Evolutionary analysis of influenza A(H1N1)pdm09 during the pandemic and post-pandemic period in Pakistan.

BACKGROUND: The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since then, it has continued to circulate causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in influenza A(H1N1)pdm09 viruses from 2009 to 2016 and their relevance to the current vaccine viruses. METHODS: Respiratory specimens (throat or nasopharyngeal swabs) were collected from patients with influenza-like illness and severe acute respiratory illness. Samples were processed following the protocol of the US Centers for Disease Control and Prevention. Sequencing and phylogenetic analysis of Haemagglutinin and neuraminidase genes were carried out on representative isolates of Pakistan viruses. RESULTS: Between January 2009 and February 2016, out of 16,024 samples analysed, 1950 (12%) were positive for influenza A. During the pandemic period (2009-2010), influenza A(H1N1)pdm09 was the dominant strain with 366 out of 808 (45%) total influenza positive cases. In the post-pandemic period (2011-2016), a total of 1078 out of 1911 (56%) cases were positive for influenza A(H1N1)pdm09 with co-circulation of different influenza A subtypes. The Pakistan A(H1N1)pdm09 viruses belonged to two genetic clades: clade 7 in the pandemic period, and clade 7 (2011) and clade 6B (2015) in the post-pandemic period. Sequence analysis of genes coding for surface glycoprotein's of Haemagglutinin and neuraminidase had a high degree of sequence similarity with corresponding genes of regional viruses circulating in South-East Asia. CONCLUSION: Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Key substitutions in the receptor binding site and a few changes indicative of virulence were also detected in the post-pandemic strains. Continued monitoring of the viruses is essential for early identification of potential variants of high virulence and their relevance to current vaccine strains.

Seroprevalence and risk factors of avian influenza H9 virus among poultry professionals in Rawalpindi, Pakistan.

BACKGROUND: Avian influenza H9 is endemic in commercial and backyard poultry in Pakistan and is a serious occupational health hazard to industry workers. This study aimed to determine the seroprevalence of avian influenza H9 infection in people working with poultry in Rawalpindi, Pakistan and assess the measures they took to protect themselves from infection. METHODS: A cross-sectional study was conducted from December 2016 to May 2017 of 419 people working with poultry in Rawalpindi Division, including farm workers, vaccinators, field veterinarians, butchers and staff working in diagnostic laboratories. Potential participants were randomly approached and gave written consent to participate. Data were collected using a standardized questionnaire and serum samples were processed to detect H9 antibodies using the haemagglutination inhibition test. RESULTS: Of the 419 participants, 406 (96.9%) were male. The mean age of the participants was 36.4 (SD 10.86) years. A total of 332 participants agreed to a blood test, 167 of whom were positive for A(H9) antibodies, giving an overall seroprevalence of 50.3%. Laboratory staff had the highest seroprevalence (100%) and veterinarians the lowest (38.5%). Vaccinators, butchers and farm workers had a seroprevalence of 83.3%, 52.4% and 45.5% respectively. Personals who used facemasks had significantly lower (P<0.002) seroprevalence (29.6%) than those who never used them (90.6%). Similarly, those who always used gloves and washed their hands with soap had a seroprevalence of 32.8% compared with 89.0% in those who never took these precautions. Of the participants who handled antigens, 92.3% were seropositive. CONCLUSION: Laboratory staff and vaccinators are exposed to viral cultures and influenza vaccines respectively which may explain their high seroprevalence.