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Complete nucleotide sequence of Middelburg virus, isolated from the spleen of a horse with severe clinical disease in Zimbabwe

¹ Department of Arbovirology, Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, UK
² Agence Française de Sécurité Sanitaire des Aliments, 22 rue Pierre Curie, 94703 Maisons-Alfort Cedex 07, France
³ Unité de Virologie Moléculaire, Etablissement Français du Sang Alpes-Méditerranée, 149 Boulevard Baille, 13005 Marseille, France

Correspondence
Houssam Attoui
houssam.attoui{at}bbsrc.ac.uk

The complete nucleotide sequence of Middelburg virus (MIDV) was determined for strain MIDV-857 from Zimbabwe. The isolation of this virus in 1993 from a horse that died showing severe clinical signs represents the first indication that MIDV can cause severe disease in equids. Full-length cDNA copies of the viral genome were successfully synthesized by an innovative RT-PCR amplification approach using an ‘anchor primer’ combined with the SMART methodology described previously for the synthesis of full-length cDNA copies from genome segments of dsRNA viruses. The MIDV-857 genome is 11 674 nt, excluding the 5'-terminal cap structure and poly(A) tail (which varies in length from approximately 180 to approximately 220 residues). The organization of the genome is like that of other alphaviruses, including a read-through stop codon between the nsP3 and nsP4 genes. However, phylogenetic analyses of the structural protein amino acid sequences suggested that the MIDV E1 gene was generated by recombination with a Semliki Forest virus-like virus. This hypothesis was supported by bootscanning analysis using a recombination-detection program. The 3' untranslated region of MIDV-857 also contains a 112 nt duplication. This study reports the first full-length sequence of MIDV, which was obtained from a single RT-PCR product.

The GenBank/EMBL/DDBJ accession number for the complete sequence of Middelburg virus strain MIDV-857 determined in this study is EF536323.

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