The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order

Abstract

The frequent emergence of coronavirus (CoV) epidemics has seriously threatened public health and stock farming. The major hosts for CoVs are birds and mammals. Although most CoVs inhabit their specific natural hosts, some may occasionally cross the host barrier to infect livestock and even people, causing a variety of diseases. Since the beginning of the new century, increasing attention has been given to research on CoVs due to the emergence of highly pathogenic and genetically diverse CoVs that have caused several epidemics, including the recent COVID-19 pandemic. CoVs belong to the Coronaviridae family of the Nidovirales order. Recently, advanced techniques for viral detection and viral genome analyses have enabled characterization of many new nidoviruses than ever and have greatly expanded the Nidovirales order with new classification and nomenclature. Here, we first provide an overview of the latest research progress in the classification of the Nidovirales order and then introduce the host range, genetic variation, genomic pattern and pathogenic features of epidemic CoVs and other epidemic viruses. This information will promote understanding of the phylogenetic relationship and infectious transmission of various pathogenic nidoviruses, including epidemic CoVs, which will benefit virological research and viral disease control.

Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2

“…All the three HP-hCoVs are single-stranded RNA (ssRNA) viruses classified into Betacoronaviruses genus of Orthocoronavirinae subfamily in Coronaviridae family (Group, 2020;Zhou et al, 2021). Specifically, SARS-CoV and SARS-CoV-2 belong to the subgenus of Sarbecovirus, while MERS-CoV is classified into the subgenus of Merbecovirus (Zhou et al, 2021). The SARS-CoV-2 genome shares around 79% identity with SARS-CoV and 30% with MERS-CoV, respectively (Zhou et al, 2020).…”

“…Their typical genomic organization contains nonstructural, structural, and accessory proteins flanked by a 5 -cap structure and a 3 -poly (A) tail (Yang and Leibowitz, 2015). The open reading frame (ORF) 1a and ORF1b occupy the two-third 5 region of the viral genome and can be directly translated into two large polyproteins, pp1a and pp1b, which are further hydrolyzed into 16 non-structural proteins (NSP1 ∼ NSP16) by two viral proteases, NSP3 (papain-like protease, PL-pro) and NSP5 (3C-like protease, 3CL-pro) (Zhou et al, 2021). These NSPs take shape the replication-transcription complex (RTC), which is necessary for viral RNA transcription and replication (Li et al, 2020b).…”

“…Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses infecting various mammals and birds, including humans (Zhou et al, 2021). In the last century, human coronaviruses (hCoVs) were recognized as mild respiratory pathogens, which were barely studied regarding their low pathogenicity (Zhou et al, 2021).…”

“…Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses infecting various mammals and birds, including humans (Zhou et al, 2021). In the last century, human coronaviruses (hCoVs) were recognized as mild respiratory pathogens, which were barely studied regarding their low pathogenicity (Zhou et al, 2021). However, highly pathogenic hCoVs (HP-hCoVs) have emerged since the year 2003 and have caused three worldwide epidemics, including severe acute respiratory syndrome (SARS) epidemic caused by SARS-CoV in 2003, Middle East Respiratory Syndrome (MERS) epidemic caused by MERS-CoV in 2012, and the recent coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2.…”

Protein Nucleotidylylation in +ssRNA Viruses

“…The order Nidovirales encompasses 14 families of positive-sense RNA viruses, within which 109 species have currently been identified [146]. Of this order, three families of biological and economic value are Arteriviridae, Mesoniviridae and Coronaviridae.…”