Need for informed providers: exploring LA-PrEP access in focus groups with PrEP-indicated communities in Baltimore, Maryland.

BACKGROUND: The approval of long-acting pre-exposure prophylaxis PrEP (LA-PrEP) in the United States brings opportunities to overcome barriers of oral PrEP, particularly among sexual and gender minority communities who bear a higher HIV burden. Little is known about real-time decision-making among potential PrEP users of LA-PrEP post-licensure. METHODS: We held focus group discussions with people assigned male at birth who have sex with men in Baltimore, Maryland to explore decision-making, values, and priorities surrounding PrEP usage. A sexual and gender minority-affirming health center that provides PrEP services supported recruitment. Discussions included a pile-sorting activity and were audio-recorded. Recordings were transcribed and analyzed iteratively, combining an inductive and deductive approach. RESULTS: We held five focus groups from Jan-June 2023 with 23 participants (21 cisgender men who have sex with men, two transgender women who have sex with men; mean age 37). Among participants, 21 were on oral PrEP, one was on injectable PrEP, and one had never taken PrEP. Most had never heard about LA-PrEP. When making decisions about PrEP, participants particularly valued efficacy in preventing HIV, side effects, feeling a sense of security, and ease of use. Perceptions varied between whether oral or injectable PrEP was more convenient, but participants valued the new opportunity for a choice in modality. Factors influencing PrEP access included cost, individual awareness, provider awareness, and level of comfort in a healthcare environment. Participants emphasized how few providers are informed about PrEP, placing the burden of being informed about PrEP on them. Comfort and trust in a provider superseded proximity as considerations for if and where to access PrEP. CONCLUSIONS: There is still low awareness about LA-PrEP among sexual and gender minority communities; thus, healthcare providers have a critical role in influencing access to LA-PrEP. Despite this, providers are still vastly underinformed about PrEP and underprepared to support clients in contextualized ways. Clients are more likely to engage in care with affirming providers who offer non-judgmental conversations about sex and life experiences. Provider education in the United States is urgently needed to better support clients in choosing a PrEP modality that is right for them and supporting adherence for effective HIV prevention.

A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.

Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.

Injection network drivers of HIV prevention service utilization among people who inject drugs: results of a community-based sociometric network cohort in New Delhi, India.

INTRODUCTION: Injection drug networks may influence their network members' health-seeking behaviours. Using data from a sociometric injecting partner network of people who inject drugs (PWID) in New Delhi, India, we assessed the role of injecting partner (alter) behaviours on individual engagement in HIV prevention services. METHODS: We enumerated injecting partner linkages among 2512 PWID using coupon referrals and biometric data from November 2017 to March 2020. Participants completed interviewer-administered questionnaires and provided information on injection behaviours, injecting partners, HIV/hepatitis C (HCV) testing and service engagement. Multilevel multiple-membership models (MMMM) evaluated individual PWID HIV testing, medication for opioid use disorder (MOUD) and syringe service engagement as a function of alter attributes, accounting for membership across multiple ego-networks. Logistic regression models assessed parallel associations among socially proximal injecting peers, defined as PWID ≤3 path length from ego. RESULTS: Median age was 26 years; 99% were male. PWID had median 2 injecting partners and 8 socially proximal peers; 14% reported HIV testing, 33% accessed MOUD and 13% used syringe services 6 months prior. In MMMM analyses, PWID with ≥1 versus 0 injecting partners who received HIV testing were significantly more likely to report HIV testing (adjusted odds ratio [aOR]: 2.27, 95% confidence interval [CI]: 1.68-3.16), MOUD (aOR: 1.99, 95% CI: 1.60-2.53) and syringe service use (aOR: 1.66, 95% CI: 1.21-2.39). We observed similar findings for individual MOUD and syringe service use. Having ≥1 versus 0 HIV-positive partners was associated with decreased HIV testing and MOUD but increased syringe service use (aOR: 1.54, 95% CI: 1.09-2.17). PWID with ≥1 versus 0 socially proximal peers who used non-sterile injection equipment reported increased HIV testing (aOR: 1.39, 95% CI: 1.01-1.92), MOUD (aOR: 1.40, 95% CI: 1.10-1.77) and syringe service use (aOR: 1.82, 95% CI: 1.23-2.68). CONCLUSIONS: We found differential associative relationships between individual HIV prevention service engagement and the health or risk behaviours of direct and indirect alters. Characterizing network exposure beyond direct injecting partnerships provided important context on possible mechanisms of behavioural influence. Findings could be leveraged to design peer-based interventions that promote network diffusion of health-seeking behaviours.

