ArticlePloS one2018
A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Genetic diversity and drug resistance mutations of HIV-1 in Ghana: a systematic review of two decades.BMC infectious diseases · 2026Pooled it
- Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America.Scientific reports · 2021Trial
- Pervasive HIV recombination limits the utility of circulating recombinant form nomenclature.PLoS pathogens · 2026Article
- Molecular transmission network reveals CRF08_BC-driven clusters of HIV-1 among low-education older adults linked to female sex workers in Taizhou, China.Frontiers in microbiology · 2026Article
- Review
- Detection of Antiretroviral Drug-Resistant Mutations and HIV-1 Subtypes in Circulation Among Men Who Have Sex With Men, SEM Females, and Female Sex Workers: Results of Vietnam's HIV Sentinel Surveillance Plus System, 2018-2020.Journal of acquired immune deficiency syndromes (1999) · 2025Article
- Identification of new circulating recombinant form of HIV-1 CRF139_02B in Japan, and search for the origin.Global health & medicine · 2024Article
- Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.Microbiology spectrum · 2024Article
- Article
- Identification of two near-identical novel HIV-1 unique recombinant forms (CRF01_AE/B) among men who have sex with men in baoding, hebei, China.Frontiers in genetics · 2023Article
- Review
- Revisiting the recombinant history of HIV-1 group M with dynamic network community detection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Identification of a New HIV-1 Circulating Recombinant Form CRF112_01B Strain in Baoding City, Hebei Province, China.Current HIV research · 2022Article
- Evidence for Recombination as an Evolutionary Mechanism in Coronaviruses: Is SARS-CoV-2 an Exception?Frontiers in public health · 2022Article
- The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China.Virus evolution · 2022Article
- Article
- Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia.BioMed research international · 2020Article
- Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain.Frontiers in microbiology · 2019Article
- Bigger and Better? Representativeness of the Influenza A Surveillance Using One Consolidated Clinical Microbiology Laboratory Data Set as Compared to the Belgian Sentinel Network of Laboratories.Frontiers in public health · 2019Article
- Near Full-length Genomic Sequencing and Molecular Analysis of HIV-Infected Individuals in a Network-based Intervention (TRIP) in Athens, Greece: Evidence that Transmissions Occur More Frequently from those with High HIV-RNA.Current HIV research · 2018Article
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Authors and funding
16 authors at 8 institutions in 1 country.
Funding
Abstract
BACKGROUND &
methodsThe ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker.
resultsThe pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset.
conclusionsThe initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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