Genetic diversity and phylogenetic analysis of Crimean Congo hemorrhagic fever virus in Pakistan

Abstract

Background: Being an endemic country for Crimean Congo hemorrhagic fever (CCHF), this study aimed to explore the genetic diversity of CCHF virus (CCHFV) detected in Pakistan. This study was conducted to confirm the etiology of suspected hemorrhagic fever cases in order to support their clinical management. The genotype classification of CCHFV strains was determined to explore their phylogenetic relationship with strains in the region. Methods and materials: Serum samples from patients with clinical signs of hemorrhagic fever attending tertiary care hospitals in Pakistan, were tested for CCHFV RNA using real-time PCR at the Department of Virology, NIH. The partial S-gene fragments were directly sequenced to determine the prevailing CCHFV genotypes and their molecular epidemiology in Pakistan. Results: During Jan–Sep 2019, 178 samples from suspected CCHF patients were tested and 14 (8%) were found positive on real-time PCR. Phylogenetic analysis showed that all 2019 strains (n = 6) belonged to Asia-1 genotype and clustered with regional strains from Oman, Iran, UAE and Afghanistan. Fourteen CCHFV samples from 2013 outbreak were also retrospectively sequenced. Among 27 positive cases, phylogenetic analysis based on partial S-gene sequences of 15 CCHFV strains revealed that 73% strains (n = 11) belonged to Asia-1 genotype and clustered with viruses from Afghanistan and Iran. Three viruses were identified as Asia-2 genotype and grouped with isolates from India and Central Asian countries. Notably, one strain CCHF2013-56-NIHPAK was reported as Euro-1 genotype and clustered with isolates from Iran and Russia. Genetic diversity estimation of Pakistan strains (Aisa-1 genotype) detected during 2013 and 2019 showed 97–99% nucleotide homology. To our knowledge, this the first report on the detection of Euro-1 genotype from Pakistan Conclusion: We conclude that Asia-1 genotype of CCHF virus remains dominant in Pakistan over a period of seven years. Our findings emphasize establishing a laboratory-based surveillance program to monitor the disease burden and identify outbreak hotspots for effective control.