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Molecular Evolution of Human Coronavirus 229E in Hong Kong and a Fatal COVID-19 Case Involving Coinfection with a Novel Human Coronavirus 229E Genogroup
mSphere ( IF 3.7 ) Pub Date : 2021-02-10 , DOI: 10.1128/msphere.00819-20 Susanna K P Lau 1, 2 , David C Lung 3 , Emily Y M Wong 4 , Kam Leng Aw-Yong 4 , Antonio C P Wong 4 , Hayes K H Luk 4 , Kenneth S M Li 4 , Joshua Fung 4 , Tony T Y Chan 4 , James Y M Tang 4 , Longchao Zhu 4 , Cyril C Y Yip 4 , Sally C Y Wong 3 , Rodney A Lee 5 , Owen T Y Tsang 6 , Kwok-Yung Yuen 2, 4 , Patrick C Y Woo 1, 2
mSphere ( IF 3.7 ) Pub Date : 2021-02-10 , DOI: 10.1128/msphere.00819-20 Susanna K P Lau 1, 2 , David C Lung 3 , Emily Y M Wong 4 , Kam Leng Aw-Yong 4 , Antonio C P Wong 4 , Hayes K H Luk 4 , Kenneth S M Li 4 , Joshua Fung 4 , Tony T Y Chan 4 , James Y M Tang 4 , Longchao Zhu 4 , Cyril C Y Yip 4 , Sally C Y Wong 3 , Rodney A Lee 5 , Owen T Y Tsang 6 , Kwok-Yung Yuen 2, 4 , Patrick C Y Woo 1, 2
Affiliation
Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient showed that the SARS-CoV-2 strain HK13 was most closely related to SARS-CoV-2 type strain Wuhan-Hu-1 (99.99% nucleotide identity), compatible with his recent history of travel to Wuhan. The HCoV-229E strain HK20-42 was most closely related to HCoV-229E strain SC0865 from the United States (99.86% nucleotide identity). To investigate if it may represent a newly emerged HCoV-229E genotype in Hong Kong, we retrieved 41 archived respiratory samples that tested positive for HCoV-229E from 2004 to 2019. Pneumonia and exacerbations of chronic airway diseases were common among infected patients. Complete RdRp, S, and N gene sequencing of the 41 HCoV-229E strains revealed that our contemporary HCoV-229E strains have undergone significant genetic drift with clustering of strains in chronological order. Two novel genogroups were identified, in addition to previously described genogroups 1 to 4, with recent circulating strains including strain HK20-42 belonging to novel genogroup 6. Positive selection was detected in the spike protein and receptor-binding domain, which may be important for viral evolution at the receptor-binding interphase. Molecular dating analysis showed that HCoV-229E shared the most recent common ancestor with bat and camel/alpaca 229E-related viruses at ∼1884, while camel/alpaca viruses had a relatively recent common ancestor at ∼1999. Further studies are required to ascertain the evolutionary origin and path of HCoV-229E.
更新日期：2021-02-11
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