SHIV-C109p5 NHP induces rapid disease progression in elderly macaques with extensive GI viral replication.

CCR5-tropic simian/human immunodeficiency viruses (SHIV) with clade C transmitted/founder envelopes represent a critical tool for the investigation of HIV experimental vaccines and microbicides in nonhuman primates, although many such isolates lead to spontaneous viral control post infection. Here, we generated a high-titer stock of pathogenic SHIV-C109p5 by serial passage in two rhesus macaques (RM) and tested its virulence in aged monkeys. The co-receptor usage was confirmed before infecting five geriatric rhesus macaques (four female and one male). Plasma viral loads were monitored by reverse transcriptase-quantitative PCR (RT-qPCR), cytokines by multiplex analysis, and biomarkers of gastrointestinal damage by enzyme-linked immunosorbent assay. Antibodies and cell-mediated responses were also measured. Viral dissemination into tissues was determined by RNAscope. Intravenous SHIV-C109p5 infection of aged RMs leads to high plasma viremia and rapid disease progression; rapid decrease in CD4+ T cells, CD4+CD8+ T cells, and plasmacytoid dendritic cells; and wasting necessitating euthanasia between 3 and 12 weeks post infection. Virus-specific cellular immune responses were detected only in the two monkeys that survived 4 weeks post infection. These were Gag-specific TNFα+CD8+, MIP1ß+CD4+, Env-specific IFN-γ+CD4+, and CD107a+ T cell responses. Four out of five monkeys had elevated intestinal fatty acid binding protein levels at the viral peak, while regenerating islet-derived protein 3α showed marked increases at later time points in the three animals surviving the longest, suggesting gut antimicrobial peptide production in response to microbial translocation post infection. Plasma levels of monocyte chemoattractant protein-1, interleukin-15, and interleukin-12/23 were also elevated. Viral replication in gut and secondary lymphoid tissues was extensive.IMPORTANCESimian/human immunodeficiency viruses (SHIV) are important reagents to study prevention of virus acquisition in nonhuman primate models of HIV infection, especially those representing transmitted/founder (T/F) viruses. However, many R5-tropic SHIV have limited fitness in vivo leading to many monkeys spontaneously controlling the virus post acute infection. Here, we report the generation of a pathogenic SHIV clade C T/F stock by in vivo passage leading to sustained viral load set points, a necessity to study pathogenicity. Unexpectedly, administration of this SHIV to elderly rhesus macaques led to extensive viral replication and fast disease progression, despite maintenance of a strict R5 tropism. Such age-dependent rapid disease progression had previously been reported for simian immunodeficiency virus but not for R5-tropic SHIV infections.

Perfil clinico-epidemiológico e factores associados à não supressão viral em pacientes vivendo com hiv/sida assistidos no centro integrado de tratamento no hospital militar de maputo (citra/hmm), 2019 à 2020 / Clinical-epidemiological profile and factors associated with viral non-suppression in patients living with hiv/aids assisted at the integrated treatment center at the maputo military hospital (citra/hmm), 2019 to 2020

: Introdução: O HIV e SIDA é um problema de saúde pública global, responsável por cerca de 32.7 milhões de mortes de doenças relacionadas à SIDA desde o início da epidemia até o final de 2019, comprometendo a saúde, a força de produção e produtividade. Esse cenário tende a ser mais grave, quando se trata de forças militares, cuja a responsabilidade da defesa e manutenção da paz, recai sobre eles. O objectivo foi avaliar o perfil clinico-epidemiológico e factores associados a não supressão viral em pacientes vivendo com HIV/SIDA assistidas no Centro Integrado de Tratamento no Hospital Militar de Maputo (CITRA/HMM). Métodos: Tratou-se de um estudo transversal analítico com uma abordagem quantitativa, utilizando dados secundários de pacientes em seguimento entre os anos de 2019-2020 no CITRA/HMM. A amostra foi composta por 9.015 indivíduos com idade igual ou superiora 15 anos de idade. A analise de dados foi feita com pacote estatístico STATA versão 16, onde recorreu-se os testes Qui-quadrado de Pearson e a razão de chances/OR com Intervalos de Confiança/IC de 95% e p<0,05, para verificar as diferenças entre às proporções e a associação entre as variáveis em análise, considerando como desfecho o estado de supressão viral: suprimido (<1000 cópias de RNA do HIV/ml) e não suprimido (≥1000 cópias de RNA do HIV/ml). Para o modelo de regressão logística múltipla, apenas foram seleccionadas as variáveis que se mostraram estatisticamente significativas na análise bivariada. Resultados: Dos 9.105 indivíduos inclusos na análise, 4.808 (52,8%) eram do sexo feminino e 1.235 (13,6%) eram militares. A média de idade foi de 47,9 anos (DP±12,1), sendo o grupo etário mais prevalente composto por indivíduos com idades entre 25 e 59 anos, totalizando 7.297 (80,2%) participantes. Entre os analisados, 5.395 (53,3%) tinham resultados de última carga viral, e destes, 4.148 (76,9%) tinham a carga viral suprimida. Embora a maior proporção de supressão viral tenha sido verificada em civis, quando ajustada, essa diferença não demonstrou significância estatística…