Network centrality and HIV prevention service use among people who inject drugs: Findings from a sociometric network cohort in New Delhi, India.

BACKGROUND AND AIMS: Network centrality, an indicator of an individual's importance and potential to drive behavioral change, is rarely used to select peer educators. Individual-level predictors of network centrality might be useful to identify people who inject drugs (PWID) for potential roles as peer navigators or change agents in network-based interventions in settings where sociometric data are unavailable. We assessed the relationship between network centrality and HIV prevention service engagement to determine whether centrally-positioned PWID share measurable commonalities. DESIGN: Observational study and survey using baseline data from a sociometric network cohort of PWID, enumerated using network software and biometric data (2017-2020). Network ties corresponded to direct injection partnerships in the prior month. SETTING: New Delhi, India. PARTICIPANTS: A total of 2512 PWID who were ≥18 years, provided written informed consent, and reported illicit injection drug use within the 24 months before study enrollment. MEASUREMENTS: Interviewer-administered questionnaires measured demographics and substance use behaviors. Central versus peripheral network position was categorized using betweenness centrality 75th%ile . Logistic regression was used to estimate adjusted odds ratios (aOR) with 95% confidence intervals (95%CI) between network position and HIV testing, medication for opioid use disorder (MOUD), or syringe service use. Lasso models selected predictors of central network position among 20 covariates detailing demographic, biologic, and substance use information. Predictive accuracy was evaluated using model performance metrics. FINDINGS: Overall, median age was 26 years (interquartile range 22-34); 99% were male; 628 were classified as central. Compared with PWID at the periphery, central PWID were more likely to use MOUD (aOR: 1.59, 95%CI: 1.30-1.94) and syringe services (aOR: 2.91, 95%CI: 2.25, 3.76) in the prior six months. Findings for HIV testing were inconclusive (aOR: 1.30, 95%CI: 1.00-1.69). The lasso variable selector identified several predictors of network centrality: HIV and hepatitis C infection, number of PWID seen in the prior month, injecting heroin and buprenorphine (vs. heroin only) six months prior, sharing injection equipment six months prior, experiencing drug overdose in the past year, and moderate/severe depression (vs. none/mild). Average agreement between model-predicted vs. observed values was 0.75; area under the receiver operator curve was 0.69. CONCLUSIONS: In a socioeconomic network of people who inject drugs (PWID) in New Delhi, India, there are common characteristics among individuals based on their network position (central vs. peripheral) but individual-level predictors have only moderate predictive accuracy. Although central network members appear to be more likely to use HIV prevention services than peripheral network members, their potential as change agents may be limited by other factors that impede their ability to adopt or promote HIV prevention service use.

Incidence of HIV and hepatitis C virus among people who inject drugs, and associations with age and sex or gender: a global systematic review and meta-analysis.

