Temporal trends and transmission dynamics of pre-treatment HIV-1 drug resistance within and between risk groups in Kenya, 1986-2020.

BACKGROUND: Evidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) among risk groups is limited in Africa. We assessed the prevalence, trends and transmission dynamics of pre-treatment HIVDR within and between MSM, people who inject drugs (PWID), female sex workers (FSWs), heterosexuals (HETs) and perinatally infected children in Kenya. METHODS: HIV-1 partial pol sequences from antiretroviral-naive individuals collected from multiple sources between 1986 and 2020 were used. Pre-treatment reverse transcriptase inhibitor (RTI), PI and integrase inhibitor (INSTI) mutations were assessed using the Stanford HIVDR database. Phylogenetic methods were used to determine and date transmission clusters. RESULTS: Of 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSWs (15.1%) and HETs (13.9%). Overall, pre-treatment HIVDR increased consistently, from 6.9% (before 2005) to 24.2% (2016-20). Among HETs, pre-treatment HIVDR increased from 6.6% (before 2005) to 20.2% (2011-15), but dropped to 6.5% (2016-20). Additionally, 32 clusters with shared pre-treatment HIVDR mutations were identified. The majority of clusters had R0 ≥ 1.0, indicating ongoing transmissions. The largest was a K103N cluster involving 16 MSM sequences sampled between 2010 and 2017, with an estimated time to the most recent common ancestor (tMRCA) of 2005 [95% higher posterior density (HPD), 2000-08], indicating propagation over 12 years. CONCLUSIONS: Compared to HETs, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2017 may have abrogated the increase in pre-treatment RTI mutations, albeit in the HET population only. Taken together, our findings underscore the need for targeted efforts towards equitable access to ART for children and key populations in Kenya.

SARS-CoV-2 in Exhaled Aerosol Particles from COVID-19 Cases and Its Association to Household Transmission.

BACKGROUND: Coronavirus disease 2019 (COVID-19) transmission via exhaled aerosol particles has been considered an important route for the spread of infection, especially during super-spreading events involving loud talking or singing. However, no study has previously linked measurements of viral aerosol emissions to transmission rates. METHODS: During February-March 2021, COVID-19 cases that were close to symptom onset were visited with a mobile laboratory for collection of exhaled aerosol particles during breathing, talking, and singing, respectively, and of nasopharyngeal and saliva samples. Aerosol samples were collected using a BioSpot-VIVAS and a NIOSH bc-251 2-stage cyclone, and all samples were analyzed by RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detection. We compared transmission rates between households with aerosol-positive and aerosol-negative index cases. RESULTS: SARS-CoV-2 RNA was detected in at least 1 aerosol sample from 19 of 38 (50%) included cases. The odds ratio (OR) of finding positive aerosol samples decreased with each day from symptom onset (OR 0.55, 95 confidence interval [CI] .30-1.0, P = .049). The highest number of positive aerosol samples were from singing, 16 (42%), followed by talking, 11 (30%), and the least from breathing, 3 (8%). Index cases were identified for 13 households with 31 exposed contacts. Higher transmission rates were observed in households with aerosol-positive index cases, 10/16 infected (63%), compared to households with aerosol-negative index cases, 4/15 infected (27%) (χ2 test, P = .045). CONCLUSIONS: COVID-19 cases were more likely to exhale SARS-CoV-2-containing aerosol particles close to symptom onset and during singing or talking as compared to breathing. This study supports that individuals with SARS-CoV-2 in exhaled aerosols are more likely to transmit COVID-19.

Airborne Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Hospitals: Effects of Aerosol-Generating Procedures, HEPA-Filtration Units, Patient Viral Load, and Physical Distance.

