Genetic diversity and phylogenetic analysis of Crimean-Congo Hemorrhagic Fever viruses circulating in Pakistan during 2019

Abstract

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 during 2019. 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 Department of Virology, National Institute of Health. The partial S-gene fragments were directly sequenced to determine the prevailing CCHFV genotypes and their molecular epidemiology in Pakistan. During January-December 2019, 280 samples from suspected CCHF patients were tested and 28 (10%) were found positive on real-time PCR. Positive cases were detected from 14 districts and across all four provinces of Pakistan with majority reported during August-September. The mean age of CCHFV positive patients was 37.25 years (range 5-65 years) with a high frequency in males (92.8%; n = 26) and a case fatality rate of 40.7% was observed. Phylogenetic analysis showed that S-segment of 2019 PAK CCHFV strains (n = 13) belonged to Asia-1 genotype and clustered with regional strains from Iran, Oman, and Afghanistan. We conclude that Asia-1 genotype of CCHF virus remains endemic in Pakistan. Our findings emphasize to establish a laboratory based surveillance program to monitor the disease burden and identify outbreak hotspots for effective control.

Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019

“…No mortality was observed in secondary cases (n = 8) with viral RNA copy number ranging from 10 6 −10 3 . The high CFR amongst CCHF cases observed in our study implies to the high viral load and bleeding [17,19,20,23,24,25]. Persistence of the CCHF viral RNA without any symptom or sign of active disease in survivors up to 76 th POD as noticed in our study has not been reported earlier.…”

“…The 33 CCHFV sequences retrieved from the 29 clinical specimens and 4 tick pools were each belonging to L and S gene clustered with the Asian clade. The Asian clade is further grouped into Asia 1 and Asia 2 subgroups [19,20]. The sequences retrieved in this study were found in both the subgroups.…”

“…CCHF cases were observed sporadically with increase in the incidence during rainy and winter seasons due to close proximity of livestock and humans, leading to increase possibility of tick bites [19,20]. Occupational vulnerability and risk factors for CCHF have been documented previously amongst the people involved in farming, animal handling, milking the animals, animal grazing, veterinary care providers, slaughtering of animals and nosocomial infection amongst healthcare workers [17,21].…”

Evaluation of seroprevalence and clinical and laboratory findings of patients admitted to health institutions in Gümüşhane with suspicion of Crimean-Congo hemorrhagic fever

“…Likewise, in a study conducted in Georgia, it was found that the disease was mostly found in farmers and people who lived in rural areas [14]. In a study investigating the molecular and clinical epidemiology of CCHF in Oman [15], the main risks of infection for contracting CCHF were animal contact (73%) and butchery (88%). When the distribution of ticks according to occupations was examined in the current study, it was found that 54.1% of the 362 patients were engaged in farming and animal husbandry, 38.1% were from other occupational groups, 3.9% were students, 3.6% were children, and 0.3% were health personnel.…”

Phylogenetic Analysis of Crimean-Congo Hemorrhagic Fever Virus in Inner Mongolia, China

“…Compared with S and L fragments, the rearrangement of the M fragment is more frequent (Deyde et al, 2006). According to phylogenetic analysis, CCHFV can be divided into seven genetic categories related to geographic origin: two from Asia, two from Europe, and three from Africa (Umair et al, 2020).…”