Molecular Epidemiology Of HIV-1 Research Articles

Characterization of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China

BackgroundSichuan province is one of the highest AIDS epidemic provinces in China, with a large number of floating population. The annual number of cases of HIV/AIDS reported in Sichuan has been the highest province in China for several successive years. There is a lack of widespread and representative data on the distribution of HIV genotypes in Sichuan. We aim to investigate the characteristics of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China.MethodArchived plasma samples (n = 1524) from HIV-1 newly-diagnosed individuals in April 2019 were selected by cross-sectional investigation from all 21 cities in Sichuan province. Phylogenetic relationship, transmission cluster, and genotypic drug resistance analyses were performed using HIV-1 polymerase (pol) gene sequences. We also analysed the association of demographic and virological factors with transmitted drug-resistance (TDR) and transmission clusters.ResultsPartial pol gene sequences were obtained from 1297 cases. HIV-1 epidemic strains in Sichuan province: the majority of genotypes were circulating recombinant form (CRF) 07_BC (675, 52.04%), CRF01_AE (343, 26.45%), CRF08_BC (115, 8.87%), CRF85_BC (67, 5.17%), subtype B (33, 2.54%), the other genotypes only accounted for 4.93%, and unique recombinant forms (URFs) (23, 1.77%) were observed in the study, and the difference of age, ethnicity, education, occupation, region and transmission pathway of different genotypes were statistically significant. According to WHO HIVDR surveillance threshold, the level of TDR has reached a medium level, with 72 of 1297 (5.55%) cases carrying drug-resistance mutation sites, TDR mutation frequency to nonnucleoside reverse transcriptase inhibitors (NNRTIs, 3.85%) was much higher than nucleoside reverse transcriptase inhibitors (NRTIs, 0.31%) and protease inhibitors (PIs, 1.70%), and CRF08_BC was a risk factor for TDR (odds ratio, 8.32; 95% CI 4.38–15.80 for CRF07_BC, P < 0.05). The most common drug resistance HIV-1 mutation pattern for NNRTI was V106 (1.31%, 17/1297) and E138 (1.16%, 15/1297), and for PI was M46 (0.69%, 9/1297). A total of 205 (15.8%) pol sequences were involved in the genetic transmission network clusters, CRF01_AE (odds ratio, 2.369; 95% CI 1.659–3.382; P < 0.05), subtype B (odds ratio, 13.723; 95% CI 6.338–29.71; P < 0.05), drug resistance (odds ratio, 0.306; 95% CI 0.106–0.881; P < 0.05) and different levels of education (P < 0.05) were significantly associated to be in clusters.ConclusionThe distribution of HIV-1 genotypes in Sichuan is more diverse and complex, and the Men who have sex with men (MSM) is underrated, arguing for behavior scaling up intervention in this specific population besides the elderly people with heterosexual transmission risk groups. The risk of TDR mutation frequency increased in newly diagnosed patients highlights the significance of genotypic drug resistance monitoring and molecular surveillance of pretreatment HIV-1 drug resistance. The regimen composed of TDF, 3TC and EFV was still currently the preferred solution used free first-line therapy.

Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016.

We aimed to elucidate the characteristics of HIV molecular epidemiology and identify transmission hubs in eastern China using genetic transmission network and lineage analyses. HIV-TRACE was used to infer putative relationships. Across the range of epidemiologically-plausible genetic distance (GD) thresholds (0.1–2.0%), a sensitivity analysis was performed to determine the optimal threshold, generating the maximum number of transmission clusters and providing reliable resolution without merging different small clusters into a single large cluster. Characteristics of genetically linked individuals were analyzed using logistic regression. Assortativity (shared characteristics) analysis was performed to infer shared attributes between putative partners. 1,993 persons living with HIV-1 were enrolled. The determined GD thresholds within subtypes CRF07_BC, CRF01_AE, and B were 0.5%, 1.2%, and 1.7%, respectively, and 826 of 1,993 (41.4%) sequences were linked with at least one other sequence, forming 188 transmission clusters of 2–80 sequences. Clustering rates for the main subtypes CRF01_AE, CRF07_BC, and B were 50.9% (523/1027), 34.2% (256/749), and 32.1% (25/78), respectively. Median cluster sizes of these subtypes were 2 (2–52, n = 523), 2 (2–80, n = 256), and 3 (2–6, n = 25), respectively. Subtypes in individuals diagnosed and residing in Hangzhou city (OR = 1.423, 95% CI: 1.168–1.734) and men who have sex with men (MSM) were more likely to cluster. Assortativity analysis revealed individuals were more likely to be genetically linked to individuals from the same age group (AIage = 0.090, P<0.001) and the same area of residency in Zhejiang (AIcity = 0.078, P<0.001). Additionally, students living with HIV were more likely to be linked with students than show a random distribution (AI student = 0.740, P<0.01). These results highlight the importance of Hangzhou City in the regional epidemic and show that MSM comprise the population rapidly transmitting HIV in Zhejiang Province. We also provide a molecular epidemiology framework for improving our understanding of HIV transmission dynamics in eastern China.