BACKGROUND: Transmission of coronavirus disease 2019 (COVID-19) can occur through inhalation of fine droplets or aerosols containing infectious virus. The objective of this study was to identify situations, patient characteristics, environmental parameters, and aerosol-generating procedures (AGPs) associated with airborne severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. METHODS: Air samples were collected near hospitalized COVID-19 patients and analyzed by RT-qPCR. Results were related to distance to the patient, most recent patient diagnostic PCR cycle threshold (Ct) value, room ventilation, and ongoing potential AGPs. RESULTS: In total, 310 air samples were collected; of these, 26 (8%) were positive for SARS-CoV-2. Of the 231 samples from patient rooms, 22 (10%) were positive for SARS-CoV-2. Positive air samples were associated with a low patient Ct value (OR, 5.0 for Ct <25 vs >25; P = .01; 95% CI: 1.18-29.5) and a shorter physical distance to the patient (OR, 2.0 for every meter closer to the patient; P = .05; 95% CI: 1.0-3.8). A mobile HEPA-filtration unit in the room decreased the proportion of positive samples (OR, .3; P = .02; 95% CI: .12-.98). No association was observed between SARS-CoV-2-positive air samples and mechanical ventilation, high-flow nasal cannula, nebulizer treatment, or noninvasive ventilation. An association was found with positive expiratory pressure training (P < .01) and a trend towards an association for airway manipulation, including bronchoscopies and in- and extubations. CONCLUSIONS: Our results show that major risk factors for airborne SARS-CoV-2 include short physical distance, high patient viral load, and poor room ventilation. AGPs, as traditionally defined, seem to be of secondary importance.

All-Cause Mortality and Serious Non-AIDS Events in Adults With Low-level Human Immunodeficiency Virus Viremia During Combination Antiretroviral Therapy: Results From a Swedish Nationwide Observational Study.

BACKGROUND: The impact of low levels of human immunodeficiency virus (HIV) RNA (low-level viremia [LLV]) during combination antiretroviral therapy (cART) on clinical outcomes is unclear. We explored the associations between LLV and all-cause mortality, AIDS, and serious non-AIDS events (SNAEs). METHODS: We grouped individuals starting cART 1996-2017 (identified from the Swedish InfCare HIV register) as virologic suppression (VS; <50 copies/mL), LLV (repeated viral load, 50-999 copies/mL), and nonsuppressed viremia (NSV; ≥1000 copies/mL). Separately, LLV was subdivided into 50-199 and 200-999 copies/mL (reflecting different definitions of virologic failure). Proportional-hazard models (including sex, age, pre-ART CD4 count and viral load, country of birth, injection drug use, treatment experience and interruptions, and an interaction term between viremia and time) were fitted for the study outcomes. RESULTS: A total of 6956 participants were followed for a median of 5.7 years. At the end of follow-up, 60% were categorized as VS, 9% as LLV, and 31% as NSV. Compared with VS, LLV was associated with increased mortality (adjusted hazard ratio [aHR], 2.2; 95% confidence interval [CI], 1.3-3.6). This association was also observed for LLV 50-199 copies/mL (aHR, 2.2; 95% CI, 1.3-3.8), but was not statistically significant for LLV 200-999 copies/mL (aHR, 2.1; 95% CI, .96-4.7). LLV 50-999 copies/mL was not linked to increased risk of AIDS or SNAEs, but in subanalysis, LLV 200-999 copies/mL was associated with SNAEs (aHR, 2.0; 95% CI, 1.2-3.6). CONCLUSIONS: In this population-based cohort, LLV during cART was associated with adverse clinical outcomes.

Sources of Airborne Norovirus in Hospital Outbreaks.

BACKGROUND: Noroviruses are the major cause of viral gastroenteritis. Disease transmission is difficult to prevent and outbreaks in health-care facilities commonly occur. Contact with infected persons and contaminated environments are believed to be the main routes of transmission. However, noroviruses have recently been found in aerosols and airborne transmission has been suggested. The aim of our study was to investigate associations between symptoms of gastroenteritis and the presence of airborne norovirus, and to investigate the size of norovirus-carrying particles. METHODS: Air sampling was repeatedly performed close to 26 patients with norovirus infections. Samples were analyzed for norovirus RNA by reverse transcription quantitative polymerase chain reaction. The times since each patient's last episodes of vomiting and diarrhea were recorded. Size-separating aerosol particle collection was performed. RESULTS: Norovirus RNA was found in 21 (24%) of 86 air samples from 10 different patients. Only air samples during outbreaks, or before a succeeding outbreak, tested positive for norovirus RNA. Airborne norovirus RNA was also strongly associated with a shorter time period since the last vomiting episode (odds ratio 8.1; P = .04 within 3 hours since the last vomiting episode). The concentrations of airborne norovirus ranged from 5-215 copies/m3, and detectable amounts of norovirus RNA were found in particles <0.95 µm and >4.51 µm. CONCLUSIONS: The results suggest that recent vomiting is the major source of airborne norovirus and imply a connection between airborne norovirus and outbreaks. The presence of norovirus RNA in submicrometre particles indicates that airborne transmission can be an important transmission route.

