Nipah virus vector sequences in COVID-19 patient samples sequenced by the Wuhan Institute of Virology

TL;DR

This study uncovers the presence of a Nipah virus infectious clone in COVID-19 patient samples sequenced by WIV, suggesting possible laboratory contamination or research activities involving high-risk pathogens.

Contribution

It provides evidence of Nipah virus sequences in patient samples, indicating WIV was working with Nipah infectious clones, which was previously unreported.

Findings

Detection of Nipah virus genes in patient samples

Identification of synthetic vector sequences indicating infectious clone presence

Implication of potential BSL-4 protocol breach

Abstract

We report the detection of Nipah virus in an infectious clone format, a BSL4-level pathogen and CDC-designated Bioterrorism Agent, in raw RNA-Seq sequencing reads deposited by the Wuhan Institute of Virology (WIV) produced from five December 2019 patients infected with SARS-CoV-2. Research involving Nipah infectious clones has never been reported to have occured at the WIV. These patient samples have been previously reported to contain reads from several other viruses: Influenza A, Spodoptera frugiperda rhabdovirus and Nipah. Previous authors have interpreted the presence of these virus sequences as indicative of co-infections of the patients in question by these pathogens or laboratory contamination. However, our analysis shows that NiV genes are encapsulated in synthetic vectors, which we infer was for assembly of a NiV infectious clone. In particular, we document the finding of internal N, P-V-W-C and L protein coding sequences as well as coverage of the G and F genes. Furthermore, the format of Hepatitis D virus ribozyme and T7 terminator downstream of the 5-prime end of the NiV sequence is consistent with truncation required at the end of the genome for a full length infectious clone. This indicates that research at WIV was being conducted on an assembled NiV infectious clone. Contamination of patient sequencing reads by an infectious NiV clone of the highly pathogenic Bangladesh strain could indicate a significant breach of BSL-4 protocols. We call on WIV to explain the purpose of this research on infectious clones of Nipah Virus, the full chronology of this work, and to explain how and at what stage of sample preparation this contamination occurred.