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

• Main Authors: Chong, Yoong Min, Chan, Yoke Fun, Jamaluddin, Mohamad Fadhil Hadi, Hasan, M. Shahnaz, Pang, Yong Kek, Ponnampalavanar, Sasheela, Omar, Sharifah Faridah Syed, Voon, Kenny Gah Leong, Sam, I-Ching
• Format: Article
• Published: Elsevier 2021
• Subjects: QR355 Virology
• Online Access: http://eprints.um.edu.my/34174/
• Institution: Universiti Malaya

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.