Molecular epidemiology of HIV-1 in Oryol Oblast, Russia.

The HIV/AIDS epidemic in Russia is growing, with approximately 100,000 people infected annually. Molecular epidemiology can provide insight into the structure and dynamics of the epidemic. However, its applicability in Russia is limited by the weakness of genetic surveillance, as viral genetic data are only available for <1 per cent of cases. Here, we provide a detailed description of the HIV-1 epidemic for one geographic region of Russia, Oryol Oblast, by collecting and sequencing viral samples from about a third of its known HIV-positive population (768 out of 2,157 patients). We identify multiple introductions of HIV-1 into Oryol Oblast, resulting in eighty-two transmission lineages that together comprise 66 per cent of the samples. Most introductions are of subtype A (315/332), the predominant HIV-1 subtype in Russia, followed by CRF63 and subtype B. Bayesian analysis estimates the effective reproduction number Re for subtype A at 2.8 [1.7–4.4], in line with a growing epidemic. The frequency of CRF63 has been growing more rapidly, with the median Re of 11.8 [4.6–28.7], in agreement with recent reports of this variant rising in frequency in some regions of Russia. In contrast to the patterns described previously in European and North American countries, we see no overrepresentation of males in transmission lineages; meanwhile, injecting drug users are overrepresented in transmission lineages. This likely reflects the structure of the HIV-1 epidemic in Russia dominated by heterosexual and, to a smaller extent, people who inject drugs transmission. Samples attributed to men who have sex with men (MSM) transmission are associated with subtype B and are less prevalent than expected from the male-to-female ratio for this subtype, suggesting underreporting of the MSM transmission route. Together, our results provide a high-resolution description of the HIV-1 epidemic in Oryol Oblast, Russia, characterized by frequent interregional transmission, rapid growth of the epidemic, and rapid displacement of subtype A with the recombinant CRF63 variant.

CRF07_BC is associated with slow HIV disease progression in Chinese patients

HIV subtypes convey important epidemiological information and possibly influence the rate of disease progression. In this study, HIV disease progression in patients infected with CRF01_AE, CRF07_BC, and subtype B was compared in the largest HIV molecular epidemiology study ever done in China. A national data set of HIV pol sequences was assembled by pooling sequences from public databases and the Beijing HIV laboratory network. Logistic regression was used to assess factors associated with the risk of AIDS at diagnosis ([AIDSAD], defined as a CD4 count < 200 cells/µL) in patients with HIV subtype B, CRF01_AE, and CRF07_BC. Of the 20,663 sequences, 9,156 (44.3%) were CRF01_AE. CRF07_BC was responsible for 28.3% of infections, followed by B (13.9%). In multivariable analysis, the risk of AIDSAD differed significantly according to HIV subtype (OR for CRF07_BC vs. B: 0.46, 95% CI 0.39─0.53), age (OR for ≥ 65 years vs. < 18 years: 4.3 95% CI 1.81─11.8), and transmission risk groups (OR for men who have sex with men vs. heterosexuals: 0.67 95% CI 0.6─0.75). These findings suggest that HIV diversity in China is constantly evolving and gaining in complexity. CRF07_BC is less pathogenic than subtype B, while CRF01_AE is as pathogenic as B.

Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.

