Introduction
Next‐generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of ...low‐abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS‐based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting.
Discussion
Essential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use.
Conclusions
While NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this “Winnipeg Consensus” may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity.
Pretreatment drug resistance in people initiating or re-initiating antiretroviral therapy (ART) containing non-nucleoside reverse transcriptase inhibitors (NNRTIs) might compromise HIV control in ...low-income and middle-income countries (LMICs). We aimed to assess the scale of this problem and whether it is associated with the intiation or re-initiation of ART in people who have had previous exposure to antiretroviral drugs.
This study was a systematic review and meta-regression analysis. We assessed regional prevalence of pretreatment drug resistance and risk of pretreatment drug resistance in people initiating ART who reported previous ART exposure. We systematically screened publications and unpublished datasets for pretreatment drug-resistance data in individuals in LMICs initiating or re-initiating first-line ART from LMICs. We searched for studies in PubMed and Embase and conference abstracts and presentations from the Conference on Retroviruses and Opportunistic Infections, the International AIDS Society Conference, and the International Drug Resistance Workshop for the period Jan 1, 2001, to Dec 31, 2016. To assess the prevalence of drug resistance within a specified region at any specific timepoint, we extracted study level data and pooled prevalence estimates within the region using an empty logistic regression model with a random effect at the study level. We used random effects meta-regression to relate sampling year to prevalence of pretreatment drug resistance within geographical regions.
We identified 358 datasets that contributed data to our analyses, representing 56 044 adults in 63 countries. Prevalence estimates of pretreatment NNRTI resistance in 2016 were 11·0% (7·5–15·9) in southern Africa, 10·1% (5·1–19·4) in eastern Africa, 7·2% (2·9–16·5) in western and central Africa, and 9·4% (6·6–13·2) in Latin America and the Caribbean. There were substantial increases in pretreatment NNRTI resistance per year in all regions. The yearly increases in the odds of pretreatment drug resistance were 23% (95% CI 16–29) in southern Africa, 17% (5–30) in eastern Africa, 17% (6–29) in western and central Africa, 11% (5–18) in Latin America and the Caribbean, and 11% (2–20) in Asia. Estimated increases in the absolute prevalence of pretreatment drug resistance between 2015 and 2016 ranged from 0·3% in Asia to 1·8% in southern Africa.
Pretreatment drug resistance is increasing at substantial rate in LMICs, especially in sub-Saharan Africa. In 2016, the prevalence of pretreatment NNRTI resistance was near WHO's 10% threshold for changing first-line ART in southern and eastern Africa and Latin America, underscoring the need for routine national HIV drug-resistance surveillance and review of national policies for first-line ART regimen composition.
Bill & Melinda Gates Foundation and World Health Organization.
HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive ...and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21-22 February, 2018), a second "Winnipeg Consensus" symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium's goals and highlights.
Clinical follow-up in people living with HIV (PLWH) has individual and public health implications. The objectives of this study were to measure variables related to follow-up failures, identify ...self-reported reasons to maintain adequate follow-up or for having follow-up failures, and know how the pandemic influenced patients’ clinical follow-up. Participants were PLWH receiving HIV-health care at a hospital-based clinic in Mexico City which became an exclusive COVID-19 health service. Participants completed a telephone semi-structured interview and online psychological questionnaires. Lower educational and socioeconomic level, longer times of transportation to the clinic, being attended by different doctors, detectable viral load, having previous dropouts, inadequate antiretroviral adherence, and less HIV knowledge were related to follow-up failures. COVID-19 had a significant negative impact, but it also had positive repercussions for patients with adequate follow-up. These results could help develop effective psychosocial programs and improve healthcare in institutions to facilitate patient retention.
Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV ...envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.
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•Pre-existing antibodies to DENV1 correlate with high ZIKV neutralizing responses•Antibodies to the EDIII lateral ridge correlate with serum neutralization of ZIKV•Recurrent VH3-23/VK1-5 antibodies to the EDIII potently neutralize ZIKV and DENV1•The structures of VH3-23/VK1-5 antibodies with the EDIIIs of DENV1 and ZIKV were solved
Individuals with high neutralizing antibody response against Zika virus have expanded clones of B cells that express the same heavy and light immunoglobulin genes and that are cross-reactive against dengue 1 virus.
Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a considerable impediment in research towards a cure for HIV. To address this, we developed a ...single-cell strategy to precisely define the unperturbed peripheral blood HIV-infected memory CD4
T cell reservoir from ART-treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by new and known surface markers within total and individual memory CD4
T cell subsets. We further uncovered new epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.
