Abstract
BackgroundUsutu virus (USUV), a flavivirus belonging to the Japanese encephalitis serocomplex, was identified in South Africa in 1959 and reported for the first time in Europe in 2001. To date, full length genome sequences have been available only for the reference strain from South Africa and a single isolate from each of Austria, Hungary, and Italy.MethodsWe sequenced four USUV isolates from Senegal and the Central African Republic (CAR) between 1974 and 2007 and compared the sequence data to USUV strains from Austria, Hungary, Italy, and South Africa using a Bayesian Markov chain Monte Carlo method. We further clarified the taxonomic status of a USUV strain isolated in CAR in 1969 and proposed earlier as a subtype of USUV due to an asymetric serological cross-reactivity with USUV reference strain.ResultsA comparison of the four newly obtained USUV sequences with those from SouthAfrica_1959, Vienna_2001, Budapest_2005, and Italy_2009 revealed that they are all 96-99% and 99% similar at the nucleotide and amino acid levels, respectively. The phylogenetic relationships between these sequences indicated that a strain isolated in Senegal in 1993 is most closely related to the USUV strains detected in Europe. Analysis of a strain isolated from a human in CAR in 1981 (CAR_1981) revealed the presence of specific amino acid substitutions and a deletion in the 3′ noncoding region. This is the first fully sequenced human USUV isolate.The putative USUV subtype, CAR_1969, was 81% and 94% identical at the nucleotide and amino acid levels, respectively, compared to the other USUV strains. Our phylogenetic analyses support the serological identification of CAR_1969 as a subtype of USUV.ConclusionsIn this study, we investigate the genetic diversity of USUV in Africa and the phylogenetic relationship of isolates from Africa and Europe for the first time. The results suggest a low genetic diversity within USUV, the existence of a distinct USUV subtype strain, and support the hypothesis that USUV was introduced to Europe from Africa. Further sequencing and analysis of USUV isolates from other African countries would contribute to a better understanding of its genetic diversity and geographic distribution.
Highlights
Usutu virus (USUV), a flavivirus belonging to the Japanese encephalitis serocomplex, was identified in South Africa in 1959 and reported for the first time in Europe in 2001
The pattern of observed sequence substitution suggests that it was not the South African strain that was introduced into Europe, it is likely that other USUV strains that are more closely related to the European isolates are circulating in Africa [18]
Sequence analysis of USUV strains circulating in Africa The full genome sequences of the USUV strains Kedougou_1974 (ArD19848), CAR_1981 (HB81P08), Barkedji_1993 (ArD101291), and Barkedji_2007 (ArD19 2495) were 10800–10837 nt long and contained an ORF between nt positions 97 and 10401 in reference to SouthAfrica_1959 (SAAR1776)
Summary
Usutu virus (USUV), a flavivirus belonging to the Japanese encephalitis serocomplex, was identified in South Africa in 1959 and reported for the first time in Europe in 2001. Full length genome sequences have been available only for the reference strain from South Africa and a single isolate from each of Austria, Hungary, and Italy. Usutu virus (USUV) is a member of the Japanese encephalitis serocomplex of flaviviruses that was isolated for the first time in 1959 in South Africa [1,2]. Four full length genome sequences are available from South Africa, Austria [AY453411], Hungary [EF206350] and Italy [JF266698], and these are 97–99.9% and 99% similar at the nucleotide and amino acid levels, respectively [8,18,22].
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