BACKGROUND: Measuring the incidence of HIV and hepatitis C virus (HCV) infection among people who inject drugs (PWID) is key to track progress towards elimination. We aimed to summarise global data on HIV and primary HCV incidence among PWID and associations with age and sex or gender. METHODS: In this systematic review and meta-analysis, we updated an existing database of HIV and HCV incidence studies among PWID by searching MEDLINE, Embase, and PsycINFO, capturing studies published between Jan 1, 2000, and Dec 12, 2022, with no language or study design restrictions. We contacted authors of identified studies for unpublished or updated data. We included studies that estimated incidence by longitudinally re-testing people at risk of infection or by using assays for recent infection. We pooled incidence and relative risk (RR; young [generally defined as ≤25 years] vs older PWID; women vs men) estimates using random-effects meta-analysis and assessed risk of bias with a modified Newcastle-Ottawa scale. This study is registered with PROSPERO, CRD42020220884. FINDINGS: Our updated search identified 9493 publications, of which 211 were eligible for full-text review. An additional 377 full-text records from our existing database and five records identified through cross-referencing were assessed. Including 28 unpublished records, 125 records met the inclusion criteria. We identified 64 estimates of HIV incidence (30 from high-income countries [HICs] and 34 from low-income or middle-income countries [LMICs]) and 66 estimates of HCV incidence (52 from HICs and 14 from LMICs). 41 (64%) of 64 HIV and 42 (64%) of 66 HCV estimates were from single cities rather than being multi-city or nationwide. Estimates were measured over 1987-2021 for HIV and 1992-2021 for HCV. Pooled HIV incidence was 1·7 per 100 person-years (95% CI 1·3-2·3; I2=98·4%) and pooled HCV incidence was 12·1 per 100 person-years (10·0-14·6; I2=97·2%). Young PWID had a greater risk of HIV (RR 1·5, 95% CI 1·2-1·8; I2=66·9%) and HCV (1·5, 1·3-1·8; I2=70·6%) acquisition than older PWID. Women had a greater risk of HIV (RR 1·4, 95% CI 1·1-1·6; I2=55·3%) and HCV (1·2, 1·1-1·3; I2=43·3%) acquisition than men. For both HIV and HCV, the median risk-of-bias score was 6 (IQR 6-7), indicating moderate risk. INTERPRETATION: Although sparse, available HIV and HCV incidence estimates offer insights into global levels of HIV and HCV transmission among PWID. Intensified efforts are needed to keep track of the HIV and HCV epidemics among PWID and to expand access to age-appropriate and gender-appropriate prevention services that serve young PWID and women who inject drugs. FUNDING: Canadian Institutes of Health Research, Fonds de recherche du Québec-Santé, Canadian Network on Hepatitis C, UK National Institute for Health and Care Research, and WHO.

Antiretroviral Drug Resistance in HIV Sequences From People Who Inject Drugs and Men Who Have Sex With Men Across 21 Cities in India.

Background: Drug resistance testing is limited in public-sector human immunodeficiency virus (HIV) care in India, and there are few systematic samplings for prevalent drug resistance mutations (DRMs), particularly among men who have sex with men (MSM) and people who inject drugs (PWID). Methods: We conducted genotypic resistance testing on 915 HIV sequences sampled from viremic self-reported antiretroviral therapy (ART) experienced and naive PWID and MSM recruited from 21 cities across India in 2016-2017. We analyzed factors associated with resistance using logistic regression and evaluated evidence for transmitted resistance using phylogenetic analyses. Results: Of the 915 participants sequenced, median age was 31, 436 were MSM, and 191 were ART experienced. Overall, 62.8% of ART-experienced participants and 14.4% of ART-naive participants were found to have low-level resistance or higher to 1 or more classes of drugs. Prevalence of tenofovir disoproxil fumarate resistance was 25.7% in ART-experienced participants and 1.11% in ART-naive participants. The highest proportion of drug resistance was seen across nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors, and resistance was significantly more common among MSM participants than PWID. Phylogenetic analyses revealed that 54.6% of ART-naive participants with resistance who clustered had shared DRMs, suggesting transmitted resistance may have occurred. Conclusions: Patients experiencing virologic failure on first-line therapy switched blindly to tenofovir/lamivudine/dolutegravir may effectively be receiving dolutegravir monotherapy due to resistance to tenofovir and lamivudine. While dolutegravir is expected to have full activity in the majority of patients in India, follow-up is needed to understand how resistance may affect long-term outcomes.

Deep learning and social network analysis elucidate drivers of HIV transmission in a high-incidence cohort of people who inject drugs.

Globally, people who inject drugs (PWID) experience some of the fastest-growing HIV epidemics. Network-based approaches represent a powerful tool for understanding and combating these epidemics; however, detailed social network studies are limited and pose analytical challenges. We collected longitudinal social (injection partners) and spatial (injection venues) network information from 2512 PWID in New Delhi, India. We leveraged network analysis and graph neural networks (GNNs) to uncover factors associated with HIV transmission and identify optimal intervention delivery points. Longitudinal HIV incidence was 21.3 per 100 person-years. Overlapping community detection using GNNs revealed seven communities, with HIV incidence concentrated within one community. The injection venue most strongly associated with incidence was found to overlap six of the seven communities, suggesting that an intervention deployed at this one location could reach the majority of the sample. These findings highlight the utility of network analysis and deep learning in HIV program design.

Analysis of antibody binding specificities in twin and SNP-genotyped cohorts reveals that antiviral antibody epitope selection is a heritable trait.

