Working Paper Brief Report Version 1 This version is not peer-reviewed

Identification of a Low Pathogenicity Clade of SARS-CoV-2

Version 1 : Received: 28 May 2020 / Approved: 29 May 2020 / Online: 29 May 2020 (12:47:07 CEST)

How to cite: KOYAMA, T.; Parida, L. Identification of a Low Pathogenicity Clade of SARS-CoV-2. Preprints 2020, 2020050466 KOYAMA, T.; Parida, L. Identification of a Low Pathogenicity Clade of SARS-CoV-2. Preprints 2020, 2020050466

Abstract

Number of confirmed cases of COVID-19 caused by SARS-CoV-2 exceeded 5 million as of May 21, 2020. Global average of the case fatality rate of COVID-19 is about 7% so far. There exist variations in case fatality rates among countries. Particularly, Singapore and Qatar have exceptionally low case fatality rates with 0.1% while France’s rate is almost 20%. Since no magic bullet treatment for COVID-19 exists, we investigated SARS-CoV-2 strains specific to Singapore in this study to identify a clade with low pathogenicity. Variant analysis revealed that a clade with variants ORF1ab L3606F, A4489V, S2015R, T2016K, and N P13L is common in Singapore. Based on our analysis of variants and historical case statistics, the clade is dominant in a recent surge. Therefore, we suggest that low case fatality rate of Singapore possibly is attributed to the clade. Although contribution of each variant to the low pathogenicity is not clear, L3606F alone does not accomplish such low pathogenicity from the comparison with case fatality data from Japan, where L3606F is dominant. Further investigation is necessary to conclude to validate this finding.

Subject Areas

COVID-19; SARS-CoV-2; variant; low pathogenicity; Singapore

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