A snapshot of SARS-CoV-2 genome availability up to April 2020 and its implications

ABSTRACT

BACKGROUND: The SARS-CoV-2 pandemic has been growing exponentially, affecting over four million people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published in scientific journals, as well as through non-peer reviewed channels, to investigate SARS-CoV-2 genetic heterogeneity and spatiotemporal dissemination. Yet, a systematic investigation of phylogenetic information and sampling bias in the available data is missing. OBJECTIVE: The objective of this study was to determine the quality of the current SARS-CoV-2 full genome data, in terms of sampling bias as well as phylogenetic and temporal signal, 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 data released between March and April 2020. RESULTS: Although number of high quality full-genomes is growing daily, and recent sequence data released in April contains sufficient phylogenetic information that would 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 at best, or hypothesis generating. Hence, the need for interpreting current reports with caution, and continuing concerted efforts to increase number and quality of sequences required for robust tracing of the epidemic. CLINICALTRIAL INTERNATIONAL REGISTERED REPORT RR2-https//doi.org/10.1101/2020.04.01.020594.