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A pneumonia outbreak associated with a new coronavirus of probable bat origin

Our take —

This study reports sequencing results from patients with acute respiratory illness in Wuhan, establishing a SARS-related coronavirus as the likely etiological agent. The similarity between the novel coronavirus and other viruses from bats suggest that bats are the likely primary hosts of the novel coronavirus, but the intermediate host is yet to be identified.

Study design


Study population and setting

Samples from seven patients with severe pneumonia admitted to the ICU at Wuhan Jin Yin-Tan Hospital in Wuhan, Hubei province, China at the beginning of the outbreak in December 2019. Six of the patients were sellers or deliverymen from the Huanan Seafood Market, identified as a key location of exposure for a majority of early cases. Symptom onset for patients started as early as December 12, 2019.

Summary of Main Findings

A SARS-related coronavirus was identified by amplification and sequencing of virus genetic material in lung fluid and oral swab samples collected from patients. The novel coronavirus (2019-nCoV) detected in human patients shared 96% similarity in its genetic code to a bat SARS-related coronavirus from the insectivorous bat species Rhinolophus affinis in Yunnan province collected in 2013 (identification code RaTG13) and 88% similarity with other bat SARS-related coronaviruses (bat-SL-CoVZXC21 and bat-SL-CoVZC45 from Rhinolophus sinicus, Zhejiang province; collected in 2015 and 2017, respectively). The virus also uses the same receptor protein (ACE2) to bind and infect human cells as SARS coronavirus.

Study Strengths

Rapid detection and identification of the infectious agent through sequencing technology. Tissue culture successfully isolated the virus and established the receptor protein for infection of human cells.


Evidence from sequencing alone is not sufficient to conclude that the SARS-CoV-2 is the cause of pneumonia in patients. The similarity of virus genetic material and the number of hosts sampled is insufficient to establish whether humans were infected directly from bats or through another intermediate animal host.

Value added

This is one of the earliest reports establishing a coronavirus as the etiological agent of the acute respiratory disease, including genetic information about the novel coronavirus and a potential zoonotic link with bats.