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Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review.

ABSTRACT: SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure-function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin-natural or synthetic-of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).

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The online version of this article (10.1007/s10311-020-01151-1) contains supplementary material, which is available to authorized users.

SUBMITTER: Sallard E

PROVIDER: S-EPMC7859469 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review.

Sallard Erwan E Halloy José J Casane Didier D Decroly Etienne E van Helden Jacques J

Environmental chemistry letters 20210204 2

SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure-function relationships of coronavirus proteins, inf ...[more]

PMID: 33558807

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Project description:The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-or protocol-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be screened and problematic variants removed, and we plan to regularly inform the scientific community with our updated results as more SARS-CoV-2 genome sequences are shared (https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 and https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480). We also develop tools for comparing and visualizing differences among very large phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse.

Project description:ObjectiveTo systematically review evidence on effectiveness of contact tracing apps (CTAs) for SARS-CoV-2 on epidemiological and clinical outcomes.DesignRapid systematic review.Data sourcesEMBASE (OVID), MEDLINE (PubMed), BioRxiv and MedRxiv were searched up to 28 October 2020.Study selectionStudies, both empirical and model-based, assessing effect of CTAs for SARS-CoV-2 on reproduction number (R), total number of infections, hospitalisation rate, mortality rate, and other epidemiologically and clinically relevant outcomes, were eligible for inclusion.Data extractionEmpirical and model-based studies were critically appraised using separate checklists. Data on type of study (ie, empirical or model-based), sample size, (simulated) time horizon, study population, CTA type (and associated interventions), comparator and outcomes assessed, were extracted. The most important findings were extracted and narratively summarised. Specifically for model-based studies, characteristics and values of important model parameters were collected.Results2140 studies were identified, of which 17 studies (2 empirical, 15 model-based studies) were eligible and included in this review. Both empirical studies were observational (non-randomised) studies and at high risk of bias, most importantly due to risk of confounding. Risk of bias of model-based studies was considered low for 12 out of 15 studies. Most studies demonstrated beneficial effects of CTAs on R, total number of infections and mortality rate. No studies assessed effect on hospitalisation. Effect size was dependent on model parameters values used, but in general, a beneficial effect was observed at CTA adoption rates of 20% or higher.ConclusionsCTAs have the potential to be effective in reducing SARS-CoV-2 related epidemiological and clinical outcomes, though effect size depends on other model parameters (eg, proportion of asymptomatic individuals, or testing delays), and interventions after CTA notification. Methodologically sound comparative empirical studies on effectiveness of CTAs are required to confirm findings from model-based studies.

Dataset Information

Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review.

Supplementary information

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Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review.

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