Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination

Abstract

Although human coronavirus OC43-OC43 (HCoV-OC43Coronaviruses cause infections in a wide variety of animals, resulting in respiratory, enteric, hepatic, and neurological diseases of various levels of severity. Based on genotypic and serological characterization, coronaviruses traditionally were classified into three distinct groups, groups 1, 2, and 3 (4). Recently, the Coronavirus Study Group of the International Committee for Taxonomy of Viruses has renamed the traditional group 1, 2, and 3 coronaviruses as Alphacoronavirus, Betacoronavirus, and Gammacoronavirus, respectively (http: //talk.ictvonline.org/media/p/1230.aspx).The recent severe acute respiratory syndrome (SARS) epidemic due to SARS coronavirus (SARS-CoV) and the identification of SARS-related coronaviruses (SARSr-CoVs) from Himalayan palm civets and horseshoe bats in mainland China have led to a boost in interest in the study of coronaviruses in both humans and animals (5,13,24,26,33,37,55). Before the SARS epidemic in 2003, there were only 19 known coronaviruses, including 2 human, 13 mammalian, and 4 avian coronaviruses. After the SARS epidemic, more than 20 additional novel coronaviruses have been described with complete genome sequences (9, 24-26, 31, 42, 45, 50, 53, 54, 57). These include 3 human coronaviruses, 15 mammalian coronaviruses, and 4 avian coronaviruses. For human coronaviruses, human coronavirus NL63 (HCoV-NL63) (an alphacoronavirus) and human coronavirus HKU1 (HCoV-HKU1) (a betacoronavirus) have been discovered in addition to the two previously known human coronaviruses, human coronavirus 229E (HCoV-229E) (an alphacoronavirus) and human coronavirus OC43 (HCoV-OC43) (a betacoronavirus), as well as SARSCoV (a betacoronavirus) (9,45,53,56). While HCoV-229E and HCoV-OC43 were thought to account for 5 to 30% of human respiratory tract infections, HCoV-NL63 and HCoV-HKU1 often were detected in Ͻ5% of respiratory tract samples (23,29,38). Outbreaks due to HCoV-OC43 also have been reported (3,32,44). Nevertheless, the different HCoVs often cocirculate, with one or two HCoVs being predominant depending on the geographical area and year (8,11,19,23).Coronaviruses are unique in having a high frequency of homologous RNA recombination, which is a result of random

Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests

“…human in the 1890s. 57 The more recent example of interspecies transmission was the jumping of the lineage B betacoronavirus SARS-CoV from bats to civets and then to humans which caused the SARS epidemic in 2003. 11,19,58e62 Though the seroprevalence of anti-HCoV-EMC antibody found no indication of positivity among residents in the Kingdom of Saudi Arabia, their demographic details, particularly the history of animal exposure, were not described.…”

Novel Betacoronavirus in Dromedaries of the Middle East, 2013

“…Divergence time was calculated on the basis of RdRp gene sequence data by using a Bayesian Markov Chain Monte Carlo approach as implemented in BEAST version 1.8.0 (http://beast.bio.ed.ac.uk), as described ( 15 , 19 , 29 , 30 ). Bayesian skyline under a relaxed-clock model with an uncorrelated exponential distribution was adopted for making inferences because Bayes factor analysis for the RdRp gene indicated that this model fitted the data better than other models tested.…”

Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains

“…Bootscan analysis was also used to detect possible recombination using the nucleotide alignment of the S gene sequences of virus species in Betacoronaviruses 1 and also CRCoV. Bootscan analysis was performed using Simplot version 3.5.1 as described previously (Lau et al, 2011;Woo et al, 2006), with BCoV, HCoV, ECoV, PHEV and CRCoV strains as the query.…”