Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition

Abstract

Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Predictions on 47 additional coronaviruses precisely conformed to conclusions or speculations by other researchers. Our approach is implemented as a web server that can be accessed at http://bioinfo.ihb.ac.cn/seq2hosts.

Structural and Evolutionary Analysis Indicate that the SARS-CoV-2 Mpro is an Inconvenient Target for Small-Molecule Inhibitors Design

“…In early December 2019, the first atypical pneumonia outbreak associated with the novel coronavirus of zoonotic origin (SARS-CoV-2) appeared in Wuhan City, Hubei Province, China [1,2]. In general, coronaviruses (CoVs) are classified into four major genera: Alphacoronavirus, Betacoronavirus (which primarily infect mammals), Gammacoronavirus, and Deltacoronavirus (which primarily infect birds) [3][4][5]. In humans, coronaviruses usually cause mild to moderate upper-respiratory tract illnesses, e.g., the common cold, however, the rarer forms of CoVs can be lethal.…”

“…In humans, coronaviruses usually cause mild to moderate upper-respiratory tract illnesses, e.g., the common cold, however, the rarer forms of CoVs can be lethal. By the end of 2019, six kinds of human CoV have been identified: HCoV-NL63, HCoV-229E, belonging to Alphacoronavirus genera, HCoV-OC43, HCoV-HKU1, severe acute respiratory syndrome SARS-CoV, and Middle East respiratory syndrome MERS-CoV, belonging to Betacoronavirus genera [4]. Of the aforementioned CoVs, the last two are the most dangerous and they were associated with the outbreak of two epidemics at the beginning of the 21st century [6].…”

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China

“…Coronaviruses mainly cause respiratory and gastrointestinal tract infections and are genetically classified into four major genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (Li, 2016). The former two genera primarily infect mammals, whereas the latter two predominantly infect birds (Tang et al, 2015). Six kinds of human CoVs have been previously identified.…”

“…Six kinds of human CoVs have been previously identified. These include HCoV-NL63 and HCoV-229E, which belong to the Alphacoronavirus genus; and HCoV-OC43, HCoV-HKU1, severe acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome coronavirus (MERS-CoV), which belong to the Beta-coronavirus genus (Tang et al, 2015). Coronaviruses did not attract worldwide attention until the 2003 SARS pandemic, followed by the 2012 MERS and, most recently, the 2019-nCoV outbreaks (China CDC, 2020;Song et al, 2019).…”

Predicting the receptor-binding domain usage of the coronavirus based on kmer frequency on spike protein

“…It could be classified into four major genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus, based on serological and genetic studies (Li, 2016). The Alphacoronavirus and Betacoronavirus mainly infect mammals, whereas the Gammacoronavirus and Deltacoronavirus mainly infect avians (Tang et al, 2015). The coronavirus poses a serious threat to human health and global security because several coronaviruses could cross-species to infect humans, such as the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) (Lu et al, 2015;Peck et al, 2015;Smith, 2006).…”