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

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’ 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 BSL4 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.