Genetic characterization of a selection of influenza virus (H5N1) samples circulating
Genetic characterization of a selection of influenza virus (H5N1) samples circulating in 8 Nigerian states over a 39-day period in early 2007 indicates a brand-new reassortant strain exists in 7 from the 8 states. to 22 from the Nesbuvir 36 Nigerian state governments also Rabbit Polyclonal to GPR152. to the Government Capital Place. In Feb 2007 1 case of avian influenza was reported in a female in Nesbuvir the southern condition of Lagos. Hence the extensive flow of Nesbuvir influenza trojan (H5N1) in Nigeria boosts concerns about individual and animal medical issues. A prior research indicated that 2 sublineages (EMA1 and EMA2) had been cocirculating in Nigeria in 2006 (1); nevertheless 3 sublineages had been identified in a far more latest research (2) specifically sublineage A (matching to EMA2) and sublineages B and C (matching to EMA1). The 2007 research by Salzberg et al. also discovered a trojan displaying a 4:4 reassortment between genes Nesbuvir of sublineages EMA1 and EMA2 (1). The purpose of our research is to supply additional information over the hereditary features of isolates which were circulating in Nigeria in early 2007. THE ANALYSIS Twelve representative influenza trojan (H5N1) examples from different Nigerian outbreaks had been selected (Desk 1) by firmly taking into consideration the geographic origins and the time of isolation. We characterized these infections by sequencing the complete genome then. Table 1 Set of influenza trojan (H5N1) samples examined in chicken Nigeria 2007 Examples were processed for disease isolation subtyping and pathotyping (3 4). The amplification of the 8 viral gene segments was carried out with reverse transcription (RT)-PCR by using gene-specific primers (available upon request). PCR products were sequenced inside a 3100 Avant Genetic Analyzer (Applied Biosystems Foster City CA USA). Phylogenetic analysis was performed by using the neighbor-joining method as implemented in the MEGA 3 system (5). GenBank accession nos. for the 8-gene segments of the 12 Nigerian strains are “type”:”entrez-nucleotide-range” attrs :”text”:”EU148356 to EU148451″ start_term :”EU148356″ end_term :”EU148451″ start_term_id :”157399691″ end_term_id :”157399905″EU148356 to EU148451. As expected all Nigerian isolates were closely related to the viruses that have been circulating in parrots throughout Europe Russia Africa and the Middle East since late 2005. According to the unified nomenclature system for highly pathogenic influenza disease (H5N1) these isolates belong to clade 2.2 (6). Phylogenetic analysis of all 8 gene segments of the Nesbuvir recent Nigerian strains showed that 10 of these strains labeled EMA1/EMA2-2:6 reassortant 2007 (EMA1/EMA2-2:6-R07) (Table 1) have the same genotype. In particular the genetic comparison of the hemagglutinin (HA) and nonstructural (NS) genes of EMA1/EMA2-2:6-R07 demonstrates they are derived from viruses of the EMA1 sublineage (1) and have the highest similarity with the 1st Nigerian strain isolated A/chicken/Nigeria/641/2006 (homology ranged between 99.3% and 99.7%). We observed different topology for the remaining gene segments (neuraminidase nucleoprotein [NP] matrix heterotrimeric polymerase complex [PA PB1 and PB2]). Phylogenetic analysis showed the nucleotide sequences of these genes fall into EMA2 sublineage; the highest homology was observed with respective gene segments of the Nigerian strains isolated in 2006 which belong to EMA2 (homology ranged between 99.4% and 99.7%). The separation of the gene segments into 2 clusters (Numbers 1 ? 2 is definitely evidence of reassortment (7). The genetic pattern of EMA1/EMA2-2:6-R07 disease is unique from that of A/chicken/Nigeria/1047-62/2006 disease isolated in June 2006 in Taraba State and identified previously as an EMA1/EMA2-4:4 reassortant disease (1) (Table 2). The remaining 2 viruses were not reassortants. They were recognized in Sokoto State and belong to sublineage EMA2. Number 1 Phylogenetic tree for the hemagglutinin gene of influenza viruses constructed by neighbor-joining method. Sequences obtained with this study were labeled having a circle (EMA1/EMA2-2:6-R07 group) and triangle (EMA2 group). The remaining sequences can be found … Nesbuvir Number 2 Phylogenetic tree for nucleoprotein gene of influenza viruses constructed by neighbor-joining method. Sequences obtained with this study were labeled having a circle (EMA1/EMA2-2:6-R07 group) and triangle (EMA2 group). The remaining sequences can be found … Table 2 Clustering of the gene segments of influenza strains.