An Exploratory Search for Novel Coronaviruses in Sarawak, Malaysia

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Date

2017

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Gray, Gregory C

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Abstract

Background: In recent years, emerging zoonotic microbes are gaining more attention from the public and policy makers. Explosive outbreaks such as those from avian influenza viruses, severe acute respiratory syndrome (SARS) virus, swine influenza viruses, Hendra virus, Nipah virus, and Middle East respiratory syndrome (MERS) have had tremendous international economic and social impact. In particular, livestock workers have been found to be at increased infection risk and some of the first impacted by a novel pathogen. One of the main obstacles in averting outbreaks of novel microbes is detecting it when it first begins to cross species from animals to man and may not cause severe disease. Often routine diagnostics will fail to detect a new pathogen. The purpose of this research was to evaluate diagnostics for emerging coronaviruses that would be missed with routine diagnostics.

Methods: In 2016, I learned how to run new diagnostics adapted at Duke University to detect novel coronaviruses. I took this molecular technology to Sarawak, Malaysia, where I applied the assays against a panel of human clinical specimens from patients seen at three hospitals for respiratory illnesses. Our collaborators in Sarawak had previously examined these specimens with other assays against human coronaviruses but did not tell me of their results.

Results: In my hands, the new pan-species coronavirus assay detected only one coronavirus among 88 clinical specimens. After I finished my assay work, I learned from our collaborators that 27of the 88 specimens had been positive for at least one previously recognized human coronavirus. Hence, the sensitivity of the new assay in my hands found to be 3.70% (95% confidence interval 0% - 11.91%). However, the assay accurately showed negative results with a specificity of 100%

Conclusion: While this low sensitivity may have been real, it may also been influenced by a number of confounding factors such as specimen nucleic acid degradation with numerous freeze-thaw cycles, imprecise adaptation of an assay to new equipment in a new laboratory, or my or our collaborators’ operator error. It is difficult to precisely identify the cause of the discordance. Nevertheless, I learned a great deal about global health in conducting this research in Sarawak and have chronicled some of these lessons in this report.

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Fatima, Hiba (2017). An Exploratory Search for Novel Coronaviruses in Sarawak, Malaysia. Master's thesis, Duke University. Retrieved from https://hdl.handle.net/10161/15256.

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