Rapid fixation of a distinctive sequence motif in the 3′ noncoding region of the clade of West Nile virus invading North America

Abstract

Phylogenetic analysis of complete genomes of West Nile virus (WNV) by a variety of methods supported the hypothesis that North American isolates of WNV constitute a monophyletic group, together with an isolate from Israel and one from Hungary. We used ancestral sequence reconstruction in order to obtain evidence for evolutionary changes that might be correlated with increased virulence in this clade (designated the N.A. clade). There was one amino acid change (I→T at residue 356 of the NS3 protein) that occurred in the ancestor of the N.A. clade and remained conserved in all N.A. clade genomes analyzed. There were four changes in the upstream portion of the 3′ noncoding region (the AT-enriched region) that occurred in the ancestor of the N.A. clade and remained conserved in all N.A. clade genomes analyzed, changes predicted to alter RNA secondary structure. The AT-enriched region showed a higher rate of substitution in the branch ancestral to the N.A. clade, relative to polymorphism, than did the remainder of the non-coding regions, synonymous sites in coding regions, or nonsynonymous sites in coding regions. The high rate of occurrence of fixed nucleotide substitutions in this region suggests that positive Darwinian selection may have acted on this portion of the 3′NCR and that these fixed changes, possibly in concert with the amino acid change in NS3, may underlie phenotypic effects associated with increased virulence in North American WNV.

The evolutionary biology of poxviruses

“…In most viral protein-coding genes, the number of synonymous substitutions per synonymous site ( d S ) typically exceeds the number of nonsynonymous substitutions per nonsynonymous site ( d N ), indicating that purifying selection has acted against the latter (Hughes 1999). This pattern has been found in the protein-coding genes of many virus taxa (e.g., Hughes 2007a; Hughes and Hughes 2007; Hughes et al 2007; Hughes and Piontkivska 2008; Irausquin and Hughes 2008). Moreover, in many viruses the rate of nucleotide substitution in non-coding regions is substantially less than d S (though usually not lower than d N ), providing evidence of purifying selection on viral genomes outside protein-coding genes (Hughes 2007a, 2009; Hughes and Piontkivska 2008).…”

“…Evidence of ongoing purifying selection against slightly deleterious nonsynonymous variants is provided by the occurrence of numerous relatively rare nonsynonymous variants (Hughes 2005; Hughes et al 2003); and such a pattern has been seen in many viruses as well as in cellular organisms (Hughes 2007a; Hughes and Hughes 2007; Hughes et al 2007; Hughes and Piontkivska 2008; Irausquin and Hughes 2008). …”

“…These VARV genomes were sequenced by Esposito et al (2006), who noted a relatively low level of sequence polymorphism in comparison to many other viral sequence data sets. In order to compare VARV with an RNA virus with similarly low polymorphism, we estimated d S and d N pairwise among the polyprotein genes of 53 West Nile virus (WNV) isolates from the North American clade (Hughes et al 2007). WNV is a flavivirus that has spread rapidly in the Americas since it was first observed in the Western Hemisphere in 1999 (Nash et al 2001).…”

Genetic Variability of West Nile Virus in US Blood Donors, 2002–2005

“…Subsequent observations showed that nucleotide changes in the 3′-UTR played a role in rapid spread of this virus in the New World because nucleotide changes in the 3′-UTR had co-evolved with amino acid changes and affected interactions of helicase and RNA polymerase with their RNA substrate (33). Mutations in 3′-UTR appear to play a role in production of small-plaque temperature-sensitive variants or mouseattenuated phenotype variants (34).…”

Genetic Analysis of West Nile Virus Isolates from an Outbreak in Idaho, United States, 2006–2007

“…However, the relevance and role of the identified motifs and associated genome lesions in viral replication and their evolutionary consequences remain to be explored. The relatively high rate of occurrence of mutations, deletions and insertions in the variable region of the 3′UTR suggests that positive Darwinian selection may have acted on this part of the WNV genome [61].…”