1  Introduction
In December 2019, the seventh human coronavirus, termed 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was found in Wuhan, China. On February 8, 2020, the total number of infections and deaths due to 2019-nCoV globally was 34,439 and 720, respectively, according to the Johns Hopkins University Center for Systems Science and Engineering.
Coronaviruses are enveloped RNA viruses that infect many species, including humans, other mammals, and birds. After infection, the host may develop respiratory, bowel, liver, and neurological diseases (Weiss and Leibowitz, 2011; Cui et al., 2019). Coronaviruses are members of the order Nidovirales and subfamily Orthocoronavirinae. This subfamily is divided into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. Generally, Alphacoronavirus and Betacoronavirus tend to infect mammals, while Gammacoronavirus and Deltacoronavirus typically infect birds. However, some Gammacoronavirus and Deltacoronavirus can infect mammals under specific conditions (Woo et al., 2012).
In immunocompromised individuals, infection with one of the four human coronaviruses—human coronavirus NL63 (HCoV-NL63), human coronavirus 229E (HCoV-229E), human coronavirus OC43 (HCoV-OC43), and human coronavirus HKU1 (ECoV-HKU1)—usually results in cold-like symptoms. These viruses can cause severe infections in some infants and the elderly. Due to the frequent interaction between wild animals and humans, wild animals are a common source of human zoonotic infections. SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic coronaviruses that can cause severe respiratory diseases in humans; both belong to Betacoronavirus (Su et al., 2016; Forni et al., 2017; Cui et al., 2019; Luk et al., 2019; Ramadan and Shaib, 2019). 2019-nCoV is the seventh coronavirus discovered that infects humans. It causes acute respiratory disease in respiratory infections. Immediately after its discovery, the complete genome sequence of 2019-nCoV was determined. The sequence (MN908947) was released by GenBank on 05 January 2020 (Lu et al., 2020). The sequence of 2019-nCoV is 96% identical, at the whole-genome level, to a bat coronavirus (Zhou et al., 2020).
The genomic characteristics and epidemiology of 2019-nCoV have been analyzed (Lu et al., 2020). Nine inpatient culture isolates were subjected to next-generation sequencing, and individual complete and partial 2019-nCoV genomic sequences were obtained. Phylogenetic analysis of these 2019-nCoV genomes and other coronaviruses was performed to determine the evolutionary history of the virus and to explore the origin of 2019-nCoV. At the first onset, homology modeling investigated the potential receptor-binding properties of the virus. However, SARS-CoV and MERS-CoV showed approximate similarities of 79% and 50% with 2019-nCoV, respectively. These findings indicated that there is not a close evolutionary relationship of 2019-nCoV with SARS-CoV and MERS-CoV. Thus, 2019-nCoV is considered the seventh novel human Betacoronavirus (Lu et al., 2020).
In this study, we comprehensively characterized the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins.