The molecular epidemiology of Kokobera virus

We describe herein the molecular epidemiology and phylogeny of Kokobera (KO K) virus, a flavivirus found in Australia and Papua New Guinea. We sequence d a region encompassing the 200 nucleotides of the 3' terminus of the NS5 g ene, and the first 300 nucleotides of the 3' untranslated region (UTR). The study included 25 isolates of the virus, including an isolate from PNG, an d several recent isolates from the south-west of Western Australia (WA), wh ere the virus had not previously been detected. We found that the KOK isola tes clustered according to geographic location and time of isolation into t hree distinct topotypes: one covering Queensland and New South Wales; anoth er represented by the single isolate from PNG; and a third covering the Nor thern Territory and WA. This latter group was further subdivided into north ern and south-west isolates. This molecular epidemiology is significantly d ifferent from other Australian flaviviruses, such as Murray Valley encephal itis (MVE) and Kunjin (KUN) viruses, which exist as single genetic types ac ross the entire Australian continent. However, it is similar to the molecul ar epidemiology of the alphavirus Ross River (RR) virus. This may be explai ned by the fact that MVE and KUN viruses are known to have birds as their m ain vertebrate hosts, whereas RR virus utilises macropods, which have also been implicated as the vertebrate host for KOK virus. In addition, the sout h-west isolates exhibited a degree of sequence heterogeneity, including one isolate that has a nine nucleotide deletion in the 3'UTR. This suggests th at KOK virus has been in the south-west of WA for some time, and was not re cently introduced. (C) 2000 Elsevier Science B.V. All rights reserved.