Human immune responses to viral infections are highly variable, but the genetic factors that contribute to this variability are not well characterized. We used VirScan, a high-throughput epitope scanning technology, to analyze pan-viral antibody reactivity profiles of twins and SNP-genotyped individuals. Using these data, we determined the heritability and genomic loci associated with antibody epitope selection, response breadth, and control of Epstein-Barr virus (EBV) viral load. 107 EBV peptide reactivities were heritable and at least two Epstein-Barr nuclear antigen 2 (EBNA-2) reactivities were associated with variants in the MHC class II locus. We identified an EBV serosignature that predicted viral load in peripheral blood mononuclear cells and was associated with variants in the MHC class I locus. Our study illustrates the utility of epitope profiling to investigate the genetics of pathogen immunity, reports heritable features of the antibody response to viruses, and identifies specific HLA loci important for EBV epitope selection.

Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 Testing Cascade in the United States: Data From Serial Cross-sectional Assessments.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing is critical for monitoring case counts, early detection and containment of infection, clinical management, and surveillance of variants. However, community-based data on the access, uptake, and barriers to testing have been lacking. METHODS: We conducted serial cross-sectional online surveys covering demographics, coronavirus disease 2019 symptoms, and experiences around SARS-CoV-2 diagnostic testing to characterize the SARS-CoV-2 testing cascade and associated barriers across 10 US states (California, Florida, Illinois, Maryland, Massachusetts, Nebraska, North Dakota, South Dakota, Texas, and Wisconsin), from July 2020 to February 2021. RESULTS: In February 2021, across 10 US states, 895 respondents (11%) reported wanting a diagnostic test in the prior 2 weeks, 63% of whom were tested, with limited variability across states. Almost all (97%) who were tested received their results; 56% received their results within 2 days. In Maryland, Florida, and Illinois, where serial data were available at 4 time points, 56% were tested the same day they wanted or needed a test in February 2021, compared with 28% in July 2020, and 45% received results the same day, compared with 17% in July 2020. Wanting a test was significantly more common among younger, nonwhite respondents and participants with a history of symptoms or exposure. Logistical challenges, including not knowing where to go, were the most frequently cited barriers. CONCLUSIONS: There were significant improvements in access and turnaround times across US states, yet barriers to testing remained consistent across states, underscoring the importance of a continued focus on testing, even amidst mass vaccination campaigns.

Role of direct and indirect social and spatial ties in the diffusion of HIV and HCV among people who inject drugs: a cross-sectional community-based network analysis in New Delhi, India.

Background: People who inject drugs (PWID) account for some of the most explosive human immunodeficiency virus (HIV) and hepatitis C virus (HCV) epidemics globally. While individual drivers of infection are well understood, less is known about network factors, with minimal data beyond direct ties. Methods: 2512 PWID in New Delhi, India were recruited in 2017-19 using a sociometric network design. Sampling was initiated with 10 indexes who recruited named injection partners (people who they injected with in the prior month). Each recruit then recruited their named injection partners following the same process with cross-network linkages established by biometric data. Participants responded to a survey, including information on injection venues, and provided a blood sample. Factors associated with HIV/HCV infection were identified using logistic regression. Results: The median age was 26; 99% were male. Baseline HIV prevalence was 37.0% and 46.8% were actively infected with HCV (HCV RNA positive). The odds of prevalent HIV and active HCV infection decreased with each additional degree of separation from an infected alter (HIV AOR: 0.87; HCV AOR: 0.90) and increased among those who injected at a specific venue (HIV AOR: 1.50; HCV AOR: 1.69) independent of individual-level factors (p<0.001). In addition, sociometric factors, for example, network distance to an infected alter, were statistically significant predictors even when considering immediate egocentric ties. Conclusions: These data demonstrate an extremely high burden of HIV and HCV infection and a highly interconnected injection and spatial network structure. Incorporating network and spatial data into the design/implementation of interventions may help interrupt transmission while improving efficiency. Funding: National Institute on Drug Abuse and the Johns Hopkins University Center for AIDS Research.

