Characterization of Nipah virus from outbreaks in Bangladesh, 2008-2010

Abstract

Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes fatal encephalitis in humans. The initial outbreak of NiV infection occurred in Malaysia and Singapore in 1998-1999; relatively small, sporadic outbreaks among humans have occurred in Bangladesh since 2001. We characterized the complete genomic sequences of identical NiV isolates from 2 patients in 2008 and partial genomic sequences of throat swab samples from 3 patients in 2010, all from Bangladesh. All sequences from patients in Bangladesh comprised a distinct genetic group. However, the detection of 3 genetically distinct sequences from patients in the districts of Faridpur and Gopalganj indicated multiple co-circulating lineages in a localized region over a short time (January-March 2010). Sequence comparisons between the open reading frames of all available NiV genes led us to propose a standardized protocol for genotyping NiV; this protcol provides a simple and accurate way to classify current and future NiV sequences.

Figure 1

Phylogenetic analyses of sequences from the complete Nipah virus N ORF (A) and the 729-nt proposed N ORF genotyping window (B). Tree created with maximum parsimony, close-neighbor-interchange algorithm, 1,000 bootstrap replicates (16). Branch lengths are in units of number of changes over the whole sequence. Available GenBank accession numbers are shown for corresponding sequences. Proposed genotype groupings are indicated by brackets (M, B). ORF, open reading frame; MY, Malaysia; KH, Cambodia; BD, Bangladesh; IN, India; HU, human; PI, pig; BA, bat. Scale bars indicate number of sequence changes corresponding to illustrated branch length.

Figure 2

Phylogenetic analyses of sequences from the complete Nipah virus P ORF (A), M ORF (B), F ORF (C), G ORF (D), and L ORF (E). Tree created with maximum parsimony, close-neighbor-interchange algorithm, 1,000 bootstrap replicates (16). Branch lengths are in units of number of changes over the whole sequence. Available GenBank accession numbers are shown for corresponding sequences. Proposed genotype groupings are indicated by brackets (M, B). ORF, open reading frame; MY, Malaysia; KH, Cambodia; BD, Bangladesh; IN, India; HU, human; PI, pig; BA, bat. Scale bars indicate number of sequence changes corresponding to illustrated branch length.