Detection of respiratory viruses in adults with suspected COVID-19 in Kuala Lumpur, Malaysia

Chong, Yoong Min and Chan, Yoke Fun and Jamaluddin, Mohamad Fadhil Hadi and Hasan, M. Shahnaz and Pang, Yong Kek and Ponnampalavanar, Sasheela and Omar, Sharifah Faridah Syed and Voon, Kenny Gah Leong and Sam, I-Ching (2021) Detection of respiratory viruses in adults with suspected COVID-19 in Kuala Lumpur, Malaysia. Journal of Clinical Virology, 145. ISSN 1386-6532, DOI

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Background: Reports of co-circulation of respiratory viruses during the COVID-19 pandemic and co-infections with SARS-CoV-2 vary. However, limited information is available from developing countries. Objectives: We aimed to investigate the incidence of respiratory viruses in adult patients with suspected COVID19 in Kuala Lumpur, Malaysia. Study Design: We collected 198 respiratory samples from adult patients hospitalized with suspected COVID-19 in a single teaching hospital in Kuala Lumpur in February-May 2020 and tested combined oro-nasopharyngeal swabs with the NxTAG Respiratory Pathogen Panel (Luminex) and Allplex RV Essential (Seegene) assays. Forty-five negative samples further underwent viral metagenomics analysis. Results: Of the 198 samples, 74 (37.4%) had respiratory pathogens, including 56 (28.3%) with SARS-CoV-2 and 18 (9.1%) positive for other respiratory pathogens. There were five (2.5%) SARS-CoV-2 co-infections, all with rhinovirus/enterovirus. Three samples (6.7%; 3/45) had viruses identified by metagenomics, including one case of enterovirus D68 and one of Saffold virus genotype 6 in a patient requiring ICU care. Most of the COVID-19 patients (91.1%; 51/56) had mild symptoms but 5.4% (3/56) died. Conclusion: During the early COVID-19 period, common respiratory viruses other than SARS-CoV-2 only accounted for 9.1% of hospitalization cases with ARI and co-infections with SARS-CoV-2 were rare. Continued surveillance is important to understand the impact of COVID-19 and its associated public health control measures on circulation of other respiratory viruses. Metagenomics can identify unexpected or rare pathogens, such as Saffold virus, which is rarely described in adults.

Item Type: Article
Funders: United States Department of Defense [Grant No: HDTRA1-6], Defense Threat Reduction Agency [Grant No: HDTRA1-17-1-0027], Seegene Inc. [Grant No: IF059-2020]
Uncontrolled Keywords: COVID-19; Malaysia; Viral metagenomics; SARS-CoV-2; Respiratory viruses; Saffold virus
Subjects: Q Science > QR Microbiology > QR355 Virology
Divisions: Faculty of Medicine
Depositing User: Ms Zaharah Ramly
Date Deposited: 14 Jun 2022 08:52
Last Modified: 14 Jun 2022 08:52

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