Understanding the social and spatial relationships that connect people is a key element to stop the spread of infectious diseases. These networks are particularly relevant to combat epidemics among populations that are hard to reach with public health interventions. Network-based approaches, for example, can help to stop HIV or hepatitis C from spreading amongst populations that use injectable drugs. Yet how social and geographic connections such as acquaintances, injection partners, or preferred drug use places impact the risk of infection is still poorly mapped out. To address this question, Clipman et al. focused on people who inject drugs in New Delhi, India, a population heavily impacted by HIV and hepatitis C. Over 2500 people were recruited, each participant inviting their injection partners to also take part. The volunteers answered survey questions, including where they used drugs, and provided a blood sample to be tested. The results showed that, even after adjusting for individual risk factors, where people used drugs and with whom affected their risk of becoming infected with HIV and hepatitis C. In terms of social ties, the likelihood of HIV and hepatitis C infection decreased by about 13% for each person separating a given individual from an infected person. However, geographical networks also had a major impact. Injecting at a popular location respectively increased the odds of HIV and hepatitis C infection by 50% and 69%. In fact, even if the participant was not using drugs at these specific places, having an injection partner who did was enough to increase the risk for disease: for each person separating an individual from the location, the likelihood of being infected with HIV and hepatitis C decreased by respectively 14% and 10%. The results by Clipman et al. highlight how the relationships between physical spaces and social networks contribute to the spread of dangerous diseases amongst people who inject drugs. Ultimately, this knowledge may help to shape better public health interventions that would take into account the importance of geographical locations.

Holiday gatherings, mobility and SARS-CoV-2 transmission: results from 10 US states following Thanksgiving.

Public health officials discouraged travel and non-household gatherings for Thanksgiving, but data suggests that travel increased over the holidays. The objective of this analysis was to assess associations between holiday gatherings and SARS-CoV-2 positivity in the weeks following Thanksgiving. Using an online survey, we sampled 7770 individuals across 10 US states from December 4-18, 2020, about 8-22 days post-Thanksgiving. Participants were asked about Thanksgiving, COVID-19 symptoms, and SARS-CoV-2 testing and positivity in the prior 2 weeks. Logistic regression was used to identify factors associated with SARS-CoV-2 positivity and COVID-19 symptoms in the weeks following Thanksgiving. An activity score measured the total number of non-essential activities an individual participated in the prior 2 weeks. The probability of community transmission was estimated using Markov Chain Monte Carlo (MCMC) methods. While 47.2% had Thanksgiving at home with household members, 26.9% had guests and 25.9% traveled. There was a statistically significant interaction between how people spent Thanksgiving, the frequency of activities, and SARS-CoV-2 test positivity in the prior 2 weeks (p < 0.05). Those who had guests for Thanksgiving or traveled were only more likely to test positive for SARS-CoV-2 if they also had high activity (e.g., participated in > one non-essential activity/day in the prior 2 weeks). Had individuals limited the number and frequency of activities post-Thanksgiving, cases in surveyed individuals would be reduced by > 50%. As travel continues to increase and the more contagious Delta variant starts to dominate transmission, it is critical to promote how to gather in a "low-risk" manner (e.g., minimize other non-essential activities) to mitigate the need for nationwide shelter-at-home orders.

Spatiotemporal Phylodynamics of Hepatitis C Among People Who Inject Drugs in India.

BACKGROUND AND AIMS: Implementing effective interventions for HCV requires a detailed understanding of local transmission dynamics and geospatial spread. Little is known about HCV phylodynamics, particularly among high-burden populations, such as people who inject drugs (PWID). APPROACH AND RESULTS: We used 483 HCV sequences and detailed individual-level data from PWID across four Indian cities. Bayesian phylogeographic analyses were used to evaluate transmission hotspots and geospatial diffusion of the virus. Phylogenetic cluster analysis was performed to infer epidemiologic links and factors associated with clustering. A total of 492 HIV sequences were used to draw comparisons within the same population and, in the case of coinfections, evaluate molecular evidence for shared transmission pathways. Overall, 139/483 (28.8%) of HCV sequences clustered with a median cluster size of 3 individuals. Genetically linked participants with HCV were significantly younger and more likely to be infected with HCV subtype 3b as well as to live and inject close to one another. Phylogenetic evidence suggests likely ongoing HCV infection/reinfection with limited support for shared HIV/HCV transmission pathways. Phylogeographic analyses trace historic HCV spread back to Northeastern India and show diffusion patterns consistent with drug trafficking routes. CONCLUSIONS: This study characterizes HCV phylodynamics among PWID in a low and middle-income country setting. Heterogeneity and recent genetic linkage of HCV across geographically disparate Indian states suggest that targeted interventions could help prevent reimportation of virus through drug trafficking routes.

