A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis
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Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been growing exponentially, affecting over 4 million people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published both in scientific journals and through non–peer-reviewed channels to investigate the genetic heterogeneity and spatiotemporal dissemination of SARS-CoV-2. However, a systematic investigation of phylogenetic information and sampling bias in the available data is lacking. Although the number of available genome sequences of SARS-CoV-2 is growing daily and the sequences show increasing phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution.
Objective
The objective of this study was to determine the quality of the currently available SARS-CoV-2 full genome data in terms of sampling bias as well as phylogenetic and temporal signals to inform and guide the scientific community.
Methods
We used maximum likelihood–based methods to assess the presence of sufficient information for robust phylogenetic and phylogeographic studies in several SARS-CoV-2 sequence alignments assembled from GISAID (Global Initiative on Sharing All Influenza Data) data released between March and April 2020.
Results
Although the number of high-quality full genomes is growing daily, and sequence data released in April 2020 contain sufficient phylogenetic information to allow reliable inference of phylogenetic relationships, country-specific SARS-CoV-2 data sets still present severe limitations.
Conclusions
At the present time, studies assessing within-country spread or transmission clusters should be considered preliminary or hypothesis-generating at best. Hence, current reports should be interpreted with caution, and concerted efforts should continue to increase the number and quality of sequences required for robust tracing of the epidemic.
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SciScore for 10.1101/2020.03.16.20034470: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Evaluation of the presence of phylogenetic signal satisfying resolved phylogenetic relationships among sequences was carried out with IQ-TREE, allowing the software to search for all possible quartets using the best-fitting nucleotide substitution model 11. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Exploration of temporal structure, i.e. presence of molecular clock in the data, was assessed by regression of divergence -root-to-tip genetic distance-against sampling time using … SciScore for 10.1101/2020.03.16.20034470: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Evaluation of the presence of phylogenetic signal satisfying resolved phylogenetic relationships among sequences was carried out with IQ-TREE, allowing the software to search for all possible quartets using the best-fitting nucleotide substitution model 11. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Exploration of temporal structure, i.e. presence of molecular clock in the data, was assessed by regression of divergence -root-to-tip genetic distance-against sampling time using TempEst 19. TempEstsuggested: (TempEst, RRID:SCR_017304)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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