The HIV care continuum and HIV-1 drug resistance among female sex workers: a key population in Guinea-Bissau.

INTRODUCTION: Female sex workers (FSW) are considered a key group for HIV transmissions in sub-Saharan Africa. The HIV Care Continuum and HIV drug resistance (HIVDR) among FSW has not been well studied in most countries in West Africa. In the current study we describe the HIV Care continuum and prevalence of HIVDR among FSW in Guinea-Bissau. METHODS: A venue-based recruitment and peer-referral of FSW was used in seven cities in Guinea-Bissau from October 2014 to September 2017. We administered a questionnaire, performed discriminatory HIV-testing and collected blood specimens for CD4 count, viral load and HIVDR genotyping. RESULTS: The survey included 440 FSW. The overall HIV-prevalence among FSW was 26.8%. Of the HIV-1 (HIV-1 single- or dually HIV-1/HIV-2) infected FSW (N = 104), 58.7% were previously diagnosed with HIV-1 at enrolment and 41.4% reported taking antiretroviral therapy (ART) compared to 28.6% of the HIV-2 single-infected FSW (N = 14). Among HIV-1 infected FSW on ART (N = 43), 55.8% were virally suppressed (< 1000 copies/ml) and of all HIV-1 infected FSW, 29.8% were virally suppressed. Among ART experienced FSW (N = 22), 50.0% had HIVDR. HIVDR was also found in 9.4% of treatment naïve FSW (N = 53). CONCLUSION: The majority of FSW who knew their HIV status received ART, however a large proportion of FSW were not aware of their HIV positive status. This translated into a great majority of the HIV-infected FSW not being virally suppressed. Amongst treatment naïve FSW nearly a tenth had HIVDR, suggesting that sexual transmission of HIVDR is occurring in this at-risk-population.

Cross-Reactive Antibodies With the Capacity to Mediate HIV-1 Envelope Glycoprotein-Targeted Antibody-Dependent Cellular Cytotoxicity Identified in HIV-2-Infected Individuals.

Disease progression of human immunodeficiency virus type 1 (HIV-1) is delayed by HIV type 2 (HIV-2) in individuals with dual HIV-1/HIV-2 infection. The protective mechanisms, however, are still to be revealed. In the current study we examined type-specific and cross-reactive antibody-dependent cellular cytotoxicity (ADCC) in HIV-1 and HIV-2 monoinfection or dual infection. Of note, intertype cross-reactive antibodies that mediated HIV-1 envelope glycoprotein (Env)-targeted ADCC were frequently identified in HIV-2-infected individuals. Furthermore, the magnitude of HIV-1 cross-reactive ADCC activity during HIV-2 infections depended on the HIV-1 Env origin and was associated with the duration of infection. These results suggest that preexisting antibodies against HIV-2, which mediate intertype ADCC, might contribute to control of HIV-1 during dual infection.

HIV-2 as a model to identify a functional HIV cure.

Two HIV virus types exist: HIV-1 is pandemic and aggressive, whereas HIV-2 is confined mainly to West Africa and less pathogenic. Despite the fact that it has been almost 40 years since the discovery of AIDS, there is still no cure or vaccine against HIV. Consequently, the concepts of functional vaccines and cures that aim to limit HIV disease progression and spread by persistent control of viral replication without life-long treatment have been suggested as more feasible options to control the HIV pandemic. To identify virus-host mechanisms that could be targeted for functional cure development, researchers have focused on a small fraction of HIV-1 infected individuals that control their infection spontaneously, so-called elite controllers. However, these efforts have not been able to unravel the key mechanisms of the infection control. This is partly due to lack in statistical power since only 0.15% of HIV-1 infected individuals are natural elite controllers. The proportion of long-term viral control is larger in HIV-2 infection compared with HIV-1 infection. We therefore present the idea of using HIV-2 as a model for finding a functional cure against HIV. Understanding the key differences between HIV-1 and HIV-2 infections, and the cross-reactive effects in HIV-1/HIV-2 dual-infection could provide novel insights in developing functional HIV cures and vaccines.

Inhibition of HIV-1 disease progression by contemporaneous HIV-2 infection.