Rapid Real-time Tracking of Nonpharmaceutical Interventions and Their Association With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity: The Coronavirus Disease 2019 (COVID-19) Pandemic Pulse Study.

BACKGROUND: Current mitigation strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on the population-wide adoption of nonpharmaceutical interventions (NPIs). Monitoring the adoption of NPIs and their associations with SARS-CoV-2 infection history can provide key information for public health. METHODS: We sampled 1030 individuals in Maryland from 17-28 June 2020 to capture sociodemographically and geographically resolved information about NPI adoption and access to SARS-CoV-2 testing, and examine associations with self-reported SARS-CoV-2 positivity. RESULTS: Overall, 92% reported traveling for essential services and 66% visited friends/family. Use of public transport was reported by 18%. In total, 68% reported strict social distancing indoors and 53% reported strict masking indoors; indoor social distancing was significantly associated with age, and race/ethnicity and income were associated with masking. Overall, 55 participants (5.3%) self-reported ever testing positive for SARS-CoV-2, with strong dose-response relationships between several forms of movement frequency and SARS-CoV-2 positivity. In a multivariable analysis, a history of SARS-CoV-2 infection was negatively associated with strict social distancing (adjusted odds ratio [aOR] for outdoor social distancing, 0.10; 95% confidence interval, .03-.33). Only public transport use (aOR for >7 times vs never, 4.3) and visiting a place of worship (aOR for ≥3 times vs never, 16.0) remained significantly associated with SARS-CoV-2 infection after adjusting for strict social distancing and demographics. CONCLUSIONS: These results support public health messaging that strict social distancing during most activities can reduce SARS-CoV-2 transmission. Additional considerations are needed for indoor activities with large numbers of persons (places of worship and public transportation), where even NPIs may not be possible or sufficient.

The Immunoglobulin M-Shed Acute Phase Antigen (SAPA)-test for the Early Diagnosis of Congenital Chagas Disease in the Time of the Elimination Goal of Mother-to-Child Transmission.

BACKGROUND: Diagnosis of congenital Chagas disease (CChD) in most endemic areas is based on low-sensitive microscopy at birth and 9-month immunoglobulin G (IgG), which has poor adherence. We aim to evaluate the accuracy of the Immunoglobulin M (IgM)-Shed Acute Phase Antigen (SAPA) test in the diagnosis of CChD at birth. METHODS: Two cohort studies (training and validation cohorts) were conducted in 3 hospitals in the department of Santa Cruz, Bolivia. Pregnant women were screened for Chagas disease, and all infants born to seropositive mothers were followed for up to 9 months to diagnose CChD. A composite reference standard was used to determine congenital infection and was based on the parallel use of microscopy, quantitative polymerase chain reaction (qPCR), and IgM-trypomastigote excreted-secreted antigen (TESA) blot at birth and/or 1 month, and/or the detection of anti-Trypanosoma cruzi IgG at 6 or 9 months. The diagnostic accuracy of the IgM-SAPA test was calculated at birth against the composite reference standard. RESULTS: Adherence to the 6- or 9-month follow-up ranged from 25.3% to 59.7%. Most cases of CChD (training and validation cohort: 76.5% and 83.7%, respectively) were detected during the first month of life using the combination of microscopy, qPCR, and/or IgM-TESA blot. Results from the validation cohort showed that when only 1 infant sample obtained at birth was evaluated, the qPCR and the IgM-SAPA test have similar accuracy (sensitivity: range, 79.1%-97.1% and 76.7%-94.3%, respectively, and specificity: 99.5% and 92.6%, respectively). CONCLUSIONS: The IgM-SAPA test has the potential to be implemented as an early diagnostic tool in areas that currently rely only on microscopy.

Rapid real-time tracking of non-pharmaceutical interventions and their association with SARS-CoV-2 positivity: The COVID-19 Pandemic Pulse Study.