HIV molecular epidemiology estimates the transmission patterns from clustering genetically similar viruses. The process involves connecting genetically similar genotyped viral sequences in the network implying epidemiological transmissions. This technique relies on genotype data which is collected only from HIV diagnosed and in-care populations and leaves many persons with HIV (PWH) who have no access to consistent care out of the tracking process. We use machine learning algorithms to learn the non-linear correlation patterns between patient metadata and transmissions between HIV-positive cases. This enables us to expand the transmission network reconstruction beyond the molecular network. We employed multiple commonly used supervised classification algorithms to analyze the San Diego Primary Infection Resource Consortium (PIRC) cohort dataset, consisting of genotypes and nearly 80 additional non-genetic features. First, we trained classification models to determine genetically unrelated individuals from related ones. Our results show that random forest and decision tree achieved over 80% in accuracy, precision, recall, and F1-score by only using a subset of meta-features including age, birth sex, sexual orientation, race, transmission category, estimated date of infection, and first viral load date besides genetic data. Additionally, both algorithms achieved approximately 80% sensitivity and specificity. The Area Under Curve (AUC) is reported 97% and 94% for random forest and decision tree classifiers respectively. Next, we extended the models to identify clusters of similar viral sequences. Support vector machine demonstrated one order of magnitude improvement in accuracy of assigning the sequences to the correct cluster compared to dummy uniform random classifier. These results confirm that metadata carries important information about the dynamics of HIV transmission as embedded in transmission clusters. Hence, novel computational approaches are needed to apply the non-trivial knowledge collected from inter-individual genetic information to metadata from PWH in order to expand the estimated transmissions. We note that feature extraction alone will not be effective in identifying patterns of transmission and will result in random clustering of the data, but its utilization in conjunction with genetic data and the right algorithm can contribute to the expansion of the reconstructed network beyond individuals with genetic data.

Identification, Genetic Characterization and Validation of Highly Diverse HIV-1 Viruses for Reference Panel Development.

The continued diversification of HIV poses potentially significant challenges to HIV diagnostics and therapeutics. The dynamic evolution of emerging variants is highlighted in countries such as Cameroon in West Central Africa, where all known subtypes and circulating recombinant forms (CRFs) have been shown to be prevalent. We obtained several hundred HIV-positive plasma and viruses from this region for characterization and identification of highly divergent HIV strains. A total of 163 viral strains were cultured to high titers and high volumes using donor peripheral blood mononuclear cells (PBMCs). Initially, 101 viruses representing 59 strains were well characterized and categorized. Results showed that the viral load (VL) range was 0.36–398.9 × 107 copies/mL, p24 values was 0.2–1134 ng/mL. Phylogenetic analysis of thirty-six near full-length HIV-1 genomic sequences demonstrated that most recombinants were highly diverse CRF02 containing unique recombinant forms (URFs). There were seven viral isolates identified as pure subtype/sub-subtypes (F2, A1, G, and D), six as CRFs (CRF06, CRF18, and CRF22), and ten as URFs. These extensively characterized reagents reflect the current dynamic and complex HIV epidemic in Cameroon and provide valuable insights into the potential phylogenetic evolutionary trend of global HIV molecular epidemiology in the future. These materials may be useful for development of HIV validation and reference panels to evaluate the performance of serologic antigen and nucleic acid assays for their ability to detect and quantitate highly divergent HIV strains.

Longitudinal typing of molecular HIV clusters in a statewide epidemic.

HIV molecular epidemiology is increasingly integrated into public health prevention. We conducted cluster typing to enhance characterization of a densely sampled statewide epidemic towards informing public health. We identified HIV clusters, categorized them into types, and evaluated their dynamics between 2004 and 2019 in Rhode Island. We grouped sequences by diagnosis year, assessed cluster changes between paired phylogenies, t0 and t1, representing adjacent years and categorized clusters as stable (cluster in t0 phylogeny = cluster in t1 phylogeny) or unstable (cluster in t0 ≠ cluster in t1). Unstable clusters were further categorized as emerging (t1 phylogeny only) or growing (larger in t1 phylogeny). We determined proportions of each cluster type, of individuals in each cluster type, and of newly diagnosed individuals in each cluster type, and assessed trends over time. A total of 1727 individuals with available HIV-1 subtype B pol sequences were diagnosed in Rhode Island by 2019. Over time, stable clusters and individuals in them dominated the epidemic, increasing over time, with reciprocally decreasing unstable clusters and individuals in them. Conversely, proportions of newly diagnosed individuals in unstable clusters significantly increased. Within unstable clusters, proportions of emerging clusters and of individuals in them declined; whereas proportions of newly diagnosed individuals in growing clusters significantly increased over time. Distinct molecular cluster types were identified in the Rhode Island epidemic. Cluster dynamics demonstrated increasing stable and decreasing unstable clusters driven by growing, rather than emerging clusters, suggesting consistent in-state transmission networks. Cluster typing could inform public health beyond conventional approaches and direct interventions.

The Epidemiological Impact of STIs among General and Vulnerable Populations of the Amazon Region of Brazil: 30 years of Surveillance

Sexually transmitted infections (STIs) represent a worldwide public health problem and, although many of them are curable, they continue to be neglected, especially in areas with a low human development index, such as in the northern region of Brazil. This review describes the results of 30 years of studies at the Virus Laboratory at the Federal University of Pará, including the prevalence and molecular epidemiology of HIV-1, HTLV-1/2, HPV, HBV, Treponema pallidum and Chlamydia trachomatis among urban and non-urban populations, and also in vulnerable groups in the Brazilian Amazon. Control strategies and challenges in preventing STIs are discussed considering this immense geographic region, where essential health services are unable to reach the entire population, especially the most vulnerable, such as female sex workers, people who use illicit drugs, remnants of quilombolos and indigenous communities.

Using molecular transmission networks to understand the epidemic characteristics of HIV-1 CRF08_BC across China

ABSTRACT HIV-1 CRF08_BC has become a major epidemic in heterosexuals and intravenous drug users (IDUs) in southern China. In order to evaluate the trends of its epidemic and facilitate targeted HIV prevention, we constructed the genetic transmission networks based on its pol sequences, derived from the National HIV Molecular Epidemiology Survey. Through retrospective network analysis, to study the epidemiological and demographic correlations with the transmission network. Of the 1,829 study subjects, 639 (34.9%) were clustered in 151 transmission networks. Factors associated with increased clustering include IDUs, heterosexual men, young adults and people with lower education (P < 0.05 for all). The IDUs, MSM, young adult and person with low education had more potential transmission links as well (P < 0.05 for all). The most crossover links were found between heterosexual women and IDUs, with 30.9% heterosexual women linked to IDUs. The crossover links heterosexual women were mainly those with middle age and single (P < 0.001). This study indicated that the HIV-1 CRF08_BC epidemic was still on going in China with more than one third of the infected people clustered in the transmission networks. Meanwhile, the study could help identify the active CRF08_BC spreader in the local community and greatly facilitate précising AIDS prevention with targeted intervention.

Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015.

The global diversity of HIV forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. We sought to determine country level HIV-1 diversity globally between 1990 and 2015. We assembled a global HIV-1 molecular epidemiology database through a systematic literature search and a global survey. We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published from 1 January 1990 to 31 December 2015. We collected additional unpublished data through a global survey of experts. Prevalence studies with original HIV-1 subtyping data collected between 1990 and 2015 were included. This resulted in a database with 383,519 subtyped HIV-1 samples from 116 countries over four time periods (1990 to 1999, 2000 to 2004, 2005 to 2009, and 2010 to 2015). We analyzed country-specific numbers of distinct HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each time period. We also analyzed country-specific proportions of infections due to HIV-1 recombinants, CRFs, and URFs and calculated the Shannon diversity index for each country. Finally, we analyzed global temporal trends in each of these measures of HIV-1 diversity. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries such as Chad, Democratic Republic of the Congo, Angola, and Republic of the Congo have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe (Spain and France) and North America (United States) (up to 39 distinct HIV-1 variants in Spain). The proportion of HIV-1 infections due to recombinants was highest in Southeast Asia (>95% of infections in Viet Nam, Cambodia, and Thailand), China, and West and Central Africa, mainly due to high proportions of CRF01_AE and CRF02_AG. Other CRFs played major roles (>75% of HIV-1 infections) in Estonia (CRF06_cpx), Iran (CRF35_AD), and Algeria (CRF06_cpx). The highest proportions of URFs (>30%) were found in Myanmar, Republic of the Congo, and Argentina. Global temporal analysis showed consistent increases over time in country level numbers of distinct HIV-1 variants and proportions of CRFs and URFs, leading to increases in country level HIV-1 diversity. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to prevention and treatment efforts. HIV-1 molecular epidemiological surveillance needs to be continued and improved.IMPORTANCE This is the first study to analyze global country level HIV-1 diversity from 1990 to 2015. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China, and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo, and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to HIV vaccine development and diagnostic, drug resistance, and viral load assays.

Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo

HIV-1 diversity may impact monitoring and vaccine development. We describe the most recent data of HIV-1 variants and their temporal trends in the Democratic Republic of Congo (DRC) from 1976 to 2018 and in Kinshasa from 1983–2018. HIV-1 pol sequencing from dried blood collected in Kinshasa during 2016–2018 was done in 340 HIV-infected children/adolescents/adults to identify HIV-1 variants by phylogenetic reconstructions. Recombination events and transmission clusters were also analyzed. Variant distribution and genetic diversity were compared to historical available pol sequences from the DRC in Los Alamos Database (LANL). We characterized 165 HIV-1 pol variants circulating in Kinshasa (2016–2018) and compared them with 2641 LANL sequences from the DRC (1976–2012) and Kinshasa (1983–2008). During 2016–2018 the main subtypes were A (26.7%), G (9.7%) and C (7.3%). Recombinants accounted for a third of infections (12.7%/23.6% Circulant/Unique Recombinant Forms). We identified the first CRF47_BF reported in Africa and four transmission clusters. A significant increase of subtype A and sub-subtype F1 and a significant reduction of sub-subtype A1 and subtype D were observed in Kinshasa during 2016–2018 compared to variants circulating in the city from 1983 to 2008. We provide unique and updated information related to HIV-1 variants currently circulating in Kinshasa, reporting the temporal trends of subtypes/CRF/URF during 43 years in the DRC, and providing the most extensive data on children/adolescents.

Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Global HIV-1 genetic diversity and evolution form a major challenge to treatment and prevention efforts. An increasing number of distinct HIV-1 recombinants have been identified worldwide, but their contribution to the global epidemic is unknown. We aimed to estimate the global and regional distribution of HIV-1 recombinant forms during 1990-2015. We assembled a global HIV-1 molecular epidemiology database through a systematic literature review and a global survey. We searched the PubMed, Embase (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) databases for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. Unpublished original HIV-1 subtyping data were collected through a survey among experts in the field who were members of the WHO-UNAIDS Network for HIV Isolation and Characterisation. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. Countries were grouped into 14 regions and analyses were done for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV in each country to generate regional and global estimates of numbers and proportions of HIV-1 recombinants in each time period. The systematic review is registered with PROSPERO, CRD42017067164. Our global data collection yielded an HIV-1 molecular epidemiology database of 383 519 samples from 116 countries in 1990-2015. We found that the proportion of recombinants increased over time, both globally and in most regions, reaching 22·8% (7 978 517 of 34 921 639) of global HIV-1 infections in 2010-15. Both the proportion and the number of distinct CRFs detected increased over time to 16·7% and 57 CRFs in 2010-15. The global and regional distribution of HIV-1 recombinants was diverse and evolved over time, and we found large regional variation in the numbers (0-44 CRFs), types (58 distinct CRFs), and proportions (0-80·5%) of HIV-1 recombinants. Globally, CRF02_AG was the most prevalent recombinant, accounting for 33·9% (2 701 364 of 7 978 517) of all recombinant infections in 2010-15. URFs accounted for 26·7% (2 131 450 of 7 978 517), CRF01_AE for 23·0% (1 838 433), and other CRFs for 16·4% (1 307 270) of all recombinant infections in 2010-15. Although other CRFs accounted for small proportions of infections globally (<1% each), they were prominent in regional epidemics, including in east and southeast Asia, west and central Africa, Middle East and north Africa, and eastern Europe and central Asia. In addition, in 2010-15, central Africa (21·3% [243 041 of 1 143 531]), west Africa (15·5% [838 476 of 5 419 010]), east Africa (12·6% [591 140 of 4 704 986]), and Latin America (9·6% [153 069 of 1 586 605]) had high proportions of URFs. HIV-1 recombinants are increasingly prominent in global and regional HIV epidemics, which has important implications for the development of an HIV vaccine and the design of diagnostic, resistance, and viral load assays. Continued and improved surveillance of the global molecular epidemiology of HIV is crucial. None.

The origin and spread of CRF85_BC, driven by heterosexual transmission among older people in Sichuan, China

BackgroundCRF_BC recombinants, including CRF07_BC and CRF08_BC, were considered the predominant subtypes in China. Since the discovery of HIV-1 circulating recombinant form CRF 85_BC in Southwest China in 2016, this BC recombinant forms had been reported in different regions of China. However, the history and magnitude of CRF85_BC transmission were still to be investigated.MethodWe conducted the most recent molecular epidemiology of HIV-1 among newly reported HIV-1 infected patients in Sichuan in 2019 by sequencing and phylogenetic analysis of 1291 pol sequences. Then, we used maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of pol sequences to reconstruct the phylogeographic and demographic dynamics of the CRF85_BC.ResultsHIV-1 CRF85_BC (68/1291, 5.27%) became the fourth most prevalent strain revealing a significant increase in local population. CRF85_BC were only found in heterosexually infected individuals and the majority of CRF85_BC (95.45%) were circulating among the people living with HIV aged 50 years and over (PLHIV50+), suggesting a unique prevalent pattern. The founder lineages of CRF85_BC were likely to have first emerged in Yunnan, a province of Southwest China bordering Sichuan, in the early 2000s. It then spread exponentially to various places (including Guangxi, Sichuan, et al) and became endemic around 2008.6 (2006.7–2010.2) in Sichuan.ConclusionTaken together, our findings on HIV-1 subtype CRF85_BC infections provided new insights into the spread of this virus and extended the understanding of the HIV epidemic in China.