Introduction: HIV and AIDS is a global public health problem, responsible for about 32.7 million deaths from AIDS-related diseases from the beginning of the epidemic to the end of 2019, compromising health, workforce and productivity. This scenario tends to be more serious when it comes to military forces, whose responsibility for the defense and maintenance of peace falls on them. The objective was to evaluate the clinical and epidemiological profile and factors associated with viral load non-suppression in patients living with HIV/AIDS at the Military Hospital (CITRA/HMM). Methods: This is a analytic cross-sectional study with a quantitative approach, using secondary data from patients being followed up between the years 2019-2020 at CITRA/HMM. The sample consisted of 9,015 individuals aged 15 years and over. Data analysis was performed with the statistical package STATA, Version 16. Pearson's chi-square test and odds ratio/OR with a confidence interval of 95%CI and p<0,05 were used to verify the differences between the proportions and association between the variables under analysis, considering the state of viral suppression as an outcome: suppressed (<1000 HIV RNA copies/ml) and non-suppressed (≥1000 HIV RNA copies/ml). For the multiple logistic regression model, only the variables that proved to be statistically significant in the bivariate analysis were selected. Results: Of the 9,105 individuals included in the analysis, 4,808 (52.8%) were female and 1,235 (13.6%) were military personnel. The average age was 47.9 years (SD±12.1), with the most prevalent age group being individuals aged between 25 and 59, totalling 7,297 (80.2%) participants. Among those analysed, 5,395 (53.3%) had their last viral load results, and of these, 4,148 (76.9%) had a suppressed viral load. Although the highest proportion of viral suppression was seen in civilians, when adjusted, this difference was not statistically significant…

Drug resistance mutations in HIV: new bioinformatics approaches and challenges.

Drug resistance mutations appear in HIV under treatment pressure. Resistant variants can be transmitted to treatment-naive individuals, which can lead to rapid virological failure and can limit treatment options. Consequently, quantifying the prevalence, emergence and transmission of drug resistance is critical to effectively treating patients and to shape health policies. We review recent bioinformatics developments and in particular describe: (1) the machine learning approaches intended to predict and explain the level of resistance of HIV variants from their sequence data; (2) the phylogenetic methods used to survey the emergence and dynamics of resistant HIV transmission clusters; (3) the impact of deep sequencing in studying within-host and between-host genetic diversity of HIV variants, notably regarding minority resistant variants.

Transmitted HIV drug resistance and subtype patterns among blood donors in Poland.

Surveillance on the HIV molecular variability, risk of drug resistance transmission and evolution of novel viral variants among blood donors remains an understudied aspect of hemovigilance. This nationwide study analyses patterns of HIV diversity and transmitted resistance mutations. Study included 185 samples from the first time and repeat blood donors with HIV infection identified by molecular assay. HIV protease, reverse transcriptase and integrase were sequenced using population methods. Drug resistance mutation (DRM) patterns were analyzed based on the Stanford Interpretation Algorithm and standardized lists of transmitted mutations. Phylogeny was used to investigate subtyping, clustering and recombination patterns. HIV-1 subtype B (89.2%) followed by subtype A6 (7.6%) were predominant, while in three (1.6%) cases, novel recombinant B/A6 variants were identified. Non-B variants were more common among repeat donors (14.5%) compared to the first time ones (1.8%), p = 0.011, with higher frequency (9.9%) of A6 variant in the repeat donor group, p = 0.04. Major NRTI DRMs were observed in 3.8%, NNRTI and PI in 0.6% and INSTI 1.1% of cases. Additionally, E157Q polymorphism was observed in 9.8% and L74I in 11.5% of integrase sequences. Transmission of drug resistance among blood donors remains infrequent. Subtype patters increase in complexity with emergence of novel intersubtype A6B recombinants.

