Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment.
Crimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown.
Department of Medical Microbiology and Virology,National Health Laboratory Service/University of the Free State,Bloemfontein,South Africa.
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D
Goedhals
Department of Medical Microbiology and Virology,National Health Laboratory Service/University of the Free State,Bloemfontein,South Africa.
P A
PA
Bester
Centre for Emerging and Zoonotic Pathogens,National Institute for Communicable Diseases,National Health Laboratory Service, Johannesburg,South Africa.
J T
JT
Paweska
Zoonoses Research Unit, Department of Medical Virology,University of Pretoria,South Africa.
R
R
Swanepoel
Department of Medical Microbiology and Virology,National Health Laboratory Service/University of the Free State,Bloemfontein,South Africa.
F J
FJ
Burt
D014644:Genetic Variation; D016679:Genome, Viral; D003225:Hemorrhagic Fever Virus, Crimean-Congo / Q000235:genetics* / Q000302:isolation & purification*; D006479:Hemorrhagic Fever, Crimean / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses / Q000235:genetics*; D013019:South Africa / Q000453:epidemiology
D012367:RNA, Viral