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      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

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          Abstract

          Background:

          TRIP (Transmission Reduction Intervention Project) was a network-based, contact tracing approach to locate and link to care, mostly people who inject drugs (PWID) with recent HIV infection.

          Objective:

          We investigated whether sequences from HIV-infected participants with high viral load cluster together more frequently than what is expected by chance.

          Methods:

          Paired end reads were generated for 104 samples using Illumina MiSeq next-generation se-quencing.

          Results:

          63 sequences belonged to previously identified local transmission networks of PWID (LTNs) of an HIV outbreak in Athens, Greece. For two HIV-RNA cut-offs (105 and 106 IU/mL), HIV transmissions were more likely between PWID with similar levels of HIV-RNA (p<0.001). 10 of the 14 sequences (71.4%) from PWID with HIV-RNA >106 IU/mL were clustered in 5 pairs. For 4 of these clusters (80%), there was in each one of them at least one sequence from a recently HIV-infected PWID.

          Conclusion:

          We showed that transmissions are more likely among PWID with high viremia.

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          Most cited references77

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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            FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

            Background We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. Methodology/Principal Findings Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the “CAT” approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100–1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. Conclusions/Significance FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
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              Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.

              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 and env 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 chi2 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.
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                Author and article information

                Journal
                Curr HIV Res
                Curr. HIV Res
                CHIVR
                Current HIV Research
                Bentham Science Publishers
                1570-162X
                1873-4251
                September 2018
                September 2018
                : 16
                : 5
                : 345-353
                Affiliations
                Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, , Greece; Department of Infection and Immunity, UCL, London, , United Kingdom; Medical School, University of Cyprus , Nicosia, , Cyprus; NIHR Biomedical Research Centre, UCLH/UCL, London, , United Kingdom; Department of Clinical Virology, UCLH, London, , United Kingdom; Division of Infection and Immunity, Faculty of Medical Sciences, UCL and Farr Institute of Health Informatics Research , London, , United Kingdom; European University Cyprus, Nicosia, , Cyprus; Transmission Reduction Intervention Project, Athens site, Athens, , Greece; National Development and Research Institutes, New York, , United States; Department of Population, Policy and Practice, UCL GOS Institute of Child Health , London, , United Kingdom
                Author notes
                [* ]Address correspondence to this author at the Medical School, University of Cyprus, Palaios dromos Lefkosias Lemesou No.215/6, 2029 Strovolos, Nicosia, Cyprus; Tel: 00357 22895223; E-mails: gknikolopoulos@ 123456gmail.com ;, nikolopoulos.georgios@ 123456ucy.ac.cy
                [§]

                Contributed equally to this work

                Article
                CHIVR-16-345
                10.2174/1570162X17666190130120757
                6446520
                30706819
                a175109e-6ce2-4d44-a529-5f9234abb821
                © 2018 Bentham Science Publishers

                This is an open access article licensed under the terms of the Creative Commons Attribution-Non-Commercial 4.0 International Public License (CC BY-NC 4.0) ( https://creativecommons.org/licenses/by-nc/4.0/legalcode), which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

                History
                : 02 December 2018
                : 21 January 2019
                : 27 January 2019
                Categories
                Article

                Infectious disease & Microbiology
                hiv,recent infection,hiv transmission,pwid,hiv-rna,trip
                Infectious disease & Microbiology
                hiv, recent infection, hiv transmission, pwid, hiv-rna, trip

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