Molecular Evolution of Human Coronavirus Genomes

Although canine respiratory coronavirus (CRCoV) is an important respiratory pathogen that is prevalent in many countries, only one complete genome sequence of CRCoV (South Korea strain K37) has been obtained to date. Genome-wide analyses and recombination have rarely been conducted, as small numbers of samples and limited genomic characterization have previously prevented further analyses. Herein, we report a unique CRCoV strain, denoted strain BJ232, derived from a CRCoV-positive dog with a mild respiratory infection. Phylogenetic analysis based on complete genome of all available coronaviruses consistently show that CRCoV BJ232 is most closely related to human coronavirus OC43 (HCoV-OC43) and BCoV, forming a separate clade that split off early from other Betacoronavirus 1. Based on the phylogenetic and SimPlot analysis we propose that CRCoV-K37 was derived from genetic recombination between CRCoV-BJ232 and BCoV. In detail, spike (S) gene of CRCoV-K37 clustered with CRCoV-BJ232. However orf1ab, membrane (M) and nucleocapsid (N) genes were more related to Bovine coronavirus (BCoV) than CRCoV-B232. Molecular epidemic analysis confirmed the prevalence of CRCoV-BJ232 lineage around the world for a long time. Recombinant events among Betacoronavirus 1 may have implications for CRCoV transmissibility. All these findings provide further information regarding the origin of CRCoV.

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a b s t r a c tSince the first case of human infection by the Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia in June 2012, more than 2260 cases of confirmed MERS-CoV infection and 803 related deaths have been reported since the 16th of October 2018. The vast majority of these cases (71%) were reported in Saudi Arabia but the epidemic has now spread to 27 countries and has not ceased 6 years later, unlike SARS-CoV that disappeared a little less than 2 years after emerging. Due to the high fatality rate observed in MERS-CoV infected patients (36%), much effort has been put into understanding the origin and pathophysiology of this novel coronavirus to prevent it from becoming endemic in humans. This review focuses in particular on the origin, epidemiology and clinical manifestations of MERS-CoV, as well as the diagnosis and treatment of infected patients. The experience gained over recent years on how to manage the different risks related to this kind of epidemic will be key to being prepared for future outbreaks of communicable disease. Mots clés : Maladies émergentes MERS-CoV Coronavirus Pneumonie r é s u m é Depuis le premier cas d'infection liée au Middle East Respiratory Syndrome -Coronavirus (MERS-CoV), détecté en Arabie Saoudite en juin 2012, le MERS-CoV a donné lieu, au 16 octobre 2018, à plus de 2260 cas d'infections confirmées et à 803 décès. La grande majorité des cas (71 %) ont été déclarés en ArabieSaoudite mais l'épidémie a depuis touché 27 pays et n'est toujours pas enrayée 6 ans après son émergence, contrairement au SRAS-CoV qui a disparu un peu moins de deux ans après sa première détection. En raison du taux important de décès observé parmi les patients infectés par le MERS-CoV (36 %), beaucoup d'efforts ont été déployés pour comprendre l'origine et la physiopathologie de ce nouveau coronavirus ainsi que pour lutter contre une éventuelle installation endémique de ce virus au sein de la population humaine. Cette revue s'attache plus particulièrement à retracer l'origine et l'épidémiologie du MERS-CoV à décrire la clinique observée chez les patients ainsi que la prise en charge diagnostique et thérapeutique des patients infectés. L'expérience acquise au cours des dernières années dans la gestion des différents risques liés à ce type d'épidémie est importante pour pouvoir faire face à la prochaine émergence d'infection transmissible.