Phylogenetic characteristics of HIV among female cross-border travelers in Yunnan province between 2003 and 2012.

Sexual transmission is currently the main mode of transmission of the human immunodeficiency virus (HIV). In this study, 181 HIV-infected female cross-border travelers entering Yunnan province were recruited between 2003 and 2012. HIV RNAs were extracted from their frozen serum and gag-pol gene sequences were obtained for phylogenetic and recombination analyses. In total, 131 gag-pol gene sequences were obtained successfully, at a rate of 72.4%. The most prevalent subtypes were CRF01_AE, followed by CRF08_BC, subtypes B and C. The other four subjects were classified as undefined subtypes and other recombinants. The subtype distribution of intravenous drug users was significantly different from that of sexually transmitted infections and unknown groups. The genetic distances of subtype B, C, and CRF01_AE strains were all close to the reference sequences from Yunnan province and Southeast Asian countries. Gene diversity and cocirculation of multiple subtypes were observed in female cross-border travelers, and CRF01_AE was the dominant epidemic subtype. The advantages of these subtype preferences for sexual transmission were obvious in HIV infection and transmission among this population. Our findings also suggest that close attention should be given to the HIV infection status of the female migrant population. In addition, a description of their epidemic characteristics is significant for the surveillance and prevention of acquired immunodeficiency syndrome in the Yunnan province.

Molecular epidemiology in the HIV and SARS-CoV-2 pandemics.

PURPOSE OF REVIEW: The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics. RECENT FINDINGS: Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges. SUMMARY: Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.

Subclinical Genital Herpes Shedding in HIV/Herpes Simplex Virus 2-Coinfected Women during Antiretroviral Therapy Is Associated with an Increase in HIV Tissue Reservoirs and Potentially Promotes HIV Evolution.

Antigen (Ag)-specific immune responses to chronic infections, such as herpes simplex virus type 2 (HSV-2) in HIV/HSV-coinfected persons, may sustain HIV tissue reservoirs by promoting T-cell proliferation but are poorly studied in women on antiretroviral therapy (ART). Mixed anogenital swabs and cervical secretions were self-collected by nine HIV/HSV-2-coinfected women during ART for 28 days to establish subclinical HSV DNA shedding rates and detection of HIV RNA by real-time PCR. Typical herpes lesion site biopsy (TLSB) and cervical biopsy specimens were collected at the end of the daily sampling period. Nucleic acids (NA) isolated from biopsy specimens had HIV quantified and HIV envC2-V5 single-genome amplification (SGA) and T-cell receptor (TCR) repertoires assessed. Women had a median CD4 count of 537 cells/µl (IQR: 483 to 741) at enrollment and HIV plasma viral loads of <40 copies/ml. HSV DNA was detected on 12% of days (IQR: 2 to 25%) from anogenital specimens. Frequent subclinical HSV DNA shedding was associated with increased HIV DNA tissue concentrations and increased divergence from the most recent common ancestor (MRCA), an indicator of HIV replication. Distinct predominant TCR clones were detected in cervical and TLSB specimens in a woman with frequent HSV DNA shedding, with mixing of minor variants between her tissues. In contrast, more limited TCR repertoire mixing was observed in two women with less frequent subclinical HSV DNA shedding. Subclinical HSV shedding in HIV/HSV-coinfected women during ART may sustain HIV tissue reservoirs via Ag exposure or HIV replication. This study provides evidence supporting further study of interventions targeting suppression of Ag-specific immune responses as a component of HIV cure strategies.IMPORTANCE Persons with HIV infection are frequently coinfected with chronic herpesviruses, which periodically replicate and produce viable herpes virions, particularly in anogenital and cervical tissues. Persistent protein expression results in proliferation of CD8+ and CD4+ T cells, and the latter could potentially expand and sustain HIV tissue reservoirs. We found HSV genital shedding rates were positively correlated with HIV DNA concentrations and HIV divergence from ancestral sequences in tissues. Our work suggests that immune responses to common coinfections, such as herpesviruses, may sustain HIV tissue reservoirs during suppressive ART, suggesting future cure strategies should study interventions to suppress replication or reactivation of chronic herpes infections.

Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics.

The emergence of a new coronavirus, in around late December 2019 which had first been reported in Wuhan, China has now developed into a massive threat to global public health. The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. The person-to-person transmission of this virus is ongoing despite drastic public health mitigation measures such as social distancing and movement restrictions implemented in most countries. Understanding the source of such an infectious pathogen is crucial to develop a means of avoiding transmission and further to develop therapeutic drugs and vaccines. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. In this context, this review is devoted to understanding the taxonomic characteristics of SARS-CoV-2 and HIV. Herein, we discuss the emergence and molecular mechanisms of both viral infections. Nevertheless, no vaccine or therapeutic drug is yet to be approved for the treatment of SARS-CoV-2, although it is highly likely that new effective medications that target the virus specifically will take years to establish. Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2.

Massively multiplexed nucleic acid detection with Cas13.

The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.

What have we researched about HIV infection in Colombia? A bibliometric review 1983 - 2018 / Qué hemos investigado acerca de la infección por VIH en Colombia? Una revisión bibliométrica 1983 - 2018

Objective: Our objective was to quantitatively describe the research on HIV infection carried out in Colombia. Materials and methods: A bibliometric review of all studies that included people infected or affected by HIV between January 1, 1983, and August 31, 2018, was performed. Results: 587 studies were identified. Most were descriptive studies. There are a lower number of studies in the fields of prevention, education and public health. Most of the published studies were carried out in 3 departments. 72% were published in Q3, Q4 or unclassified journals. Discussion: The research performed has given priority to the description of figures and is not enough to understand and know how to treat factors like late diagnosis, the stigma and the prevention of the disease. Conclusion: There does not seem to be a national strategy to define the research needs. There is a low dissemination of the results and a low cover of the research in the country.

Objetivo: Describir cuantitativamente la investigación sobre infección por VIH realizada en Colombia. Materiales y métodos: Se realizó una revisión bibliométrica de estudios que incluyeran personas infectadas o afectadas por el VIH entre el 1 de enero de 1983 y el 31 de agosto de 2018. Resultados: Se identificaron 587 estudios. La mayoría fueron descriptivos. Hay un menor número en los campos de prevención, educación y salud pública. La mayoría se llevaron a cabo en 3 departamentos. El 72% se publicaron en Q3, Q4 o revistas no clasificadas. Discusión: La investigación realizada ha dado prioridad a la descripción de las cifras y no es suficiente para comprender y saber cómo tratar factores como el diagnóstico tardío, el estigma y la prevención de la enfermedad. Conclusión: No parece haber una estrategia nacional para definir las necesidades de investigación. Hay una baja difusión de los resultados y una baja cobertura de la investigación en el país.

High rates of tenofovir failure in a CRF01_AE-predominant HIV epidemic in the Philippines.

BACKGROUND: The Philippines has the fastest growing HIV epidemic in the Asia-Pacific. This increase was accompanied by a shift in the predominant HIV subtype from B to CRF01_AE. Increasing evidence points to a difference in treatment responses between subtypes. We examined treatment failure and acquired drug resistance (ADR) in people living with HIV (PLHIVs) after one year on antiretrovirals (ARVs). METHODS: PLHIV maintained on ARVs for one year were recruited. Treatment failure was defined as a viral load of ≥1000 copies/mL. Sanger sequencing for genotyping and drug resistance mutation (DRM) detection was performed on patients failing treatment. RESULTS: 513 PLHIV were enrolled. The most common antiretroviral regimens were TDF+3TC + EFV (269) and AZT+3TC + EFV (155). 53 (10.3%) subjects failed treatment. Among these, 48 (90.6%) had DRMs, 84.9% were subtype CRF01_AE. Tenofovir-based regimens performed worse than zidovudine-based regimens (OR 3.28, 95% CI 1.58-7.52 p < 0.001). Higher rates of NRTI, NNRTI, K65R tenofovir resistance, and multi-class resistance were found compared to those reported in literature. CONCLUSIONS: HIV treatment failure at one year of treatment in the Philippines is 10.3%. We found unusually high tenofovir and multiclass resistance, and optimal ARV regimens may need to be reevaluated for CRF01_AE-predominant epidemics.

Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission.

Tailoring public health responses to growing HIV transmission clusters depends on accurately mapping the risk network through which it spreads and identifying acute infections that represent the leading edge of cluster growth. HIV transmission links, especially those involving persons with acute HIV infection (AHI), can be difficult to uncover, or confirm during partner services investigations. We integrated molecular, epidemiologic, serologic and behavioral data to infer and evaluate transmission linkages between participants of a prospective study of AHI conducted in North Carolina, New York City and San Francisco from 2011-2013. Among the 547 participants with newly diagnosed HIV with polymerase sequences, 465 sex partners were reported, of whom only 35 (7.5%) had HIV sequences. Among these 35 contacts, 23 (65.7%) links were genetically supported and 12 (34.3%) were not. Only five links were reported between participants with AHI but none were genetically supported. In contrast, phylodynamic inference identified 102 unreported transmission links, including 12 between persons with AHI. Importantly, all putative transmission links between persons with AHI were found among large clusters with more than five members. Taken together, the presence of putative links between acute participants who did not name each other as contacts that are found only among large clusters underscores the potential for unobserved or undiagnosed intermediaries. Phylodynamics identified many more links than partner services alone and, if routinely and rapidly integrated, can illuminate transmission patterns not readily captured by partner services investigations.

HIV transmission and source-sink dynamics in sub-Saharan Africa.

Multiple phylogenetic studies of HIV in sub-Saharan Africa have shown that mobility-driven transmission frequently occurs: many communities export and import strains. Mobility-driven transmission can result in source-sink dynamics: one community can sustain a micro-epidemic in another community in which transmission is too low to be self-sustaining. In epidemiology, the basic reproduction number (R0) is used to specify the sustainability threshold. R0 represents the average number of secondary infections generated by one infected individual in a community in which everyone is susceptible. If R0 is greater than 1, transmission is high enough to sustain an epidemic; if R0 is less than 1, it is not. Here, we discuss the conditions that are needed (in terms of R0) for source-sink transmission dynamics to occur in generalised HIV epidemics in sub-Saharan Africa, present an example of where these conditions could occur (ie, Namibia), and discuss the necessity of considering mobility-driven transmission when designing control strategies. Additionally, we discuss the need for a new generation of HIV transmission models that are more realistic than the current models. The new models should reflect not only geographical variation in epidemiology and demography, but also the spatial-temporal complexity of population-level movement patterns.

HIV Outbreak Control With Effective Access to Care and Harm Reduction in North Carolina, 2017-2018.

Objectives. To assess and control a potential outbreak of HIV among people who inject drugs in Western North Carolina.Methods. Disease intervention specialists offered testing for hepatitis B and hepatitis C, harm reduction materials, and linkage to care to 7 linked people recently diagnosed with HIV who also injected drugs. Contacts were offered the same services and HIV testing. HIV genotype analysis was used to characterize HIV spread. We assessed testing and care outcomes by using state surveillance information.Results. Disease intervention specialists contacted 6 of 7 linked group members and received information on 177 contacts; among 96 prioritized contacts, 42 of 96 (44%) were exposed to or diagnosed with hepatitis C, 4 of 96 (4%) had hepatitis B, and 14 of 96 (15%) had HIV (2 newly diagnosed during the investigation). HIV genotype analysis suggested recent transmission to linked group members and 1 contact. Eleven of 14 with HIV were virally suppressed following the outbreak response.Conclusions. North Carolina identified and rapidly responded to an HIV outbreak among people reporting injecting drugs. Effective HIV care, the availability of syringe exchange services, and the rapid response likely contributed to controlling this outbreak.

No evidence of ongoing HIV replication or compartmentalization in tissues during combination antiretroviral therapy: Implications for HIV eradication.

HIV persistence during combination antiretroviral therapy (cART) is the principal obstacle to cure. Mechanisms responsible for persistence remain uncertain; infections may be maintained by persistence and clonal expansion of infected cells or by ongoing replication in anatomic locations with poor antiretroviral penetration. These mechanisms require different strategies for eradication, and determining their contributions to HIV persistence is essential. We used phylogenetic approaches to investigate, at the DNA level, HIV populations in blood, lymphoid, and other infected tissues obtained at colonoscopy or autopsy in individuals who were on cART for 8 to 16 years. We found no evidence of ongoing replication or compartmentalization of HIV; we did detect clonal expansion of infected cells that were present before cART. Long-term persistence, and not ongoing replication, is primarily responsible for maintaining HIV. HIV-infected cells present when cART is initiated represent the only identifiable source of persistence and is the appropriate focus for eradication.

