Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis

Abstract

The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus.

Discovery of a novel canine respiratory coronavirus support genetic recombination among betacoronavirus1

“…Recombination is a common phenomenon in coronaviruses and thought to contribute to the emergence of new pathotypes (Gorbalenya, 2008;Wang et al, 2015). Thus far, most of the recombination events of coronaviruses have been reported between species of the same group (Herrewegh et al, 1998;Keck et al, 1988), such as among the batassociated CoVs (Corman et al, 2014) and 229E-related CoVs (Corman et al, 2015), and the major recombination breakpoint has mainly been within the S gene.…”

Whole genome analysis of Japanese bovine toroviruses reveals natural recombination between porcine and bovine toroviruses

“…Approximately 76% of the genomes of BToV Ishi and BToV Kago are similar to that of PToV. Natural recombination events are common in coronaviruses, resulting in evolution and emergence of new variants that are pathogenic to poultry, cats, pigs, and humans (Graham and Baric, 2010;Herrewegh et al, 1998;Hewson et al, 2014;Lau et al, 2015;Song et al, 2013;Terada et al, 2014;Tian et al, 2014;Wang et al, 2015;T. Zhang et al, 2015;Y.…”

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

“…Lineages 3 and 5 viruses were predominant during July and December 2014; however, lineage 5 became dominant within the camel population by 2015. Lineage 5, which is closely associated with the MERS-CoV causing the outbreak in South Korea in 2015, as well as recent human infections in Riyadh, Saudi Arabia, is a recombinant virus between lineages 3 and 4, or groups 3 and 5 of clade B (Figure 4) [62,80].…”