Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study

Abstract

Background: Human infections with zoonotic coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, have raised great public health concern globally. Here, we report a novel batorigin CoV causing severe and fatal pneumonia in humans. Methods: We collected clinical data and bronchoalveolar lavage (BAL) specimens from five patients with severe pneumonia from Jin Yin-tan Hospital of Wuhan, Hubei province, China. Nucleic acids of the BAL were extracted and subjected to next-generation sequencing. Virus isolation was carried out, and maximum-likelihood phylogenetic trees were constructed. Results: Five patients hospitalized from December 18 to December 29, 2019 presented with fever, cough, and dyspnea accompanied by complications of acute respiratory distress syndrome. Chest radiography revealed diffuse opacities and consolidation. One of these patients died. Sequence results revealed the presence of a previously unknown b-CoV strain in all five patients, with 99.8% to 99.9% nucleotide identities among the isolates. These isolates showed 79.0% nucleotide identity with the sequence of SARS-CoV (GenBank NC_004718) and 51.8% identity with the sequence of MERS-CoV (GenBank NC_019843). The virus is phylogenetically 1 closest to a bat SARS-like CoV (SL-ZC45, GenBank MG772933) with 87.6% to 87.7% nucleotide identity, but is in a separate clade. Moreover, these viruses have a single intact open reading frame gene 8, as a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor. Conclusion: A novel bat-borne CoV was identified that is associated with severe and fatal respiratory disease in humans.

The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak

“…It was shorter among patients > 70-years old compared with those under the age of 70 [8]. The most common symptoms at onset of COVID-19 illness are fever, cough, and fatigue, while other symptoms include sputum production, headache, haemoptysis, diarrhoea, dyspnoea, and lymphopenia [5,6,8,13]. Clinical features revealed by a chest CT scan presented as pneumonia, however, there were abnormal features such as RNAaemia, acute respiratory distress syndrome, acute cardiac injury, and incidence of grand-glass opacities that led to death [6].…”

“…Ten genome sequences of COVID-19 obtained from a total of nine patients exhibited 99.98% sequence identity [19]. Another study showed there was 99.8-99.9% nucleotide identity in isolates from five patients and the sequence results revealed the presence of a new beta-CoV strain [5]. The genetic sequence of the COVID-19 showed more than 80% identity to SARS-CoV and 50% to the MERS-CoV [5,19], and both SARS-CoV and MERS-CoV originate in bats [24].…”

“…Another study showed there was 99.8-99.9% nucleotide identity in isolates from five patients and the sequence results revealed the presence of a new beta-CoV strain [5]. The genetic sequence of the COVID-19 showed more than 80% identity to SARS-CoV and 50% to the MERS-CoV [5,19], and both SARS-CoV and MERS-CoV originate in bats [24]. Thus, the evidence from the phylogenetic analysis indicates that the COVID-19 belongs to the genus betacoronavirus, which includes SARS-CoV, that infects humans, bats, and wild animals [25].…”

“…Moreover, these viruses have a single intact open reading frame on gene 8, which is a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor [5].…”

“…The first cases were reported in December 2019 [4]. From December 18, 2019 through December 29, 2019, five patients were hospitalized with acute respiratory distress syndrome and one of these patients died [5]. By January 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed COVID-19 infection, less than half of these patients had underlying diseases, including diabetes, hypertension, and cardiovascular disease [6].…”