Genetic diversity and phylogenetic analysis of Crimean-Congo Hemorrhagic Fever viruses circulating in Pakistan during 2019.
Adolescent
Adult
Aged
Child
Child, Preschool
Female
Genetic Variation
Genotype
Hemorrhagic Fever Virus, Crimean-Congo
/ classification
Hemorrhagic Fever, Crimean
/ epidemiology
Humans
Male
Middle Aged
Pakistan
/ epidemiology
RNA, Viral
/ genetics
Sequence Analysis, DNA
Serum
/ virology
Tertiary Care Centers
Young Adult
Journal
PLoS neglected tropical diseases
ISSN: 1935-2735
Titre abrégé: PLoS Negl Trop Dis
Pays: United States
ID NLM: 101291488
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
17
01
2020
accepted:
20
03
2020
revised:
10
07
2020
pubmed:
1
7
2020
medline:
6
8
2020
entrez:
30
6
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32598383
doi: 10.1371/journal.pntd.0008238
pii: PNTD-D-20-00001
pmc: PMC7351229
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0008238Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
J Arthropod Borne Dis. 2016 Jan 05;10(2):127-40
pubmed: 27308271
BMC Infect Dis. 2013 May 04;13:201
pubmed: 23641865
J Virol. 2006 Sep;80(17):8834-42
pubmed: 16912331
Int J Infect Dis. 2019 Nov;88:135-140
pubmed: 31442628
Antiviral Res. 2013 Oct;100(1):20-8
pubmed: 23872313
Lancet Infect Dis. 2016 Dec;16(12):1332-1333
pubmed: 27998596
Trans R Soc Trop Med Hyg. 2015 Aug;109(8):503-13
pubmed: 26142451
J Gen Virol. 2010 Jan;91(Pt 1):199-207
pubmed: 19812264
Virus Res. 2004 Jun 15;102(2):185-9
pubmed: 15084400
Trans R Soc Trop Med Hyg. 2005 Aug;99(8):577-84
pubmed: 15935414
Emerg Infect Dis. 2013 Jun;19(6):1017-9
pubmed: 23735999
J Gen Virol. 2005 Aug;86(Pt 8):2333-2338
pubmed: 16033981
J Vector Borne Dis. 2010 Dec;47(4):211-6
pubmed: 21178213
J Coll Physicians Surg Pak. 2007 Sep;17(9):543-5
pubmed: 17903402
Genome Announc. 2013 May 16;1(3):
pubmed: 23682136
J Clin Virol. 2010 Feb;47(2):110-4
pubmed: 20006541
Rev Infect Dis. 1989 May-Jun;11 Suppl 4:S794-800
pubmed: 2749111
Am J Epidemiol. 1970 Sep;92(3):197-202
pubmed: 5458948
Lancet Infect Dis. 2006 Apr;6(4):203-14
pubmed: 16554245
Lancet Infect Dis. 2017 Apr;17(4):367-368
pubmed: 28346174
Int J Infect Dis. 2005 Jan;9(1):37-42
pubmed: 15696649
Epidemiol Infect. 2005 Aug;133(4):659-66
pubmed: 16050511
J Clin Microbiol. 2002 Mar;40(3):1122-3
pubmed: 11880460
J Coll Physicians Surg Pak. 2019 Jun;29(6):563-573
pubmed: 31133158
PLoS Negl Trop Dis. 2019 Apr 25;13(4):e0007100
pubmed: 31022170
Emerg Infect Dis. 2002 Aug;8(8):852-4
pubmed: 12141973
Lancet Infect Dis. 2017 Aug;17(8):806
pubmed: 28741546
Emerg Infect Dis. 2002 Jan;8(1):50-3
pubmed: 11749748
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
MMWR Suppl. 1988 Feb 26;37(3):1-16
pubmed: 3126390
J Clin Virol. 2015 Jun;67:25-30
pubmed: 25959153
Int J Prev Med. 2019 Jul 05;10:117
pubmed: 31367281
Am J Trop Med Hyg. 1997 Nov;57(5):512-8
pubmed: 9392588
Am J Trop Med Hyg. 1980 Sep;29(5):941-7
pubmed: 7435795