1
|
Abdullahi A, Kida IM, Maina UA, Ibrahim AH, Mshelia J, Wisso H, Adamu A, Onyemata JE, Edun M, Yusuph H, Aliyu SH, Charurat M, Abimiku A, Abeler-Dorner L, Fraser C, Bonsall D, Kemp SA, Gupta RK. Limited emergence of resistance to integrase strand transfer inhibitors (INSTIs) in ART-experienced participants failing dolutegravir-based antiretroviral therapy: a cross-sectional analysis of a Northeast Nigerian cohort. J Antimicrob Chemother 2023; 78:2000-2007. [PMID: 37367727 PMCID: PMC10393879 DOI: 10.1093/jac/dkad195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Due to the high prevalence of resistance to NNRTI-based ART since 2018, consolidated recommendations from the WHO have indicated dolutegravir as the preferred drug of choice for HIV treatment globally. There is a paucity of resistance outcome data from HIV-1 non-B subtypes circulating across West Africa. AIMS We characterized the mutational profiles of persons living with HIV from a cross-sectional cohort in North-East Nigeria failing a dolutegravir-based ART regimen. METHODS WGS of plasma samples collected from 61 HIV-1-infected participants following virological failure of dolutegravir-based ART were sequenced using the Illumina platform. Sequencing was successfully completed for samples from 55 participants. Following quality control, 33 full genomes were analysed from participants with a median age of 40 years and median time on ART of 9 years. HIV-1 subtyping was performed using SNAPPy. RESULTS Most participants had mutational profiles reflective of exposure to previous first- and second-line ART regimens comprised NRTIs and NNRTIs. More than half of participants had one or more drug resistance-associated mutations (DRMs) affecting susceptibility to NRTIs (17/33; 52%) and NNRTIs (24/33; 73%). Almost a quarter of participants (8/33; 24.4%) had one or more DRMs affecting tenofovir susceptibility. Only one participant, infected with HIV-1 subtype G, had evidence of DRMs affecting dolutegravir susceptibility-this was characterized by the T66A, G118R, E138K and R263K mutations. CONCLUSIONS This study found a low prevalence of resistance to dolutegravir; the data are therefore supportive of the continual rollout of dolutegravir as the primary first-line regimen for ART-naive participants and the preferred switch to second-line ART across the region. However, population-level, longer-term data collection on dolutegravir outcomes are required to further guide implementation and policy action across the region.
Collapse
Affiliation(s)
- Adam Abdullahi
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ibrahim Musa Kida
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Umar Abdullahi Maina
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Maiduguri, Borno, Nigeria
| | | | - James Mshelia
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Haruna Wisso
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Abdullahi Adamu
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Maiduguri, Borno, Nigeria
| | | | - Martin Edun
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Haruna Yusuph
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Sani H Aliyu
- Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | | | - Lucie Abeler-Dorner
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - David Bonsall
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
| |
Collapse
|
2
|
Souto B, Triunfante V, Santos-Pereira A, Martins J, Araújo PMM, Osório NS. Evolutionary dynamics of HIV-1 subtype C in Brazil. Sci Rep 2021; 11:23060. [PMID: 34845263 PMCID: PMC8629974 DOI: 10.1038/s41598-021-02428-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/12/2021] [Indexed: 11/29/2022] Open
Abstract
The extensive genetic diversity of HIV-1 is a major challenge for the prevention and treatment of HIV-1 infections. Subtype C accounts for most of the HIV-1 infections in the world but has been mainly localized in Southern Africa, Ethiopia and India. For elusive reasons, South Brazil harbors the largest HIV-1 subtype C epidemic in the American continent that is elsewhere dominated by subtype B. To investigate this topic, we collected clinical data and viral sequences from 2611 treatment-naïve patients diagnosed with HIV-1 in Brazil. Molecular epidemiology analysis supported 35 well-delimited transmission clusters of subtype C highlighting transmission within South Brazil but also from the South to all other Brazilian regions and internationally. Individuals infected with subtype C had lower probability to be deficient in CD4+ T cells when compared to subtype B. The HIV-1 epidemics in the South was characterized by high female-to-male infection ratios and women-to-child transmission. Our results suggest that HIV-1 subtype C probably takes advantage of longer asymptomatic periods to maximize transmission and is unlikely to outcompete subtype B in settings where the infection of women is relatively less relevant. This study contributes to elucidate factors possibly underlying the geographical distribution and expansion patterns of the most spread HIV-1 subtypes.
Collapse
Affiliation(s)
- Bernardino Souto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.,Department of Medicine, Federal University of São Carlos, São Carlos, Brazil
| | - Vera Triunfante
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Joana Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Pedro M M Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
| |
Collapse
|
3
|
Nationwide Study of Drug Resistance Mutations in HIV-1 Infected Individuals under Antiretroviral Therapy in Brazil. Int J Mol Sci 2021; 22:ijms22105304. [PMID: 34069929 PMCID: PMC8157590 DOI: 10.3390/ijms22105304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/02/2022] Open
Abstract
The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p < 0.001). Among the two most prevalent HIV-1 subtypes (B and C) there was a significant (p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.
Collapse
|
4
|
Prasanna A, Niranjan V. Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200608130029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background:
Since bacteria are the earliest known organisms, there has been significant
interest in their variety and biology, most certainly concerning human health. Recent advances in
Metagenomics sequencing (mNGS), a culture-independent sequencing technology, have facilitated
an accelerated development in clinical microbiology and our understanding of pathogens.
Objective:
For the implementation of mNGS in routine clinical practice to become feasible, a
practical and scalable strategy for the study of mNGS data is essential. This study presents a robust
automated pipeline to analyze clinical metagenomic data for pathogen identification and
classification.
Method:
The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible,
and user-friendly framework scripted using the Snakemake workflow management software. The
implementation avoids the hassle of manual installation and configuration of the multiple commandline
tools and dependencies. The approach directly screens pathogens from clinical raw reads and
generates consolidated reports for each sample.
Results:
The pipeline is demonstrated using publicly available data and is tested on a desktop Linux
system and a High-performance cluster. The study compares variability in results from different
tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality
check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of
bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors
identification. The results obtained from the pipeline are evaluated based on sensitivity and positive
predictive value.
Conclusion:
Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial
clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance
prediction.
Collapse
Affiliation(s)
- Akshatha Prasanna
- Department of Biotechnology, Rashtreeya Vidyalaya College of Engineering, Bengaluru,India
| | - Vidya Niranjan
- Department of Biotechnology, Rashtreeya Vidyalaya College of Engineering, Bengaluru,India
| |
Collapse
|
5
|
Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
Collapse
Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| |
Collapse
|
6
|
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
Collapse
Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | |
Collapse
|