Recurrent Aspergillus contamination in a biomedical research facility: a case study

Zhang

et al. 2022

Preprint

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here we examine thenovel SARS2r-CoV we previously identified in game animal metatranscriptomic datasetssequenced by He et al. (2022) and find that sections of the partial genome phylogenetically groupwith Guangxi (GX) pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, the same CoV isalso found in 10 additional NGS datasets from 5 separate mammalian species and is likelyrelated to contamination by a laboratory researched virus. Absence of bat mitochondrialsequences from the datasets, the fragmentary nature of the virus sequence and the presence of apartial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has beencloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated withsignificant Homo sapiens genetic material, and numerous viruses not associated with the hostanimals sampled. We further identify the dominant human haplogroup of the contaminatingH.sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association ofthis novel CoV with both bat CoV and the Guangxi pangolin CoV (GX PCoV) clades is animportant step towards identifying the origin of the GX PCoVs.

Section: Mitochondrial Mapping Analysismentioning

confidence: 99%

Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentation

Zhang

et al. 2022

Preprint

“…Several species of Aspergillus and Candida yeasts are also found. The widespread yeast occurrences may be indicative of cell culture with yeast growth contaminating the samples, contamination during incubation [49], or yeast contamination of materials during the library preparation stage.…”

Section: Mitochondrial Mapping Analysismentioning

confidence: 99%

Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation

Zhang³

et al. 2022

Applied Microbiology

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs.

“…Several species of Aspergillus and Candida yeasts are also found. The widespread yeast occurrences may be indicative of cell culture with yeast growth contaminating the samples, contamination during incubation (Cornelison et al 2012), or yeast contamination of materials during the library preparation stage.…”

Section: Mitochondrial Mapping Analysismentioning

confidence: 99%

Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentation

Zhang

et al. 2022

Preprint

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by He et al. (2022) and find that sections of the partial genome phylogenetically group with Guangxi (GX) pangolin CoVs (GX PCoVs) while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, the same CoV is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H.sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel CoV with both bat CoV and the Guangxi pangolin CoV (GX PCoV) clades is an important step towards identifying the origin of the GX PCoVs.