Current Molecular Epidemiology of Lassa Virus in Nigeria

Abstract

Recent Lassa virus strains from Nigeria were completely or partially sequenced. Phylogenetic analysis revealed the predominance of lineage II and III strains, the existence of a previously undescribed (sub)lineage in Nigeria, and the directional spread of virus in the southern part of the country. The Bayesian analysis also provided estimates for divergence times within the Lassa virus clade.

Sequence Variability and Geographic Distribution of Lassa Virus, Sierra Leone

“…The analysis of phylogenetic trees constructed by using all available partial sequences of NP, GPC, and L genes from Sierra Leone confirmed previous findings that the strains circulating in this country belong to lineage IV and are closely related to each other ( 17 , 19 ). The topology of the largest NP-based tree (Figure 2) strongly supports the hypothesis that the isolates from Sierra Leone belong to at least 3 distinct major clades (posterior probability 1.00 in all cases): the first clade (A), including a large cluster of strains originating from a group of villages to the north and east of Kenema in the Eastern Province (Bumpeh, Gondama, Koi, Konia, Largo, Ngiehun, Panguma, Segbwema, Taiama, Tongo, and Yawei; Figure 1); the second clade (B), including several strains isolated from rodents captured in Barlie (located a few kilometers southeast of Bo) and 1 isolate from Saama (located northeast of Kenema); and the third clade (C) represented by just 2 older human isolates from Mano and Mobai.…”

“…This kind of clustering has been reported previously over large geographic distances and is believed to have resulted from limited dispersal and migration of the host species ( 17 , 19 ). Results of this study show that this phenomenon also can be observed over relatively short distances.…”

“…Forty-seven unique partial LASV sequences from Sierra Leone were available in GenBank at the time of this analysis, which included fragments of NP (27 sequences), GPC (9 sequences), L (9 sequences), and Z (2 sequences) genes plus full sequences of small and large segments of 2 strains—Josiah and NL. Most of these sequences are from isolates collected >30 years ago; only 2 more recent sequences (GPC and L gene fragments) from strain SL06-2057 were isolated in 2006 ( 17 , 19 ). …”

Arenavirus Diversity and Phylogeography ofMastomys natalensisRodents, Nigeria

“…Phylogenetic analyses of the GPC and L gene sequences showed that 15 of the viruses were Lassa and 1 was a Mobala-like virus (Figure 2). The LASV sequences from Ekpoma and Eguare-Egoro belonged to lineage II and clustered with strains Nig08-A4, A37, A41, and A47 from patients in Edo State ( 14 ). Nucleotide identities between the sequences of LASV from the rodents and those from the human patients were 82%–96% (GPC) and 85%–97% (L), and amino acid identities were 95%–99% (GPC) and 93%–100% (L), respectively (Technical Appendix 2).…”

Rapid and Specific Detection of Lassa Virus by Reverse Transcription-PCR Coupled with Oligonucleotide Array Hybridization

“…Most of the clinical strains had previously been sequenced in the PCR target region (3,5). In addition, in vitro transcripts of 11 reference strains were tested.…”