BACKGROUND: Progressive immune dysfunction and the acquired immunodeficiency syndrome (AIDS) develop in most persons with untreated infection with human immunodeficiency virus type 1 (HIV-1) but in only approximately 20 to 30% of persons infected with HIV type 2 (HIV-2); among persons infected with both types, the natural history of disease progression is poorly understood. METHODS: We analyzed data from 223 participants who were infected with HIV-1 after enrollment (with either HIV-1 infection alone or HIV-1 and HIV-2 infection) in a cohort with a long follow-up duration (approximately 20 years), according to whether HIV-2 infection occurred first, the time to the development of AIDS (time to AIDS), CD4+ and CD8+ T-cell counts, and measures of viral evolution. RESULTS: The median time to AIDS was 104 months (95% confidence interval [CI], 75 to 133) in participants with dual infection and 68 months (95% CI, 60 to 76) in participants infected with HIV-1 only (P=0.003). CD4+ T-cell levels were higher and CD8+ T-cell levels increased at a lower rate among participants with dual infection, reflecting slower disease progression. Participants with dual infection with HIV-2 infection preceding HIV-1 infection had the longest time to AIDS and highest levels of CD4+ T-cell counts. HIV-1 genetic diversity was significantly lower in participants with dual infections than in those with HIV-1 infection alone at similar time points after infection. CONCLUSIONS: Our results suggest that HIV-1 disease progression is inhibited by concomitant HIV-2 infection and that dual infection is associated with slower disease progression. The slower rate of disease progression was most evident in participants with dual infection in whom HIV-2 infection preceded HIV-1 infection. These findings could have implications for the development of HIV-1 vaccines and therapeutics. (Funded by the Swedish International Development Cooperation Agency-Swedish Agency for Research Cooperation with Developing Countries and others.).

Faster progression to AIDS and AIDS-related death among seroincident individuals infected with recombinant HIV-1 A3/CRF02_AG compared with sub-subtype A3.

BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) is divided into subtypes and circulating recombinant forms (CRFs) but the impact of subtype/CRF on disease progression is not fully understood. METHODS: We determined the HIV-1 subtype/CRF of 152 seroincident individuals from Guinea-Bissau, based on the C2-V3 region of env. Disease progression was measured as time from estimated seroconversion to AIDS and AIDS-related death. Hazard ratios (HRs) were calculated using a Cox proportional hazard model, adjusting for gender and age at seroconversion. RESULTS: The major subtypes/CRFs identified were CRF02_AG (53%), A3 (29%), and A3/02 (a recombinant of A3 and CRF02_AG) (13%). Infection with A3/02 was associated with a close to 3-fold increased risk of AIDS and AIDS-related death compared to A3 (HR = 2.6 [P = 0.011] and 2.9 [P = 0.032], respectively). The estimated time from seroconversion to AIDS and AIDS-related death was 5.0 and 8.0 years for A3/02, 6.2 and 9.0 years for CRF02_AG, and 7.2 and 11.3 years for A3. CONCLUSION: Our results show that there are differences in disease progression between HIV-1 A-like subtypes/CRFs. Individuals infected with A3/02 have among the fastest progression rates to AIDS reported to date. Determining the HIV-1 subtype of infected individuals could be important in the management of HIV-1 infections.

HIV-2 mediated effects on target and bystander cells induce plasma proteome remodeling.

Despite low or undetectable plasma viral load, people living with HIV-2 (PLWH2) typically progress toward AIDS. The driving forces behind HIV-2 disease progression and the role of viremia are still not known, but low-level replication in tissues is believed to play a role. To investigate the impact of viremic and aviremic HIV-2 infection on target and bystander cell pathology, we used data-independent acquisition mass spectrometry to determine plasma signatures of tissue and cell type engagement. Proteins derived from target and bystander cells in multiple tissues, such as the gastrointestinal tract and brain, were detected at elevated levels in plasma of PLWH2, compared with HIV negative controls. Moreover, viremic HIV-2 infection appeared to induce enhanced release of proteins from a broader range of tissues compared to aviremic HIV-2 infection. This study expands the knowledge on the link between plasma proteome remodeling and the pathological cell engagement in tissues during HIV-2 infection.

Size distribution of exhaled aerosol particles containing SARS-CoV-2 RNA.

