April 5, 2023

expert reaction to study looking at SARS-CoV-2 in environmental samples from the Huanan Seafood Market

A study published in Nature looks at surveillance of SARS-CoV-2 at the Huanan Seafood Market.

Prof Alice Hughes, Group Leader Biodiversity Analytics of Terrestrial Ecosystems (BAT) group, University of Hong Kong, said:

“Sadly this study has not progressed since the preprint, and the analysis is incredibly weak.  In one of the figures in their paper, you can see that their analysis suggests the presence of Pandas, Chimpanzees, degus, two genera of molerats – among others.  None of those can possibly have been in the market.  (Killing a Panda carries the death sentence, so there is no way they could be in a market.)  This either relates to very poor species assignment, or contamination of the genomic samples (or both).  Some of these animals would be in Chinese labs (molerats are model species), so contamination of genomic samples when being analysed in the lab is possible.  The text itself switches between the Latin and common names of species, which again creates inconsistencies (like whether ferret badgers, Asian badgers, hog badgers or even Eurasian badgers were present in their analysis).  Also the paper states it uses methods to exclude human DNA, but it is still there, highlighting inconsistencies in methods in addition to major flaws in analysis.

“The issue of the origins of SARS-CoV-2 is so important.  It’s a shame there couldn’t have been more collaboration in working on this analysis, as there do appear to be errors in the analysis.  We should be looking for further analysis on these datasets, where necessary care is applied to ensure reliable and accurate results.

“The good news is that this paper legitimises the analysis of the data by others.”

‘Surveillance of SARS-CoV-2 at the Huanan Seafood Market’ by William J. Liu was published in Nature on Wednesday 5 April 2023.

DOI: 10.1038/s41586-023-06043-2

https://www.nature.com/articles/s41586-023-06043-2

Declared interests

Prof Alice Hughes: “No COI.  Some of my work has been on bats and covid in China, and until the end of 2021 I was working in Yunnan (as I had been since 2013).  These are my comments based on my work and that of various collaborators, as well as my experiences within China and how things operate within China.”