Molecular Epidemiology of HIV-1 in Jiangsu Province, Southeast China: Genotypes and HIV-1 Transmission Networks Among Newly Diagnosed Men Having Sex with Men in 2017.

Investigation of disease and intervention in populations of men having sex with men (MSM) has garnered attention globally, a primary reason being the rapid increase in the prevalence of human immunodeficiency virus (HIV)-1 among MSM. The purpose of this study was to understand the current HIV-1 molecular characteristics and characterize HIV-1 transmission networks in the MSM population. Nine hundred and fourteen newly diagnosed HIV-positive MSM were included in this study. The HIV-1 pol gene region was amplified and sequenced. A maximum likelihood phylogenetic tree was constructed, and transmission clusters were identified using 1.5% distance and 0.9 bootstrap values. In total, 767 sequences were successfully obtained, with CRF01_AE being the major genotype (43.3%, 332/767), followed by CRF07_BC (31.3%, 240/767), CRF67_01B (7.2%, 55/767), and URF (6.4%, 49/767). The transmitted HIV drug resistance rate was 4.0% (31/767), and the most common mutations were E138G (n = 4) and G190A (n = 4). A total of 182 (23.7%) sequences were included in the HIV-1 transmission networks, forming 79 clusters. Four clusters were identified as fast-growing, and the proportion of young MSM was higher than that of non-MSM (51.6% vs. 31.8%). The genetic diversity of HIV-1 in Jiangsu was complex, and cross-region transmission might exist for CRF67_01B. Transmission among young MSM within networks was greater than the other age groups; thus, they could be essential in the control of the HIV epidemic in Jiangsu. This study was approved by the ethical review board of the National Center for AIDS/STD Control and Prevention (Project No. X140617334).

Identification of a Novel HIV-1 Unique CRF01_AE/C Recombinant in Yan'an City, Shaanxi Province

A wide variety of HIV-1 recombinants are constantly discovered in China. Comprehensively monitoring the genetic diversity of HIV-1 is very essential for understanding the molecular epidemiology and controlling the spread of the HIV-1 epidemic. In this study, we presented a novel HIV-1 unique CRF01_AE/C recombinant (19YA001) isolated from a female patient infected HIV-1 through heterosexual transmission in Yan'an city, Shaanxi province. The near full-length genome analyses showed 19YA001 was divided into two CRF01_AE and one C segments by two breakpoints observed in the vif/vpr region. To date, this is the first report revealing the characteristic of HIV-1 subtype in Yan'an city. And this unique recombinant strain might imply that the genetic diversity of HIV-1 in Yan'an city is complex. However, the sample size is too small. Further larger studies of HIV-1 molecular epidemiology are urgently needed to provide a better understanding of HIV-1 diversity and transmission in this region.

Pre-treatment drug resistance and HIV-1 genetic diversity in the rural and urban settings of Northwest-Cameroon.

