Clinical performance of Roche cobas 6800, Luminex ARIES, MiRXES Fortitude Kit 2.1, Altona RealStar, and Applied Biosystems TaqPath for SARS‐CoV‐2 detection in nasopharyngeal swabs

Lee, Chun Kiat; Tham, Jason Wei Ming; Png, Siyu; Chai, Chean Nee; Ng, Shu Chi; Tan, Eunice Jia Min; Ng, Li Jie; Chua, Rui Ping; Sani, Musa; Seow, Yiqi; Yan, Gabriel; Tang, Julian W.

doi:10.1002/jmv.26940

Cited by 12 publications

(6 citation statements)

References 9 publications

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“…To ensure assay specificity, a subset of 25 positive and 25 negative samples were additionally tested with the TaqPath kit (ThermoFisher Scientific) that targets the SARS-CoV-2 ORF1ab, N gene, and S gene (39,40). All results were concordant with both assays.…”

Section: Methodsmentioning

confidence: 99%

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Kuchipudi

Nair

Ruden

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

196

211

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Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ∼75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

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Section: Methodsmentioning

confidence: 99%

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Kuchipudi

Nair

Ruden

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

196

211

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“…All samples were found to be negative for the presence of the human RP gene by RT-PCR. Samples were also tested using a TaqPath kit (ThermoFisher Scientific) that targets the SARS-CoV-2 ORF1ab, N gene, and S gene 19,20 as the first screen for Omicron, which typically presents as an S gene drop out in these assays 21 .…”

Section: Rna Extraction and Rt-pcr For Sars-cov-2 Detectionmentioning

confidence: 99%

Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer

Vandegrift

Yon

Nair

et al. 2022

Preprint

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White-tailed deer (Odocoileus virginianus) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly (χ2, p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a breakthrough infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans.

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“…Similar results were found in this study where nine different dilutions, ranging from 25 copies/ml to 6,250 copies/ml were tested, and 25 copies/ml was found to be the lowest detectable concentration for both the target genes. Other studies have also supported this claim that the Cobas 6,800 has a lower limit of detection for SARS-COV-2 detection and that the Cobas E gene is more sensitive among the various other target genes in low viral load samples (Pujadas et al, 2020;Lee et al, 2021).…”

Section: Limit Of Detectionmentioning

confidence: 68%

Diagnostic accuracy of the Cobas 6800 RT-PCR assay for detection of SARS-CoV-2 RNA

Mahmoud¹,

Ganesan²,

Raheja³

et al. 2022

Front. Anal. Sci.

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Introduction: The COVID-19 pandemic has led to the rapid development and launch of several commercial RT-PCR-based assays for identification of SARS-CoV-2. However, there is need for peer-reviewed evaluation of these assays that can support their clinical performance. In this study, we, therefore, conduct an in-house evaluation of the automated Cobas 68000 RT-PCR assay in detecting SARS-CoV-2 infections using different pooling techniques.Methods: An observational study is conducted to evaluate the clinical performance of the Cobas 6800 SARS-CoV-2 assay in comparison with the Labgun Exofast RT-PCR kit, using both pooled and non-pooled sample techniques. A total of 300 nasopharyngeal swab samples, 40 known positive samples and 260 negative samples, are used for pooling, while the performance is evaluated in three different sample pool sizes of 4, 5, and 6.Results: The sensitivity and specificity of the Cobas 6,800 was 100% when compared to the comparable assay. The sample pooling technique showed that specificity was 100% in all pool sizes and the sensitivity varied from 95% in the 6-pooled sample to 100% in both the 5- and 4-pooled samples. The lower limit of detection was verified as 25 copies/ml for un-pooled samples, and, therefore, the limit of detection was 100, 125, and 150 copies/ml for the 4, 5, and 6 sample pools, respectively. Strong correlation was observed between the Ct values of the target genes of both assays.Conclusion: Cobas 6800 RT-PCR assay is a reliable platform for qualitative and rapid detection of SARS-CoV-2 and can be effectively utilized for pooling of samples with highly efficient performance when disease prevalence is lower.

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Clinical performance of Roche cobas 6800, Luminex ARIES, MiRXES Fortitude Kit 2.1, Altona RealStar, and Applied Biosystems TaqPath for SARS‐CoV‐2 detection in nasopharyngeal swabs

Cited by 12 publications

References 9 publications

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer

Diagnostic accuracy of the Cobas 6800 RT-PCR assay for detection of SARS-CoV-2 RNA

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