Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.
Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.
Infect Genet Evol. 2019 Nov;75:103989. doi: 10.1016/j.meegid.2019.103989. Epub 2019 Jul 31.
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.
登革病毒 1 型（DENV-1）亚洲和美洲/非洲（AM/AF）基因型据报道在印度南部和西部各州共同循环，这是基于对少数代表性样本的包膜（E）基因测序。本研究的目的是开发一种一步实时 RT-PCR 来区分 DENV-1 的亚洲和 AM/AF 基因型，并调查印度南部和西部各州 DENV-1 基因型的时空分布。使用 40 个样本（17 个亚洲和 23 个 AM/AF）开发并验证了一种一步实时 RT-PCR，用于区分 DENV-1 的亚洲和 AM/AF 基因型，这些样本的包膜（E）基因序列数据可用。该检测还检测了 1 个 DENV-2、DENV-3 和 DENV-4 分离株和 17 个 DENV 阴性样本。使用实时 RT-PCR 检测从印度选定的南部和西部各州采集的另外 296 个 DENV-1 阳性样本。在用于验证的样本中，39 个样本的基因分型结果与测序结果一致。在一个测序结果为 AM/AF 的不一致样本中，基因分型检测对亚洲和 AM/AF 两种基因型均呈阳性。该检测对 DENV-2、DENV-3 和 DENV-4 分离株均无反应。没有一个 DENV 阴性样本呈阳性（灵敏度 100%，特异性 98.2%）。总共 336 个样本（40 个有序列数据的样本和 296 个没有序列数据的样本）用于时空分布分析。结果表明，亚洲基因型是泰米尔纳德邦和喀拉拉邦等南部州的主要基因型。在印度西部的马哈拉施特拉邦，AM/AF 基因型是主要基因型。在马哈拉施特拉邦的纳西克区，2017 年 DENV-1 样本中观察到亚洲基因型占 32.6%，而 2018 年则降至 7.3%。在浦那区，2018 年仅观察到 40.0%的 DENV-1 样本为亚洲基因型。总之，已经开发了一种一步实时 RT-PCR 来区分 DENV-1 的亚洲和 AM/AF 基因型。该检测可以作为测序的补充，但不能替代，可在资源有限的情况下用于 DENV-1 的分子监测。DENV-1 亚洲基因型是印度南部的主要基因型，而 AM/AF 基因型是印度西部的主要基因型。
