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.