With the scale-up of antiretroviral therapy (ART), pre-treatment drug resistance (PDR) appears ≥10% amongst ART-initiators in many developing countries, including Cameroon. Northwest region-Cameroon having the second epidemiological burden of HIV infection, generating data on PDR in these geographical settings, will enhance evidence-based decision-making. We sought to ascertain levels of PDR and HIV-1 clade dispersal in rural and urban settings, and their potential association with subtype distribution and CD4-staging. A cross-sectional study was conducted from February to May 2017 among patients recently diagnosed with HIV-infection and initiating ART at the Bamenda regional Hospital (urban setting) and the Mbingo Baptist hospital (rural setting). Protease and reverse transcriptase sequencing was performed using an in-house protocol and pre-treatment drug resistance mutations were interpreted using Stanford HIVdb.v8.3. Phylogeny was performed for subtype assignation. A total of 61 patient sequences were generated from ART initiators (median age: 37 years old; 57.4% female; median CD4 cell count: 184 [IQR: 35-387] in urban vs. 161 [IQR: 96-322] cells/mm3 in rural). Overall, the level of PDR was 9.8% (6/61). Of note, burden of PDR was almost doubled in urban (12.9% [4/31]) compared to rural setting 6.7% (2/30), p = 0.352). Fifteen (15) PDR mutations were found among four patients the urban settings [6 resistance mutations to NRTIs:[M41L (2), E44D (1), K65R (1), K70E (1), M184V/I (2), K219R (1)] and 6 resistance mutations to NNRTIs: K103N (1), E138A/G (2), V179E (1), M230L (1), K238T (1), P225H (1)] against two (02) mutations found in two patients in the rural setting[2 resistant mutations to NNRTIs: E138A (1) and Y188H (1)]. The rural setting showed more genetic diversity (8 subtypes) than the urban setting (5 subtypes), with CRF02_AG being the most prevalent clade (72.1% [44/61]). Of note, level of PDR was similar between patients infected with CRF02_AG and non-CRF02_AG infected (9.1% [4/44]) vs. 11.8% [2/17]), p = 1.000). Moreover, PDR appeared higher in patients with CD4 cell count <200 cells/mm3 compared to those with CD4 cell count ≥200 cells/mm3 (14.7% [5/34]) vs. 3.7% [1/27]), p = 0.214). PDR is at a moderate rate in the Northwest region of Cameroon, with higher burden within urban populations. CRF02_AG is the most predominant clade in both urban and rural settings. No effect of HIV molecular epidemiology and CD4-staging on the presence of PDR in patients living in these settings was found. Our findings suggest close monitoring, NNRTI-sparing regimens or sequencing for patients initiating ART, especially in urban settings.

HIV-1 pol gene diversity and molecular dating of subtype C from Sri Lanka.

BackgroundThe first case of HIV infection in Sri Lanka was reported in 1987 and at the end of 2018 there were 3500 people living with HIV. There have been commendable efforts made towards the detection, treatment, and prevention of HIV in the country. Even though the genetic diversity of HIV has been shown to affect the parameters ranging from detection to vaccine development, there is no data available with respect to the molecular epidemiology of HIV-1 in Sri Lanka.MethodsIn this report we have performed the ancillary analysis of pol gene region sequences (n = 85) obtained primarily for the purpose of HIV-1 drug resistance genotyping. Briefly, dried blood spot specimens (DBS) collected from HIV-1 infected individuals between December 2015 and August 2018 were subjected to pol gene amplification and sequencing. These pol gene sequences were used to interpret the drug resistance mutation profiles. Further, sequences were subjected to HIV-1 subtyping using REGA 3.0, COMET, jPHMM and, RIP online subtyping tools. Moreover, Bayesian phylogenetic analysis was employed to estimate the evolutionary history of HIV-1 subtype C in Sri Lanka.ResultsOur analysis revealed that the majority (51.8%) of pol gene sequences were subtype C. Other than subtype C, there were sequences categorized as subtypes A1, B, D and G. In addition to pure subtypes there were sequences which were observed to be circulating recombinant forms (CRFs) and a few of the recombinants were identified as potential unique recombinants (URFs). We also observed the presence of drug resistance mutations in 56 (65.9%) out of 85 sequences. Estimates of the Bayesian evolutionary analysis suggested that the HIV-1 subtype C was introduced to Sri Lanka during the early 1970s (1972.8).ConclusionThe findings presented here indicate the presence of multiple HIV-1 subtypes and the prevalence of drug resistance mutations in Sri Lanka. The majority of the sequences were subtype C, having their most recent common ancestor traced back to the early 1970s. Continuous molecular surveillance of HIV-1 molecular epidemiology will be crucial to keep track of drug resistance, genetic diversity, and evolutionary history of HIV-1 in Sri Lanka.

HIV-1 molecular epidemiology and drug resistance-associated mutations among treatment-na\xefve blood donors in China

