-circulating in the country of infection in the two weeks prior to the sample being collected. Our results indicate that recombination among SARS-CoV-2 strains is occurring, but is either not widespread or often remains undetectable given current levels of viral genetic diversity. Efforts to monitor the emergence of new recombinant genomes should therefore be sustained.

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No detectable signal for ongoing genetic recombination in SARS-CoV-2

Cited by 19 publications

References 61 publications

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

Recombinant SARS-CoV-2 genomes are currently circulating at low levels

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