【病毒外文文獻(xiàn)】2017 A47_Origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first im

Middle East Respiratory Syndrome Coronavirus MERS CoV caus ing infections in humans is genetically indistinguishable from the virus found in Arabian camels dromedaries in the Middle East Although no primary human case of MERS was reported outside the Arabian Peninsula camel populations in Africa are known to have high prevalence of antibodies against MERS CoV We carried out surveillance for MERS CoV in dromedaries in Africa and Central Asia By MERS CoV spike pseudoparticle neu tralization assay we confirmed that camel serum samples from African countries have high prevalence of MERS CoV antibodies Using RT qPCR we detected MERS CoV positives in camel nasal swabs from all different African countries from which samples were collected However dromedary serum and swab samples from Kazakhstan in Central Asia were negative for MERS CoV by these assays Phylogenetic analysis of the spike gene revealed that MERS CoVs from Africa formed a cluster closely related to but distinct from the viruses from the Arabian Peninsula Results from this study suggest that MERS CoV is actively circulating in dromedary populations in Africa and the virus in Africa is phylo genetically distinct from that in the Middle East A47 Origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in china phylogenetics and coalescence analysis Yanqun Wang 1 Di Liu 2 3 Weifeng Shi 4 Roujian Lu 1 Wenling Wang 1 Yanjie Zhao 1 Yao Deng 1 Weimin Zhou 1 Hongguang Ren 5 Jun Wu 2 Yu Wang 6 Guizhen Wu 1 George F Gao 1 2 6 Wenjie Tan 1 1 Key Laboratory of Medical Virology Ministry of Health National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing China 2 CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing China 3 Network Information Center Institute of Microbiology Chinese Academy of Sciences Beijing China 4 Institute of Pathogen Biology Taishan Medical College Taian China 5 State Key Laboratory of Pathogen and Biosecurity Beijing China and 6 Office of Director General Chinese Center for Disease Control and Prevention Beijing China The Middle East respiratory syndrome coronavirus MERS CoV causes a severe acute respiratory tract infection with a high fatal ity rate in humans Coronaviruses are capable of infecting multi ple 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 recom bination 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 A48 Inference of biological functionality in individual genomic secondary structural elements found within capulavirus genomes P Hartnady 1 D Martin 1 B Muhire 1 P Roumagnac 2 1 UCT Faculty Of Health Sciences Institute of Infectious Disease and Molecular Medicine Cape Town and 2 Cirad France The seeming simplicity of the iconic DNA double helix is decep tive The genomes of single stranded DNA and RNA viruses often contain numerous nucleic acid secondary structures Whilst a number of these secondary structural elements have been found to play crucial roles during the life cycles of these viruses the majority have neither any identified function nor known impact on viral fitness and evolution Secondary struc tures can be predicted using nearest neighbour free energy parameters that quantify the stability of a given secondary structure Using an array of bioinformatic techniques we inves tigated the influence of inferred secondary structures on the sequence evolution of capulaviruses a diverse genera of single stranded DNA viruses We detected a significant association between structured regions of the genome and selective con straints on synonymous substitutions in coding regions This is suggestive of either natural selection acting to preserve these structures or a predisposition toward lower mutation rates in base paired regions of the genome In addition coevolution analyses revealed a significant tendency for nucleotides that are base paired in predicted structures to coevolve in a comple mentary manner Combined these results highlight the perva siveness of conserved genomic secondary structures within capulavirus genomes and support the notion that natural selec tion is favouring the maintenance of these structures providing compelling evidence of their likely biological relevance This structure first strategy for comparative analysis of genome wide secondary structures can be broadly applied to understand the contributions of higher order genome structures to viral replication and pathogenicity A49 Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya James R Otieno 1 Charles N Agoti 1 2 Caroline W Gitahi 1 Ann Bett 1 Mwanajuma Ngama 1 Graham F Medley 3 Patricia A Cane 4 D James Nokes 1 5 1 Epidemiology and Demography Department Kenya Medical Research Institute KEMRI Wellcome Trust Research Programme Kilifi Kenya 2 Department of Biomedical Sciences Pwani University Kilifi Kenya 3 Department of Global Health Development London School of Hygiene and Tropical Medicine London UK 4 Public Health England Salisbury UK and 5 School of Life Sciences and WIDER University of Warwick Coventry UK The characteristic recurrent epidemics of human respiratory syncytial virus RSV within communities may result from the genetic variability of the virus and associated evolutionary adaptation reducing efficiency of pre existing immune responses We analyzed the molecular evolutionary changes in the attachment G glycoprotein of RSV A viruses collected over 13 epidemic seasons 2000 12 in Kilifi n 649 Kenya and con temporaneous sequences n 1 131 collected elsewhere within Kenya and 28 other countries Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics charac terized by frequent new variant introductions and limited var iant persistence between consecutive epidemics Four RSV A genotypes were detected in Kilifi ON1 11 9 GA2 75 5 GA5 12 3 and GA3 0 3 with predominant genotype replace ment of GA5 by GA2 then GA2 by ON1 Within these genotypes there was considerable variation in potential N glycosylation sites with GA2 and ON1 viruses showing up to 15 different pat terns involving eight possible sites Further we identified 15 positively selected and 34 genotype distinguishing codon sites with six of these sites exhibiting both characteristics The mean substitution rate of the G ectodomain for the Kilifi dataset was estimated at 3 58 C2 10 C03 95 HPD 3 04 4 16 nucleotide substi tutions site year Kilifi viruses were interspersed in the global phylogenetic tree clustering mostly with Kenyan and European 21st International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology S17 Downloaded from by guest on 10 January 2019