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 We contacted authors of identified studies for unpublished or updated data.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 Including 28 unpublished records, 125 records met the inclusion criteria.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; I 2=98·4%) and pooled HCV incidence was 12·1 per 100 person-years (10·0-14·6; I 2=97·2%). Young PWID had a greater risk of HIV (RR 1·5, 95% CI 1·2-1·8; I 2=66·9%) and HCV (1·5, 1·3-1·8; I 2=70·6%) acquisition than older PWID. Women had a greater risk of HIV (RR 1·4, 95% CI 1·1-1·6; I 2=55·3%) and HCV (1·2, 1·1-1·3; I 2=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.</p

PHYLOGENETIC AND NETWORK APPROACHES TO UNDERSTANDING HIV AND HEPATITIS C TRANSMISSION DYNAMICS AMONG KEY POPULATIONS IN INDIA

Injection drug use is increasingly accounting for new HIV and hepatitis C virus (HCV) infections in low- and middle-income countries (LMICs); however, much of what is known about transmission among people who inject drugs (PWID) comes from high-income settings. Additionally, very little is known about real-world injection networks that include indirect ties, particularly from an LMIC. We used viral sequences, individual-level data, and comprehensive social and spatial network data to examine key questions related to HIV/HCV transmission among PWID in India. Our aims were to (1) evaluate methodologies for inferring molecular transmission clusters, (2) examine evidence for sexual transmission of HCV, (3) analyze HCV phylodynamics and factors associated with clustering, and (4) utilize sociometric network data to investigate the role space and network ties. In analyzing genetic and epidemiologic data from 4,994 men who have sex with men in India, we failed to find strong evidence of sexual HCV transmission, with infections appearing to be driven largely by injection drug use. We then used phylogeographic analyses to infer HCV transmission hotspots and geospatial diffusion of virus among PWID populations across four Indian cities. We supplemented these analyses with HIV sequences to draw comparisons within the same population, and in the case of co-infections, evaluate molecular evidence for shared transmission pathways. We found that genetically linked participants with HCV were significantly younger and more likely to live and inject close to one another. Phylogenetic evidence suggested recent and ongoing HCV infection/reinfection with limited support for shared HIV/HCV transmission pathways. Phylogeographic analyses traced HCV spread back to Northeastern India and showed diffusion patterns consistent with drug trafficking routes. Finally, we collected social and spatial network data from 2,512 PWID in New Delhi to examine the role of network-level factors on HIV/HCV transmission. We found that the odds of prevalent HIV and HCV decreased with each additional degree of separation from an infected person and increased among those who injected at a specific location, factors that were independent of individual-level predictors. Together, these findings paint a more complete picture of HIV/HCV transmission among PWID in India and may better inform public health programs

COI alignment MEGA format

COI alignment formatted for analysis in MEGA. Missing data coded as '?

Data from: Characterization of Pythium spp. associated with asymptomatic soybeans in southeastern Pennsylvania

Soybean production in Pennsylvania has increased substantially over the past twenty 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 species were isolated via baiting, and tested for aggressiveness on both soybean and corn using laboratory pathogenicity assays. In addition to our culture-based survey, we also assessed the use of cytochrome oxidase subunit 1 (COI) pyrosequencing as a culture-independent method for measuring Pythium species 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 species previously characterized as soybean and/or corn pathogens are present in southeastern Pennsylvania, including P. irregulare, P. sylvaticum, and P. ultimum var. sporangiiferum, with isolates showing aggressive phenotypes in lab assays

COI Neighbor-joining Tree with Reference Sequences

PDF of neighbor-joining tree from alignment with Pythium and other oomycete reference sequences included

COI alignment

COI alignment file in Nexus format. NCBI block included after data block, which gives organism and isolation information for each sequence (as submitted to GenBank)

COI alignment with Reference Sequences in MEGA format

Pythium (and select other oomycetes) included with COI sequences generated here. Sequences were obtained from NCBI

Suggestive association results of SNPs in NLRP, CARD, CASP1 genes under an additive model unconditional logistic regression adjusted for population substructure, age, and sex.

<p>P-values reflect Bonferroni adjustment for multiple testing.</p

Principle component analysis of bolivian chagas samples along with HapMap 3 populations.

<p>Each point represents one individual with different colors representing each population. Bolivian Chagas samples are coded in magenta. The HapMap populations include: ASW: African ancestry in Southwest USA; CEU: Utah residents with Northern and Western European ancestry from the CEPH collection; CHB: Han Chinese in Beijing, China; CHD: Chinese in Metropolitan Denver, Colorado; GIH: Gujarati Indians in Houston, Texas; JPT: Japanese in Tokyo, Japan; LWK: Luhya in Webuye, Kenya; MEX: Mexican ancestry in Los Angeles, California; MKK: Maasai in Kinyawa, Kenya; TSI: Tuscans in Italy; YRI: Yoruba in Ibadan, Nigeria.</p