BACKGROUND: Current mitigation strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Collecting demographically and geographically resolved data on NPIs and their association with SARS-CoV-2 infection history can provide critical information related to reopening geographies. METHODS: We sampled 1,030 individuals in Maryland from June 17 - June 28, 2020 to capture socio-demographically and geographically resolved information about NPI adoption, access to SARS-CoV-2 testing, and examine associations with self-reported SARS-CoV-2 positivity. RESULTS: Median age of the sample was 43 years and 45% were men; Whites and Blacks/African Americans represented 60% and 23%, respectively. Overall, 96% of the sample reported traveling outside their home for non-employment related services: most commonly cited reasons were essential services (92%) and visiting friends/family (66%). Use of public transport was reported by 18% of respondents. 68% reported always social distancing indoors and 53% always wearing masks indoors; indoor social distancing was significantly less common among younger vs. older individuals, and race/ethnicity and income were significantly associated with mask use (p<0.05 for all). 55 participants (5.3%) self-reported ever testing positive for SARS-CoV-2 with strong dose-response relationships between movement frequency and SARS-CoV-2 positivity that were significantly attenuated by social distancing. In multivariable analysis, history of SARS-CoV-2 infection was negatively associated with the practice of social distancing (adjusted Odd Ratio [aOR]: 0.10; 95% Confidence Interval: 0.03 - 0.33); the only travel associated with higher likelihood of SARS-CoV-2 infection was use of public transport (aOR for ≥7 times vs. never: 4.29) and visiting a place of worship (aOR for ≥3 times vs. never: 16.0) after adjusting for social distancing. CONCLUSIONS: Using a rapid cost-efficient approach, we highlight the role of movement and social distancing on SARS-CoV-2 transmission risk. Continued monitoring of NPI uptake, access to testing, and the subsequent impact on SARS-CoV-2 transmission will be critical for pandemic control and decisions about reopening geographies.

Prevalence and Phylogenetic Characterization of Hepatitis C Virus Among Indian Men Who Have Sex With Men: Limited Evidence for Sexual Transmission.

BACKGROUND: Data from high-income countries suggest increasing hepatitis C virus (HCV) prevalence/incidence among human immunodeficiency virus (HIV)-infected men who have sex with men (MSM), but limited data derive from low-and-middle-income countries. METHODS: We recruited 4994 MSM from 5 states across India using respondent-driven sampling. Logistic regression incorporating respondent-driven sampling weights and machine learning feature selection were used to identify correlates of prevalent HCV, and Bayesian phylogenetic analysis was used to examine genetic clustering. RESULTS: The median age was 25 years, the HIV prevalence was 7.2%, and 49.3% of participants reported recent unprotected anal intercourse. The HCV prevalence was 1.3% (95% confidence interval, 1.0%-1.6%; site range, 0.2%-3.4%) and was 3.1% in HIV-positive versus 1.1% among HIV-negative men. HCV infection was significantly associated with injection drug use (odds ratio, 177.1; 95% confidence interval, 72.7-431.5) and HIV infection (4.34; 1.88-10.05). Machine learning did not uncover any additional epidemiologic signal. Phylogenetic analysis revealed 3 clusters suggestive of linked transmission; each contained ≥1 individual reporting injection drug use. CONCLUSIONS: We observed a low HCV prevalence in this large sample of MSM despite a high prevalence of known risk factors, reflecting either the need for a threshold of HCV for sexual transmission and/or variability in sexual practices across settings.

SARS-CoV-2 Testing in Florida, Illinois, and Maryland: Access and Barriers.

Objective: To characterize the SARS-CoV-2 testing cascade and associated barriers in three US states. Methods: We recruited participants from Florida, Illinois, and Maryland (~1000/state) for an online survey September 16 - October 15, 2020. The survey covered demographics, COVID-19 symptoms, and experiences around SARS-CoV-2 PCR testing in the prior 2 weeks. Logistic regression was used to analyze associations with outcomes of interest. Results: Overall, 316 (10%) of 3,058 respondents wanted/needed a test in the two weeks prior to the survey. Of these, 166 (53%) were able to get tested and 156 (94%) received results; 53% waited ≥ 8 days to get results from when they wanted/needed a test. There were no significant differences by state. Among those wanting/needing a test, getting tested was significantly less common among men (aOR: 0.46) and those reporting black race (aOR: 0.53) and more common in those reporting recent travel (aOR: 3.35). Conclusions: There is an urgent need for a national communication strategy on who should get tested and where one can get tested. Additionally, measures need to be taken to improve access and reduce turn-around-time.

