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Abstract
Lassa virus (LASV) is endemic to parts of West Africa and causes highly fatal hemorrhagic fever. The multimammate rat (Mastomys natalensis) is the only known reservoir of LASV. Most human infections result from zoonotic transmission. The very diverse LASV genome has 4 major lineages associated with different geographic locations. We used reverse transcription PCR and resequencing microarrays to detect LASV in 41 of 214 samples from rodents captured at 8 locations in Sierra Leone. Phylogenetic analysis of partial sequences of nucleoprotein (NP), glycoprotein precursor (GPC), and polymerase (L) genes showed 5 separate clades within lineage IV of LASV in this country. The sequence diversity was higher than previously observed; mean diversity was 7.01% for nucleoprotein gene at the nucleotide level. These results may have major implications for designing diagnostic tests and therapeutic agents for LASV infections in Sierra Leone.
Highlights
Lassa virus (LASV) is endemic to parts of West Africa and causes highly fatal hemorrhagic fever
Lassa fever (LF) differs from most viral hemorrhagic fevers in that it is endemic to a large geographic area of sub-Saharan Africa
Their analysis revealed the existence of high sequence diversity and 4 major lineages of LASV, which correlate with geographic location [17]
Summary
Rodent Sample Collection The rodent samples collected were part of a separate project RT-PCR and Sequencing RNA were reverse-transcribed by using the SuperScript III Reverse Transcriptase kit (Life Technologies) according to the manufacturer’s instructions, and RT products were stored at –20°C. NP targets were amplified by using an initial 2-min denaturation at 95°C, followed by 40 cycles of 95°C for 30 sec, 55°C for 30 sec, and 72°C for 1 min. GPC targets were amplified by using 36E2 and LVS339-rev primers [24] and a PCR profile consisting of 2-min denaturation at 95°C, followed by 45 cycles of 95°C for 30 sec, 58°C for 30 sec, and 72°C for 1 min. L gene targets were amplified by using modified primers, LVL3359-F and LVL3754-R, based on published sequences [28] and a PCR program consisting of 2-min denaturation at 95°C followed by 45 cycles of 95°C for 30 sec,
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