Spatio-temporal distribution analysis of circulating genotypes of dengue virus type 1 in western and southern states of India by a one-step real-time RT-PCR assay

被引：4
作者：
Alagarasu, K. [1 ]
Patil, J. A. [1 ]
Kakade, M. B. [1 ]
More, A. M. [1 ]
Bote, M. [1 ]
Chowdhury, D. [1 ]
Seervi, M. [1 ]
Rajesh, N. T. [2 ]
Ashok, M. [3 ]
Anukumar, B. [4 ]
Abraham, A. M. [5 ]
Parashar, D. [1 ]
Shah, P. S. [1 ]
机构：
[1] Natl Inst Virol, ICMR, Dengue Chikungunya Grp, Pune 411001, Maharashtra, India
[2] PSG Inst Med Sci & Res, Coimbatore, Tamil Nadu, India
[3] ICMR Natl Inst Virol, Bangalore Field Unit, Bengaluru, Karnataka, India
[4] ICMR Natl Inst Virol, Kerala Field Unit, Alappuzha, Kerala, India
[5] Christian Med Coll & Hosp, Vellore, Tamil Nadu, India
来源：
INFECTION GENETICS AND EVOLUTION | 2019年 / 75卷
基金：
美国国家卫生研究院;
关键词：
Dengue virus; Asian genotype; American/African genotype; Real-time RT-PCR; SEROTYPE; 3; EVOLUTION; EMERGENCE; OUTBREAK;
D O I：
10.1016/j.meegid.2019.103989
中图分类号：
R51 [传染病];
学科分类号：
100401 ;
摘要：
Dengue virus type 1 (DENV-1) Asian and American/African (AM/AF) genotypes were reported to be co-circulating in southern and western states of India based on envelope (E) gene sequencing of few representative samples. The objective of the present study was to develop a one-step real-time RT-PCR to discriminate between Asian and AM/AF genotypes of DENV-1 and investigate the spatio-temporal distribution of the DENV-1 genotypes in southern and western states of India. A one-step real-time RT-PCR to discriminate the Asian and AM/AF genotypes of DENV-1 was developed and validated using 40 samples (17 Asian and 23 AM/AF), for which the envelope (E) gene sequence data was available. DENV-2, DENV-3 and DENV-4 isolates, one each and DENV negative samples (n = 17) were also tested by the assay. Additional 296 samples positive for DENV-1 from selected Southern and Western states of India were genotyped using the real-time RT-PCR assay. Among the samples used for validation, the genotyping results were concordant with sequencing results for 39 samples. In the one discordant sample which was positive for AM/AF by sequencing, the genotyping assay tested positive for both Asian and AM/AF genotype. DENV-2, DENV-3 and DENV-4 isolates were not reactive in the assay. None of the DENV negative samples were positive (sensitivity 100% and specificity 98.2%). A total of 336 samples (40 samples with sequence data and 296 samples without sequence data) were used for spatio-temporal distribution analysis. The results revealed that the Asian genotype was the predominant genotype in Tamil Nadu and Kerala, the southern states. The AM/AF genotype was the predominant genotype in Maharashtra, a western state of India. In Nashik district of Maharashtra, Asian genotype was observed in 32.6% of DENV-1 samples during 2017 while the same decreased to 7.3% during 2018. In Pune district, Asian genotype was observed in 40.0% of DENV-1 samples during 2018 only. To conclude, a one step real-time RT-PCR has been developed for discriminating Asian and AM/AF genotypes of DENV-1. This assay can act as a complement to sequencing but not a substitute and can be utilized in resource limited settings for molecular surveillance of DENV-1. DENV-1 Asian genotype was the dominant genotype in South India while, AM/AF genotype was dominant in Western India.
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页数：8
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