Genetic association study of NLRP1, CARD, and CASP1 inflammasome genes with chronic Chagas cardiomyopathy among Trypanosoma cruzi seropositive patients in Bolivia.

About 20-30% of people infected with Chagas disease present with chronic Chagas cardiomyopathy (CCC), the most serious and frequent manifestation of the disease, while others remain asymptomatic and often do not experience Chagas-specific mortality. It is not currently well understood what causes these differential disease outcomes, but a genetic predisposition within the host could play an important role. This study examined variants in the NLRP1, CARD, and CASP1 inflammasome genes among 62 T. cruzi seropositive patients from Bolivia (38 cases with CCC and 24 asymptomatic controls) to uncover associations with CCC. All subjects underwent a complete medical examination including electrocardiogram (EKG) and echocardiogram. After genotype calling and quality control filtering with exclusion of 3 cases and 3 controls, association analysis was performed across 76 directly genotyped SNPs in NLRP1, CARD, and CASP1 genes, adjusting for age, sex, and population stratification. One SNP (rs11651270; Bonferroni-corrected p = 0.036) corresponding to a missense mutation in NLPR1 was found to be significant after adjustment for multiple testing, and a suggestive association was seen in CARD11 (rs6953573; Bonferroni-corrected p = 0.060). Although limited by sample size, the study results suggest variations in the inflammasome, particularly in NLRP1 and CARD11, may be associated with CCC.

Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers.

The adult Taenia solium, the pork tapeworm, usually lives as a single worm in the small intestine of humans, its only known definitive host. Mechanisms of genetic variation in T. solium are poorly understood. Using three microsatellite markers previously reported [1], this study explored the genetic variability of T. solium from cysts recovered from experimentally infected pigs. It then explored the genetic epidemiology and transmission in naturally infected pigs and adult tapeworms recovered from human carriers from an endemic rural community in Peru. In an initial study on experimental infection, two groups of three piglets were each infected with proglottids from one of two genetically different tapeworms for each of the microsatellites. After 7 weeks, pigs were slaughtered and necropsy performed. Thirty-six (92.3%) out of 39 cysts originated from one tapeworm, and 27 (100%) out of 27 cysts from the other had exactly the same genotype as the parental tapeworm. This suggests that the microsatellite markers may be a useful tool for studying the transmission of T. solium. In the second study, we analyzed the genetic variation of T. solium in cysts recovered from eight naturally infected pigs, and from adult tapeworms recovered from four human carriers; they showed genetic variability. Four pigs had cysts with only one genotype, and four pigs had cysts with two different genotypes, suggesting that multiple infections of genetically distinct parental tapeworms are possible. Six pigs harbored cysts with a genotype corresponding to one of the identified tapeworms from the human carriers. In the dendrogram, cysts appeared to cluster within the corresponding pigs as well as with the geographical origin, but this association was not statistically significant. We conclude that genotyping of microsatellite size polymorphisms is a potentially important tool to trace the spread of infection and pinpoint sources of infection as pigs spread cysts with a shared parental genotype.

Characterization of Pythium spp. Associated with Asymptomatic Soybean in Southeastern Pennsylvania.

Soybean production in Pennsylvania has increased substantially over the past 20 years and is a highly valued field crop, together with corn. Soilborne pathogens such as Pythium spp. can contribute to soybean stand establishment issues, particularly under the conservation tillage practices that are common in the state. In this study, we collected soil samples from eight asymptomatic soybean-corn rotation fields across six counties in southeastern Pennsylvania between May and June 2012. Pythium spp. were isolated via baiting, and tested for aggressiveness on both soybean and corn using laboratory assays. In addition to our culture-based survey, we also assessed the use of cytochrome oxidase subunit 1 pyrosequencing as a culture-independent method for measuring Pythium spp. diversity from environmental samples. Diversity estimates were consistent between the culture-based and pyrosequencing datasets; however, important methodological biases inherent to culture-independent methods may have led to some differences. Our results show that several Pythium spp. previously characterized as soybean or corn pathogens are present in southeastern Pennsylvania, including Pythium irregulare, P. sylvaticum, and P. ultimum var. sporangiiferum, with isolates showing aggressive phenotypes in lab assays.