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. 2021 Dec:145:105000.
doi: 10.1016/j.jcv.2021.105000. Epub 2021 Oct 20.

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

Yoong Min Chong  1 , Yoke Fun Chan  1 , Mohamad Fadhil Hadi Jamaluddin  2 , M Shahnaz Hasan  2 , Yong Kek Pang  3 , Sasheela Ponnampalavanar  3 , Sharifah Faridah Syed Omar  3 , Kenny Gah Leong Voon  4 , I-Ching Sam  5
Affiliations

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

Yoong Min Chong et al. J Clin Virol. 2021 Dec.

Abstract

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 COVID-19 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.

Keywords: COVID-19; Malaysia; SARS-CoV-2; Saffold virus; respiratory viruses; viral metagenomics.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Figure 1:
Fig. 1
Phylogenetic tree of EV-D68 virus partial VP1 gene sequences. Strain names are in the format: accession number_strain name_country of isolation_year of isolation. The numbers refer to percentage of bootstrap support at key nodes. Malaysian sequences are colored red. The newly identified sequence from this study is denoted with the red circle. The tree is rooted with prototype Fermon strain.
Figure 2:
Fig. 2
Phylogenetic tree of Saffold virus full genome sequences. Strain names are in the format: accession number_strain name_country of isolation_year of isolation. The numbers refer to percentage of bootstrap support at key nodes. Malaysian sequences are colored red. The newly identified sequence from this study is denoted with the red circle. The tree is rooted with the earliest Saffold virus whole genome sequence (NC_009448).
See this image and copyright information in PMC

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