Reclassification of respiratory syncytial virus genotypes in India

Abstract

Respiratory syncytial virus (RSV) is known to be the major cause of lower respiratory tract infections in infants and in the elderly. RSV was recently reclassified and simplified into three genotypes of the RSV-A subgroup (GA1-GA3) and into seven genotypes of the RSV-B subgroup (GB1-GB7). This classification strategy was not implemented globally. This study intended to reclassify the sequences that were submitted in GenBank till September 2021 from India. The gene sequences of the ectodomain region, second hypervariable region (SHR), and the partial second hypervariable region (PSHR) of the G gene were selected for the analysis. 25 ectodomain, 36 s hypervariable, and 19 partial second hypervariable regions of the RSV-A subgroup and 42-ectodomain, 49-s hypervariable region and 11-partial second hypervariable region of RSV-B subgroup were used for phylogenetic analysis. P-distance was calculated to support the genotype determination done by phylogenetic analysis. Phylogenetic analysis revealed that GA2.3.1, GA2.3.3, GA2.3.4, GA2.3.5, and GA2.3.6b lineages of GA2 genotype for RSV-A; and GB5.0.1, GB5.0.2, GB5.0.3, GB5.0.4a, GB5.0.4c, GB5.0.5a, GB5.0.5c lineages of GB5 genotype and GB7 genotype for RSV-B were that circulated in India. This work has implication for RSV vaccine research, and also for strategies for the prevention and control of RSV infection in humans.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-022-00802-x.

Keywords: Ectodomain region; Genotype; India; Respiratory syncytial virus; Second hypervariable region.

Fig. 1

The flow diagram of the methodology is given in (a). The schematic representation of G-gene is given in (b). Ecto—Ectodomain region sequences, SHR—Second Hypervariable Region sequences, and PSHR—Partial Second Hypervariable Region sequences

Fig. 2

Seasonal trends of RSV-A and RSV-B genotypes, a cumulative yearly distribution of ectodomain, second hyper variable region, and partial second hyper variable region of RSV-A subgroup from 2007 to 2018 in India. b Cumulative yearly distribution of ectodomain, second hyper variable region, and partial second hyper variable region of RSV-B subgroup from 2005 to 2017 in India

Fig. 3

Mid-rooted phylogenetic tree of RSV-A subgroup. Mid-rooted phylogenetic tree of the ectodomain region of the RSV-A G protein gene constructed by using Maximum Likelihood method, by GTR + G substitution model with 1000 bootstrap replicates in PhyML software. The reference sequences used to construct the tree were downloaded from the Gen-Bank database. The two lettered words in the labels of the Indian sequences represent the state name, where: MH = Maharashtra. The tip labels of the Indian sequences were labelled in red

Fig. 4

Mid-rooted phylogenetic tree of RSV-A subgroup. Mid-rooted phylogenetic tree of the second hyper variable region of the RSV-A G protein gene constructed by using Maximum Likelihood method, by GTR + G substitution model with 1000 bootstrap replicates in PhyML software. The reference sequences used to construct the tree were downloaded from the Gen-Bank database. The two lettered words in the labels of the Indian sequences represent the state name, where: MH = Maharashtra, JH = Jharkhand, MP = Madhya Pradesh, TN = Tamil Nadu, and UP = Uttar Pradesh. The tip labels of the Indian sequences were labelled in red

Fig. 5

Mid-rooted phylogenetic tree of RSV-A subgroup. Mid-rooted phylogenetic tree of the partial second hyper variable region of the RSV-A G protein gene constructed by using Maximum Likelihood method, by GTR + G substitution model with 1000 bootstrap replicates in PhyML software. The reference sequences used to construct the tree were downloaded from the Gen-Bank database. The two lettered words in the labels of the Indian sequences represent the state name, where: MH = Maharashtra. The tip labels of the Indian sequences were labelled in red

Fig. 6

Mid-rooted phylogenetic tree of RSV-B subgroup. Mid-rooted phylogenetic tree of the ectodomain region of the RSV-B G protein gene constructed by using Maximum Likelihood method, by GTR + G substitution model with 1000 bootstrap replicates in PhyML software. The reference sequences used to construct the tree were downloaded from the Gen-Bank database. The two lettered words in the labels of the Indian sequences represent the state names, where: DL = Delhi and MH = Maharashtra. The tip labels of the Indian sequences were labelled in red

Fig. 7

Mid-rooted phylogenetic tree of RSV-B subgroup. Mid-rooted phylogenetic tree of the second hyper variable region of the RSV-B G protein gene constructed by using Maximum Likelihood method, by GTR + G substitution model with 1000 bootstrap replicates in PhyML software. The reference sequences used to construct the tree were downloaded from the Gen-Bank database. The two lettered words in the labels of the Indian sequences represent the state names, where: DL = Delhi, MP = Madhya Pradesh, UP = Uttar Pradesh, WB = West Bengal, and MH = Maharashtra. The tip labels of the Indian sequences were labelled in red

Fig. 8

Mid-rooted phylogenetic tree of RSV-B subgroup. Mid-rooted phylogenetic tree of the partial second hyper variable region of the RSV-B G protein gene constructed by using Maximum Likelihood method, by HKY85 + G substitution model with 1000 bootstrap replicates in PhyML software. The reference sequences used to construct the tree were downloaded from the Gen-Bank database. The two lettered words in the labels of the Indian sequences represent the state names, where: DL = Delhi and KA = Karnataka. The tip labels of the Indian sequences were labelled in red