TreeCluster: Clustering biological sequences using phylogenetic trees.

Clustering homologous sequences based on their similarity is a problem that appears in many bioinformatics applications. The fact that sequences cluster is ultimately the result of their phylogenetic relationships. Despite this observation and the natural ways in which a tree can define clusters, most applications of sequence clustering do not use a phylogenetic tree and instead operate on pairwise sequence distances. Due to advances in large-scale phylogenetic inference, we argue that tree-based clustering is under-utilized. We define a family of optimization problems that, given an arbitrary tree, return the minimum number of clusters such that all clusters adhere to constraints on their heterogeneity. We study three specific constraints, limiting (1) the diameter of each cluster, (2) the sum of its branch lengths, or (3) chains of pairwise distances. These three problems can be solved in time that increases linearly with the size of the tree, and for two of the three criteria, the algorithms have been known in the theoretical computer scientist literature. We implement these algorithms in a tool called TreeCluster, which we test on three applications: OTU clustering for microbiome data, HIV transmission clustering, and divide-and-conquer multiple sequence alignment. We show that, by using tree-based distances, TreeCluster generates more internally consistent clusters than alternatives and improves the effectiveness of downstream applications. TreeCluster is available at https://github.com/niemasd/TreeCluster.

Envelope-Specific Recognition Patterns of HIV Vaccine-Induced IgG Antibodies Are Linked to Immunogen Structure and Sequence.

Background: A better understanding of the parameters influencing vaccine-induced IgG recognition of individual antigenic regions and their variants within the HIV Envelope protein (Env) can help to improve design of preventive HIV vaccines. Methods: Env-specific IgG responses were mapped in samples of the UKHVC003 Standard Group (UK003SG, n = 11 from UK) and TaMoVac01 (TMV01, n = 17 from Tanzania) HIV vaccine trials. Both trials consisted of three immunizations with DNA, followed by two boosts with recombinant Modified Vaccinia Virus Ankara (MVA), either mediating secretion of gp120 (UK003SG) or the presentation of cell membrane bound gp150 envelopes (TMV01) from infected cells, and an additional two boosts with 5 µg of CN54gp140 protein adjuvanted with glucopyranosyl lipid adjuvant (GLA). Env immunogen sequences in UK003SG were solely based on the clade C isolate CN54, whereas in TMV01 these were based on clades A, C, B, and CRF01AE. The peptide microarray included 8 globally representative Env sequences, CN54gp140 and the MVA-encoded Env immunogens from both trials, as well as additional peptide variants for hot spots of immune recognition. Results: After the second MVA boost, UK003SG vaccinees almost exclusively targeted linear, non-glycosylated antigenic regions located in the inter-gp120 interface. In contrast, TMV01 recipients most strongly targeted the V2 region and an immunodominant region in gp41. The V3 region was frequently targeted in both trials, with a higher recognition magnitude for diverse antigenic variants observed in the UK003SG (p < 0.0001). After boosting with CN54gp140/GLA, the overall response magnitude increased with a more comparable recognition pattern of antigenic regions and variants between the two trials. Recognition of most immunodominant regions within gp120 remained significantly stronger in UK003SG, whereas V2-region recognition was not boosted in either group. Conclusions: IgG recognition of linear antigenic Env regions differed between the two trials particularly after the second MVA boost. Structural features of the MVA-encoded immunogens, such as secreted, monomeric gp120 vs. membrane-anchored, functional gp150, and differences in prime-boost immunogen sequence variability most probably contributed to these differences. Prime-boosting with multivalent Env immunogens during TMV01 did not improve variant cross-recognition of immunodominant peptide variants in the V3 region.

Injection of cocaine is associated with a recent HIV outbreak in people who inject drugs in Luxembourg.

