Virus Genes 26:3, 317±327, 2003 # 2003 Kluwer Academic Publishers. Manufactured in The Netherlands. Complete Genomic Sequence of the Australian South-West Genotype of Sindbis Virus: Comparisons with Other Sindbis Strains and Identification of a Unique Deletion in the 3 0 -Untranslated Region SUHA M. SALEH, 1,y MICHAEL POIDINGER, 1,2 JOHN S. MACKENZIE, 1 ANNETTE K. BROOM, 3 MICHAEL D. LINDSAY 4 & ROY A. HALL 1, * 1 Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia 2 Australian National Genomic Information Service, University of Sydney, Australia 3 Arbovirus Surveillance and Research Laboratory, Department of Microbiology, University of Western Australia, Nedlands, WA, Australia 4 Mosquito-Borne Disease Control Unit, Health Department of Western Australia, WA, Australia Received March 5, 2003; Accepted March 6, 2003 Abstract. OurpreviousstudieshaveshownthattwodistinctgenotypesofSindbis(SIN)virusoccurinAustralia. One of these, the Oriental/Australian type, circulates throughout most of the Australian continent, whereas the recentlyidentifiedsouth-west(SW)genetictypeappearstoberestrictedtoadistinctgeographicregionlocatedin the temperate south-west of Australia. We have now determined the complete nucleotide and translated amino acid sequences of a SW isolate of SIN virus (SW6562) and performed comparative analyses with other SIN viruses at the genomic level. The genome of SW6562 is 11,569 nucleotides in length, excluding the cap nucleotide and poly (A) tail. Overall this virus differs from the prototype SIN virus (strain AR339) by 23% in nucleotide sequence and 12.5% in amino acid sequence. Partial sequences of four regions of the genome of four SW isolates were determined and compared with the corresponding sequences from a number of SIN isolates from different regions of the World. These regions are the non-structural protein (nsP3), the E2 gene, the capsid gene, and the repeated sequence elements (RSE) of the 3 0 UTR. These comparisons revealed that the SW SIN viruses were more closely related to South African and European strains than to other Australian isolates of SIN virus. Thus the SW genotype of SIN virus may have been introduced into this region of Australia by viremic humans or migratory birds and subsequently evolved independently in the region. The sequence data also revealed that the SW genotype contains a unique deletion in the RSE of the 3 0 UTR region of the genome. Previous studies have shown that deletions in this region of the SIN genome can have significant effects on virus replication in mosquito and avian cells, which may explain the restricted distribution of this genotype of SIN virus. Key words: alphavirus, nucleotide sequence, repeat sequence elements, Sindbis virus Introduction Sindbis (SIN) virus is the most widely distributed of all known arboviruses and has been isolated in several countries in Europe, Africa, Asia, and Australia (for review see [1]). Although SIN virus has been isolated from a variety of mosquitoes and vertebrate species, its basic maintenance cycle is thought to involve principally Culex mosquitoes and wild birds [2]. While SIN has been responsible for significant outbreaks of disease in South Africa [3] and northern Europe [4,5], clinical infection with *Author for all correspondence. E-mail: roy.hall@mailbox.uq.edu.au y Present address: Department of Microbiology, Monash Univer- sity, Melbourne, Victoria, 3800, Australia.