Certain open access publishers based on the article processing charges model have found it highly profitable to operate within a gray zone that encompasses both legitimate and predatory publishing ...practices. In this context, maximum profits can be obtained by adequate combinations of journal acceptance rates and elevated article processing charges. Considering that the gray zone can be particularly challenging to identify and that it poses risks for authors aiming to establish academic carreers, we believe it is important to provide a comprehensive description of it.
Abstract
Background
Evolutionary analyses of well-annotated human immunodeficiency virus (HIV) sequence data can provide insights into viral transmission patterns and associated factors. Here, we ...explored the transmission dynamics of the HIV-1 subtype B epidemic across the San Diego (US) and Tijuana (Mexico) border region to identify factors that could help guide public health policy.
Methods
HIV pol sequences were collected from people with HIV in San Diego County and Tijuana between 1996–2018. A multistep phylogenetic approach was used to characterize the dynamics of spread. The contributions of geospatial factors and HIV risk group to the local dynamics were evaluated.
Results
Phylogeographic analyses of the 2034 sequences revealed an important contribution of local transmission in sustaining the epidemic, as well as a complex viral migration network across the region. Geospatial viral dispersal between San Diego communities occurred predominantly among men who have sex with men, with central San Diego being the main source (34.9%) and recipient (39.5%) of migration events. HIV migration was more frequent from San Diego county towards Tijuana than vice versa. Migrations were best explained by the driving time between locations.
Conclusions
The US-Mexico border may not be a major barrier to the spread of HIV, which may stimulate coordinated transnational intervention approaches. Whereas a focus on central San Diego has the potential to avert most spread, the substantial viral migration independent of central San Diego shows that county-wide efforts will be more effective. Combined, this work shows that epidemiological information gleaned from pathogen genomes can uncover mechanisms that underlie sustained spread and, in turn, can be a building block of public health decision-making.
Several studies indicate that some cognitive changes occur after COVID-19. Visuospatial alterations have been reported in 24–40 %. These alterations may be useful as early biomarkers of ...neurodegenerative disease. Thus, we can emphasize the importance of visuospatial processes in cognition through quantitative and qualitative analysis of performance on the Clock Test (CDT) and the Rey-Osterrieth Complex Figure (FCRO). Our objective was to describe the performance of post COVID 19 patients in visuospatial tests, with different degrees of respiratory impairment and to perform a qualitative analysis of the performance to check its relationship with alterations in attention and executive functions. This will allow highlighting the executive component of the performance of the CDT and ROCF and differentiate patients with possible cognitive impairment. 77 patients with SARS-CoV-2 infection were evaluated (3 months post-infection) with a complete neuropsychological battery and MRI. Overall, there is a significant difference between FCRO and CDT, with FCRO having only 9 % change and CDT having 51.9 % change. Regarding the correlations observed between groups (VM Inv, VM non I and non hospitalized) the highest correlations were observed between Boston with FCRO copy (r=0.497; p=0.001) and with FCRO memory (r=0.429; p=0.001). Comparing the performance between groups by severity, significant differences were observed only in the TMT A (13.706 p=0.001) and B (9.583 p=0.008) tests and in the phonological fluency letter A (13.445 p=0.001), we observed that the group of non-hospitalized patients had a better performance. Neuropsychological deficits often have a direct impact on daily life by affecting the ability to learn and adapt. Thus, a useful strategy for the neuropsychological characterization of post-COVID-19 patients is the qualitative analysis of visuospatial abilities in conjunction with executive functions that cannot be analyzed in isolation.
Abstract
The level of knowledge that people living with human immunodeficiency virus (HIV) have about their disease can impact their adherence to treatment. The aim of this study was to develop a ...tool to assess the knowledge about HIV among people receiving treatment at a specialized clinic in Mexico City. To establish content validity, expert judges were invited to conceptualize the tool and propose items for the defined dimensions. A total of 490 individuals living with HIV completed the 91-item questionnaire, with 82.2% being male and a mean age of 36.1 years. We conducted an exploratory factor analysis, resulting in a reduced questionnaire of 45 questions. A three-factor solution explained 36.2% of the variance in HIV knowledge. The total scale had a reliability coefficient of 0.937, and each subscale had reliabilities of 0.828, 0.856 and 0.859. Lower educational level (F(336) = 8.488, p < 0.001) and female gender (t(399) = 2.003, p = 0.046) were associated with lower scores on the HIV knowledge questionnaire. This tool appears suitable for measuring HIV knowledge in people living with HIV, although future studies are required to confirm its structure and reduce its extension.
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