By Neha MathurMay 1 2023Reviewed by Benedette Cuffari, M.Sc. In a recent study posted to the bioRxiv* preprint server, American computational virologist Dr. Jesse D. Bloom analyzes the association between the severe acute respiratory syndrome coronavirus 2 genetic material and the genetic material obtained from environmental and animal samples collected by the Chinese Centers for Disease Control and Prevention from the Huanan Seafood Market in Wuhan, China.
Where did SARS-CoV-2 originate? At the end of 2019, Chinese officials claimed that SARS-CoV-2 infections were only identified in patients who previously attended the Huanan Seafood Market, thus indicating that human-to-human transmission of the virus was not occurring. However, by January 2020, it became clear that SARS-CoV-2 was spreading between humans, with some of the earliest coronavirus disease 2019 cases having no relation to the Huanan Seafood Market.
Nevertheless, the Chinese CDC eventually uploaded the raw sequencing data for some of the environmental samples to the Global Initiative on Sharing All Influenza Data database. Thereafter, bioinformatic analysis of this data led to the identification that some of the environmental samples contained genetic material from animals like raccoon dogs that are susceptible to SARS-CoV-2.
When the author’s computational pipeline was applied to the environmental samples, over 75% of these samples did not exhibit any reads that aligned to the SARS-CoV-2 genetic material, with most of the remaining 25% also exhibiting only a small number of viral reads. In fact, only two samples had over 1,000 reads that aligned with SARS-CoV-2.
Although the degree of correlation increased between SARS-CoV-2 and human genetic material when samples collected before January 12, 2020, were excluded, Dr. Bloom found that the genetic material of goats and spotted doves were also similarly correlated. Notably, neither analysis indicated that the genetic material of raccoon dogs nor bamboo rats was positively correlated with SARS-CoV-2 reads.