Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment.

D Goedhals,F J Burt,R Swanepoel,J T Paweska,P A Bester

doi:10.1017/s0950268814000818

Abstract

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.

Highlights

Crimean Congo haemorrhagic fever virus (CCHFV) is a member of the family Bunyaviridae, genus Nairovirus [1]
CCHFV has a negative-sense, single-stranded RNA genome consisting of three segments designated large (L), medium (M) and small (S)
This study aimed to make use of nextgeneration sequencing (NGS) techniques to obtain whole genome sequences of southern African CCHFV isolates in order to perform genetic analysis including identification of reassortment events

Summary

Introduction

Crimean Congo haemorrhagic fever virus (CCHFV) is a member of the family Bunyaviridae, genus Nairovirus [1] This tick-borne zoonotic virus is associated with clinical disease ranging from a non-specific febrile illness to severe disease manifesting as haemorrhagic fever. CCHFV has a negative-sense, single-stranded RNA genome consisting of three segments designated large (L), medium (M) and small (S). The highly conserved complementary terminal nucleotide sequences result in loosely circular RNAs which together with the nucleocapsid protein, make up the three helical nucleocapsids. The L segment encodes the viral RNA polymerase while the S segment encodes the viral nucleocapsid protein. The M segment encodes a polyprotein which undergoes proteolytic processing to yield the viral glycoproteins, Gc and Gn [2]

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