ArticleJMIR public health and surveillance2020
A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.
Article in JMIR public health and surveillance, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.Scientific reports · 2026Article
- Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.Microorganisms · 2025Article
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- The importance of utilizing travel history metadata for informative phylogeographical inferences: a case study of early SARS-CoV-2 introductions into Australia.Microbial genomics · 2023Article
- Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink.Virus evolution · 2023Article
- New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia.PLoS genetics · 2022Article
- SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods.Pathogens (Basel, Switzerland) · 2022Review
- Single-cell sequencing of brain tissues reveal the central nervous system's susceptibility to SARS-CoV-2 and the drug.Frontiers in pharmacology · 2022Article
- Article
- Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.Molecular biology and evolution · 2021Article
- European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients.Journal of applied genetics · 2021Article
- SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.Communications biology · 2021Article
- SARS-CoV-2 within-host diversity and transmission.Science (New York, N.Y.) · 2021Article
- Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation.Scientific reports · 2021Article
- Phylogenetic analysis of SARS-CoV-2 in the first few months since its emergence.Journal of medical virology · 2021Article
- Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants.Microorganisms · 2021Article
- Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo.Current protocols · 2021Article
- Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia.Viruses · 2021Article
- Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on "A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis".JMIR public health and surveillance · 2020Article
- Authors' Reply to: Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on "A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis".JMIR public health and surveillance · 2020Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
objectiveThe 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.
methodsWe 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.
resultsAlthough 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.
conclusionsAt 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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