Whole‐genome sequencing of Crimean−Congo hemorrhagic fever virus circulating in Pakistan during 2022

Abstract

Pakistan is an endemic country for Crimean−Congo hemorrhagic fever (CCHF) and its Balochistan province is considered a hotspot region for circulation of the virus whereas sporadic cases have been reported from other parts of the country. Our study aims to investigate the genomic diversity of the CCHF virus circulating in Punjab and Khyber Pakhtunkhwa provinces of Pakistan. Between April to September 2022, 46 samples from suspected CCHF patients were tested, with 6 (13%) showing positive RT-PCR results. Among the positive cases, all were male, aged 14−48 years among which 4 were butchers. Three CCHF patients succumbed to the disease. The complete S-M-L-gene fragments of 4 positive samples were sequenced. The S and L segments belonged to the Asia-1 clade and clustered with regional strains from Iran, India, and Afghanistan. One M segment sequence grouped into Africa-2 along with those reported from India during 2016−2019. We report the detection of a reassorted virus (NIH-PAK-CCHF-03|2022) having Asia-1-Africa-2-Asia-1 (S-M-L) segment pattern for the first time from Pakistan. Mutational analysis showed M segments harboring eight mutations (T55A,

WITHDRAWN: Genomic characterization of Crimean-Congo Hemorrhagic Fever Virus detected during nosocomial outbreak (2023) in Balochistan province of Pakistan

“…Molecular analysis of CCHF samples from Balochistan, conducted at the NIH in Islamabad for the period 2008−2011, confirmed the circulation of the Asia-1 genotype [7,24]. Further genetic studies in 2019 and 2022 reinforced the endemic presence of Asia-1 in Pakistan [9,12].…”

“…Molecular analysis of CCHF samples from Balochistan, conducted at the NIH in Islamabad for the period 2008−2011, confirmed the circulation of the Asia-1 genotype [7, 24]. Further genetic studies in 2019 and 2022 reinforced the endemic presence of Asia-1 in Pakistan [9, 12]. Consistent with these findings, the CCHF viruses identified in Pakistan towards the end of 2023 were also classified as belonging to Asia-1, specifically Clade IVa, across all three genomic segments.…”

“…The subsequent years saw varying numbers of cases: 55 in 2017, 63 in 2018, 75 in 2019, 19 in 2020, and 28 in 2021, with most cases typically recorded between June and September annually [9–11]. Moreover, from January to September 2022, there were 123 reported CCHF cases and 25 fatalities as of September 7, 2022 [12]. In 2023, sporadic cases were reported from various parts of the country.…”

Is Asia Moving to a New Epidemic? Exploring the Impending Threat and Its Ramifications

“…To prevent CCHF from becoming epidemic, eventually the next global pandemic, it is crucial to take proactive measures to minimize its transmission. 9 There is a need of stricter screening, continuous surveillance of affected animals and humans, and investment in the development of new therapies and vaccines. 10 Furthermore, mass awareness about safe waste disposal and slaughter practices should be promoted.…”