BACKGROUND: An outbreak of HIV infections among people who inject drugs (PWID) started in 2014 in Luxembourg. OBJECTIVES: We conducted phylogenetic and epidemiological analyses among the PWID infected with HIV in Luxembourg or attending the supervised drug consumption facility (SDCF) to understand the main causes of the outbreak. METHODS: Between January 2013 and December 2017, analysis of medical files were performed from all PWID infected with HIV at the National Service of Infectious Diseases (NSID) providing clinical care nationwide. PWID were interviewed at NSID and SDCF using a standardized questionnaire focused on drug consumption and risk behaviours. The national drug monitoring system RELIS was consulted to determine the frequency of cocaine/heroin use. Transmission clusters were analysed by phylogenetic analyses using approximate maximum-likelihood. Univariate and multivariate logistic regression analyses were performed on epidemiological data collected at NSID and SDCF to determine risk factors associated with cocaine use. RESULTS: From January 2013 to December 2017, 68 new diagnosis of HIV infection reported injecting drug use as the main risk of transmission at NSID. The proportion of female cases enrolled between 2013-2017 was higher than the proportion among cases enrolled prior to 2013. (33% vs 21%, p < 0.05). Fifty six viral sequences were obtained from the 68 PWID newly diagnosed for HIV. Two main transmission clusters were revealed: one HIV-1 subtype B cluster and one CRF14_BG cluster including 37 and 9 patients diagnosed since 2013, respectively. Interviews from 32/68 (47%) newly diagnosed PWID revealed that 12/32 (37.5%) were homeless and 27/32 (84.4%) injected cocaine. Increased cocaine injection was indeed reported by the RELIS participants from 53 to 63% in drug users with services contacts between 2012 and 2015, and from 5 to 22% in SDCF users between 2012 and 2016. Compared with PWID who injected only heroin (n = 63), PWID injecting cocaine and heroin (n = 107) were younger (mean of 38 vs 44 years, p≤0.001), reported more frequent piercing (≤0.001), shared and injected drugs more often (p≤0.01), and were more frequently HIV positive (p<0.05) at SDCF using univariate logistic regression analysis. Finally, in the multivariate analysis, use of heroin and cocaine was independently associated with younger age, piercing, sharing of drugs, and regular consumption (p<0.05). CONCLUSIONS: Injecting cocaine is a new trend of drug use in Luxembourg associated with HIV infection in this recent outbreak among PWID.

Production of IgG2 Antibodies to Pneumococcal Polysaccharides After Vaccination of Treated HIV Patients May Be Augmented by IL-7Rα Signaling in ICOS+ Circulating T Follicular-Helper Cells.

Greater understanding of factors influencing the maturation of antibody responses against pneumococcal polysaccharides (PcPs) may improve pneumococcal vaccination strategies. Although PcPs are type 2 T cell-independent antigens thought not to induce follicular immune responses, we have previously shown that IgG2 antibody responses against antigens in the 23-valent unconjugated PcP vaccine (PPV23) are associated with expansion of ICOS+ circulating T follicular helper (cTFH) cells in HIV seronegative subjects but not HIV patients. As IL-7Rα signaling in CD4+ T cells may affect TFH cell function and is adversely affected by HIV-1 infection, we have examined the relationship of IL-7Rα expression on ICOS+ cTFH cells with PcP-specific IgG2 antibody responses. PPV23 vaccination was undertaken in HIV patients receiving antiretroviral therapy (n = 25) and HIV seronegative subjects (n = 20). IL-7Rα expression on ICOS+ and ICOS- cTFH cells was assessed at day(D) 0, 7, and 28. Fold increase between D0 and D28 in serum IgG1 and IgG2 antibodies to PcP serotypes 4, 6B, 9V, and 14 and the frequency of IgG1+ and IgG2+ antibody secreting cells (ASCs) at D7 were also assessed. Decline in IL-7Rα expression on ICOS+ cTFH cells between D0 and D7 occurred in 75% of HIV seronegative subjects and 60% of HIV patients (Group A), with changes in IL-7Rα expression being more pronounced in HIV patients. Group A patients exhibited abnormally high IL-7Rα expression pre-vaccination, an association of serum IgG2, but not IgG1, antibody responses with a decline of IL-7Rα expression on ICOS+ cTFH cells between D0 and D7, and an association of higher IgG2+ ASCs with lower IL-7Rα expression on ICOS+ cTFH cells at D7. As decline of IL-7Rα expression on CD4+ T cells is an indicator of IL-7Rα signaling, our findings suggest that utilization of IL-7 by cTFH cells affects production of IgG2 antibodies to PPV23 antigens in some HIV patients.