Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination

Abstract

The development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag andenv genes. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. Likewise, little is known about sequence variation of HIV-1 in India, the country facing the largest burden of HIV worldwide. Therefore, the objective of this study was to clone and characterize the complete genome of HIV-1 from seroconverters infected with subtype C variants in India. Cocultured HIV-1 isolates were obtained from six seroincident individuals from Pune, India, and virtually full-length HIV-1 genomes were amplified, cloned, and sequenced from each. Sequence analysis revealed that five of the six genomes were of subtype C, while one was a mosaic of subtypes A and C, with multiple breakpoints in env,nef, and the 3′ long terminal repeat as determined by both maximal χ2 analysis and phylogenetic bootstrapping. Sequences were compared for preservation of known cytotoxic T lymphocyte (CTL) epitopes. Compared with those of the HIV-1LAI sequence, 38% of well-defined CTL epitopes were identical. The proportion of nonconservative substitutions for Env, at 61%, was higher (P < 0.001) than those for Gag (24%), Pol (18%), and Nef (32%). Therefore, characterized CTL epitopes demonstrated substantial differences from subtype B laboratory strains, which were most pronounced in Env. Because these clones were obtained from Indian seroconverters, they are likely to facilitate vaccine-related efforts in India by providing potential antigens for vaccine candidates as well as for assays of vaccine responsiveness.

Emergence of a novel coronavirus causing respiratory illness from Wuhan, China

“…10 To avoid false positives, we recorded a recombination event only if it was detected to have a significant signal by at least three different methods. Using this approach, we detected three H3-HA sequences and seven N2-NA sequences that had strong signals for recombination ( Table 1 ), however, these sequences did not include the two H3N2 viruses (A/duck/Guangdong/F138/2017 (H3N2) and A/duck/Guangdong/F352/2018 (H3N2)) that were suggested to have recombination signals by Hu et al 1 To determine whether our strict criteria lead to the conflict with the result of Hu et al, 1 we reanalyzed the data used by Hu et al for potential recombination signals with the SimPlot program 11 used in their study. Our SimPlot graphs, which are the same as those in Hu et al, 1 clearly show a high degree of similarity within the HA and NA sequences ( Figs.…”

Molecular and antigenic characteristics of Massachusetts genotype infectious bronchitis coronavirus in China

“…To further identify the recombinant events, the BLASTN program (Liu et al, 2013) was used to search GenBank for IBV sequences that were homologous to those of the five IBV isolates, ck/CH/LHB/111172, ck/CH/LSD/111219, ck/CH/LHB/130598, ck/CH/ LDL/110931, and ck/CH/LHB/130573. The Similarity Plot of the complete genomic sequences (Lole et al, 1999), the nucleotide similarities and phylogenetic trees for each deduced recombinant fragment were analyzed with the MEGA 5.0 program (Schierup and Hein, 2000).…”

Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin

“…7. Similarity plots of the structural gene region of Armidale and VicS (subgroup 1), N1/88 (subgroup 2) and N1/03 (subgroup 3) strains created with SimPlot, version 3.5.1 (Lole et al, 1999). A: Armidale strain sequence used as the query, as in Mardani et al (2010).…”

“…The similarity plots were constructed using the maximum likelihood distance model, an empirical transition/transversion (Ts/Tv) ratio calculated for each window, a window size of 200 bp and a step size of 20 bp. The analyses were performed using SimPlot, version 3.5.1 (Lole et al, 1999).…”