A pan-coronavirus RT-PCR assay for rapid viral screening of animal, human, and environmental specimens

Xiu, Leshan; Binder, Raquel A.; Toh, Teck-Hock; Lee, Jeffrey Soon-Yit; Ting, Jakie; Than, Son T.; Qi, Wenhao; Coleman, Kristen K.; Perera, David; Ma, Mai‐Juan; Gray, Gregory C.

doi:10.1016/j.onehlt.2021.100274

Cited by 4 publications

(3 citation statements)

References 19 publications

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“…However, from individual analysis, X-CoV PCR was the method of choice for γ-CoV and δ-CoV testing. X-CoV PCR should be used for the study of CoVs from the environment, including wastewater or air samples that may contain CoV from birds or swines [ 21 , 37 ]. To avoid false negative results, the use of two protocols during testing is recommended.…”

Section: Discussionmentioning

confidence: 99%

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Wacharapluesadee,

Thippamom,

Hirunpatrawong

et al. 2024

Viruses

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Emerging coronaviruses (CoVs) are understood to cause critical human and domestic animal diseases; the spillover from wildlife reservoirs can result in mild and severe respiratory illness in humans and domestic animals and can spread more readily in these naïve hosts. A low-cost CoV molecular method that can detect a variety of CoVs from humans, animals, and environmental specimens is an initial step to ensure the early identification of known and new viruses. We examine a collection of 50 human, 46 wastewater, 28 bat, and 17 avian archived specimens using 3 published pan-CoV PCR assays called Q-, W-, and X-CoV PCR, to compare the performance of each assay against four CoV genera. X-CoV PCR can detect all four CoV genera, but Q- and W-CoV PCR failed to detect δ-CoV. In total, 21 (42.0%), 9 (18.0%), and 21 (42.0%) of 50 human specimens and 30 (65.22%), 6 (13.04%), and 27 (58.70%) of 46 wastewater specimens were detected using Q-, W-, and X-CoV PCR assays, respectively. The X-CoV PCR assay has a comparable sensitivity to Q-CoV PCR in bat CoV detection. Combining Q- and X-CoV PCR assays can increase sensitivity and avoid false negative results in the early detection of novel CoVs.

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Section: Discussionmentioning

confidence: 99%

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Wacharapluesadee,

Thippamom,

Hirunpatrawong

et al. 2024

Viruses

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“…Real-time PCR (RT-PCR) and quantitative PCR (qPCR) are highly precise and efficient techniques used in bioaerosol research for the detection and quantification of DNA samples [27]. RT-PCR, a specific form of qPCR, enables accurate quantification of microbial DNA in air samples by monitoring fluorescent signals in real time during the PCR process.…”

Section: Analysis Of Research Trendsmentioning

confidence: 99%

Navigating the Aerosolized Frontier: A Comprehensive Review of Bioaerosol Research Post-COVID-19

Zhang,

Dai,

Gebrezgiabhier

et al. 2024

Atmosphere

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In the wake of the COVID-19 pandemic, the scientific community has been galvanized to unravel the enigmatic role of bioaerosols in the transmission of infectious agents. This literature review, anchored in the extensive Web of Science Core Collection database covering the period from 1990 to 2023, utilizes a bibliometric approach to chart the dynamic landscape of bioaerosol research. It meticulously documents the paradigm shifts and burgeoning areas of inquiry that have emerged in the aftermath of the pandemic. This review meticulously maps out the sources and detection strategies of pathogens in a variety of ecosystems. It clearly shows that impaction and filtration sampling methods, followed by colony counting and PCR-based detection techniques, were predominantly used in the scientific works within the previous three decades. It synthesizes the progress and limitations inherent in a range of models for predicting aerosol-mediated pathogen spread and provides a comparative analysis of eDNA technology and traditional analytical techniques for bioaerosols. The accuracy of these detection methods and forecasting models is paramount for the early recognition of transmission risks, which, in turn, paves the way for prompt and effective disease mitigation strategies. By providing a thorough analysis of the historical progression and current state of bioaerosol research, this review illuminates the path ahead, identifying the critical research needs that will drive the field’s advancement in the years to come.

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“…Our One Health study called for studying livestock farms in United States and Mexico for novel respiratory viruses. [10][11][12] We planned to prospectively sample sick and healthy farm livestock, the farm environments, and a cohort of healthy animal workers for evidence of novel coronaviruses and other respiratory viruses. At enrollment and every four months for a total of 12 months, we planned to collect questionnaire data about each farm and its animal workers, and an array of samples: 20 nasal swabs from livestock (up to 70% from animals with signs of respiratory illness), NP swabs and sera from up to 10 animal workers, and 4 three-hour bioaerosol samples.…”

Section: Study Sites and Sampling Protocolmentioning

confidence: 99%

A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms

Shittu,

Silva,

Oguzie

et al. 2024

Preprint

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Background: In early April 2024 we studied two Texas dairy farms which had suffered incursions of H5N1 highly pathogenic avian influenza virus (HPAIV) the previous month. Methods: We employed molecular assays, cell and egg culture, Sanger and next generation sequencing to isolate and characterize viruses from multiple farm specimens (cow nasal swab, milk specimens, fecal slurry, and a dead bird). Results: We detected H5N1 HPAIV in 64% (9/14) of milk specimens, 2.6% (1/39) of cattle nasal swab specimens, and none of 17 cattle worker nasopharyngeal swab specimens. We cultured and characterized virus from eight H5N1-positive specimens. Sanger and next-generation sequencing revealed the viruses were closely related into other recent Texas epizootic H5N1 strains of clade 2.3.4.4b. Our isolates had multiple mutations associated with increased spillover potential. Surprisingly, we detected SARS-CoV-2 in a nasal swab from a sick cow. Additionally, 14.3% (2/14) of the farm workers who donated sera were recently symptomatic and had elevated neutralizing antibodies against a related H5N1 strain. Conclusions: While our sampling was limited, these data offer additional insight into the large H5N1 HPAIV epizootic which thus far has impacted at least 96 cattle farms in twelve US states. Due to fears that research might damage dairy businesses, studies like this one have been few. We need to find ways to work with dairy farms in collecting more comprehensive epidemiological data that are necessary for the design of future interventions against H5N1 HPAIV on cattle farms.

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A pan-coronavirus RT-PCR assay for rapid viral screening of animal, human, and environmental specimens

Cited by 4 publications

References 19 publications

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Navigating the Aerosolized Frontier: A Comprehensive Review of Bioaerosol Research Post-COVID-19

A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms

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