Molecular Evolution of Human Coronavirus 229E in Hong Kong and a Fatal COVID-19 Case Involving Coinfection with a Novel Human Coronavirus 229E Genogroup
Susanna K. P. Lau, David Christopher Lung, Emily Wong, Kam Leng Aw‐Yong, Antonio C. P. Wong, Hayes K. H. Luk, Kenneth S. M. Li, Joshua Fung, Tony Tat-Yin Chan, James Y. M. Tang, Longchao Zhu, Cyril Chik‐Yan Yip, Sally C. Y. Wong, Rodney A. Lee, Owen Tak-Yin Tsang, Kwok‐Yung Yuen, Patrick C. Y. Woo
Abstract
Since its first appearance in the 1960s, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) have been relatively understudied. In this study, we report a fatal case of COVID-19 coinfected with HCoV-229E in Hong Kong. Genome sequencing revealed that our SARS-CoV-2 strain is highly identical to the SARS-CoV-2 strain from Wuhan, compatible with the patient's recent travel history, whereas our HCoV-229E strain in this study is highly identical to a recent strain in the United States. We also retrieved 41 archived HCoV-229E strains from 2004 to 2019 in Hong Kong for sequence analysis. Pneumonia and exacerbations of chronic airway diseases were common diagnoses among the 41 patients. The results showed that HCoV-229E was evolving in chronological order. Two novel genogroups were identified in addition to the four preexisting HCoV-229E genogroups, with recent circulating strains belonging to novel genogroup 6. Molecular clock analysis dated bat-to-human and bat-to-camelid transmission to as early as 1884.