Surveillance of human immunodeficiency virus (HIV) molecular diversity and drug resistance-associated mutations (DRMs) among treatment-naïve blood donors is critical for monitoring viral evolution and blood safety. From 2016-2017, 199 plasma samples were collected from 24 blood centers and confirmed as HIV viral load positive or serologically reactive in National Centers for Clinical Laboratories (NCCL), of which 179 were sequenced and subtyped in the gag, protease (PR)-reverse transcriptase (RT), integrase (IN) and/or envelope (env) regions. DRMs in PR-RT and IN regions were analyzed in Stanford HIVdb Program. The majority of subtypes were circulating recombinant form (CRF) 07_BC (34.6%) and CRF01_AE (32.4%); many unique recombinant forms (URFs) (39, 21.8%) and other rare CRFs were observed in the study. Notably, CRF02_AG and CRF06_cpx strains typically found in Africa were firstly identified amongst Chinese blood donors. DRMs were common, with 28 of 179 (15.6%) specimens carrying DRMs, including the PR N88S and RT K103N mutations, which have been implicated in elevated resistance to antiretroviral drugs. Furthermore, 4 HIV-1 isolates (2.4%, 4/168) had surveillance drug-resistance mutation (SDRM), including 3 nonnucleosidereverse transcriptase inhibitors (NNRTI) SDRMs (1 K101E, 2 K103N) and 1 protease inhibitor (PI) SDRM (M46I). The HIV viral diversity among blood donors observed in this study suggest that ongoing HIV-1 recombination is becoming progressively complex in China, and lots of DRMs found in the study exacerbate the primary drug resistance landscape, which highlight the necessity of timely genotypic drug resistance monitoring and molecular surveillance of HIV-1 among blood donors.

Characterization of HIV-1 genetic diversity and antiretroviral resistance in the state of Maranhão, Northeast Brazil.

The HIV-1 epidemic in Brazil has been growing in northeast and north regions, particularly an increase in AIDS cases among the younger male population has been observed. This study aims to characterize the HIV-1 genetic diversity and to evaluate its antiretroviral resistance profile among individuals presenting virological failure in the state of Maranhão—Brazil. HIV-1 pol gene sequences from 633 patients on antiretroviral therapy were obtained from the Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis of the Brazilian Ministry of Health. Phylogenetic and recombination analyses were performed to characterize viral genetic diversity. The presence of antiretroviral resistance mutations was assessed using the HIV Drug Resistance Database online platform of Stanford University. A predominance of subtype B (84.5%) was observed, followed by recombinant BF (9.5%), where more than half of the sequences were dispersed in 3 clusters. Antiretroviral resistance was detected in 74.1% of the sequences, and it was significantly higher for nucleoside analogue reverse-transcriptase inhibitors (NRTIs) than for non-nucleoside analogue reverse-transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs). Inference of putative transmissions clusters identified 11 clusters with 22 query sequences (22/633, 3.5%). Thus, we conclude that continuous monitoring of the molecular epidemiology of HIV-1 is essential for prevention strategies, epidemic control, and treatment adequacy.

Characterization of subtypes and transmitted drug resistance strains of HIV among Beijing residents between 2001-2016.

Beijing is a national and international hub potentially containing a broad diversity of HIV variants. Previous studies on molecular epidemiology of HIV in Beijing pooled together samples from residents and non-residents. Pooling residents and non-residents has potentially introduced bias and undermined a good assessment and the intervention among the autochthonous population. Here, we aimed to define HIV subtype diversity and investigate the TDR in Beijing residents exclusively. We analyzed the demographic, clinical, and virological data collected between 2001 and 2016 from residents in Beijing. A population-based sequencing of the HIV pol gene was carried out using plasma specimens. Phylogenetic analysis was performed in order to classify sequences into their corresponding subtypes using an automated subtyping tool, the Context-Based Modeling for Expeditious Typing (COMET). Furthermore, the drug resistance mutations were determined using the World Health Organization list for surveillance of TDR mutations. Data on TDR were available for 92% of 2,315 individuals with HIV infection, of whom 7.1% were women. The bioinformatic analysis of HIV strains from this study revealed that a combined 17 subtypes were circulating in Beijing, China between 2001 and 2016. The most common ones were CRF01_AE, CRF07_BC, and subtype B in Beijing during this period. The overall prevalence of TDR was 4.5% (95% confidence intervals[CI]: 3.6%-5.4%), with a declining trend over the period of spanning 2001 through 2016. In-depth class-specific analysis revealed that the prevalence of TDR for the nucleoside reverse-transcriptase inhibitors (NRTIs) was 1.0% (95% CI: 0.6-1.5), 0.9% (95% CI:0.6-1.4) for non-NRTIs and 2.8% (95% CI:2.1-3.5) for protease inhibitors. The prevalence of TDR was lower in individuals infected with the CRF07_BC HIV strain than those infected with CRF01_AE. Our data showed that the HIV epidemic in Beijing displayed a high genetic heterogeneity and a low and declining prevalence of TDR. In sharp contrast to Europe and North America, the declining trend of TDR between 2001 through 2016 was noticed while there was a widespread distribution of antiretroviral treatment in Beijing, China.