BACKGROUND: SARS-CoV-2 in exhaled aerosols is considered an important contributor to the spread of COVID-19. However, characterizing the size distribution of virus-containing aerosol particles has been challenging as high concentrations of SARS-CoV-2 in exhaled air is mainly present close to symptom onset. We present a case study of a person with COVID-19 who was able to participate in extensive measurements of exhaled aerosols already on the day of symptom onset and then for the following three days. METHODS: Aerosol collection was performed using an eight-stage impactor while the subject was breathing, talking and singing, for 30 min each, once every day. In addition, nasopharyngeal samples, saliva samples, room air samples and information on symptom manifestations were collected every day. Samples were analyzed by RT-qPCR for detection of SARS-CoV-2 RNA. RESULTS: SARS-CoV-2 RNA was detected in seven of the eight particle size fractions, from 0.34 to >8.1 µm, with the highest concentrations found in 0.94-2.8 µm particles. The concentration of SARS-CoV-2 RNA was highest on the day of symptom onset, and declined for each day thereafter. CONCLUSION: Our data showed that 90% of the exhaled SARS-CoV-2 RNA was found in aerosol particles <4.5 µm, indicating the importance of small particles for the transmission of COVID-19 close to symptom onset. These results are important for our understanding of airborne transmission, for developing accurate models and for selecting appropriate mitigation strategies.

Performance of Galectin-9 for Identification of HIV Viremia in Adults Receiving Antiretroviral Therapy in a Resource-Limited Setting.

BACKGROUND: Targeted viral load (VL) testing has been proposed for antiretroviral treatment (ART) monitoring in resource-limited settings. In this study, we have investigated the performance of the host biomarker galectin-9 (Gal-9), alone and in combination with interferon-γ-inducible protein 10 (IP-10), in identifying individuals at increased likelihood of viremia during ART. SETTING: Cohort of HIV-positive adults receiving ART at Ethiopian health centers. METHODS: We included participants with detectable viremia (VL ≥150 copies/mL) 12 months after starting ART and sex-matched nonviremic controls. Performance to identify individuals with VL ≥1000 copies/mL was determined for Gal-9 and the Gal-9/IP-10 combination, respectively, using receiver operating characteristic (ROC) analysis. RESULTS: Among 191 participants (50.3% women), 46 (24.1%) had VL ≥1000 copies/mL, 23 (12.0%) had 150-999 copies/mL, and 122 (63.9%) had <150 copies/mL. Gal-9 and VL were positively correlated (r s = 0.451, P < 0.001). Sensitivity and specificity for Gal-9 to identify individuals with VL ≥1000 copies/mL were 91.3% (95% CI: 79.2-97.6) and 54.5% (95% CI: 46.0-62.8), respectively. The area under the ROC curve for Gal-9 was 0.810 (95% CI: 0.745-0.875), which was similar to that of the combination of Gal-9 and IP-10 [0.849 (95% CI: 0.792-0.905)]. Assuming 10% prevalence of VL ≥1000 copies/mL, using Gal-9 for targeted VL testing instead of universal VL testing would reduce the number of VL tests from 10 to 5 to identify 1 viremic individual, with misclassification of 1 in 10 viremic individuals. CONCLUSIONS: Gal-9 is a potential screening marker for targeted VL monitoring in ART recipients. Further studies are needed to determine optimal threshold levels.

Infectivity of exhaled SARS-CoV-2 aerosols is sufficient to transmit covid-19 within minutes.

Exhaled SARS-CoV-2-containing aerosols contributed significantly to the rapid and vast spread of covid-19. However, quantitative experimental data on the infectivity of such aerosols is missing. Here, we quantified emission rates of infectious viruses in exhaled aerosol from individuals within their first days after symptom onset from covid-19. Six aerosol samples from three individuals were culturable, of which five were successfully quantified using TCID50. The source strength of the three individuals was highest during singing, when they exhaled 4, 36, or 127 TCID50/s, respectively. Calculations with an indoor air transmission model showed that if an infected individual with this emission rate entered a room, a susceptible person would inhale an infectious dose within 6 to 37 min in a room with normal ventilation. Thus, our data show that exhaled aerosols from a single person can transmit covid-19 to others within minutes at normal indoor conditions.

Increase of ß-lactam-resistant invasive Haemophilus influenzae in Sweden, 1997 to 2010.

The proportions of Haemophilus influenzae resistant to ampicillin and other ß-lactam antibiotics have been low in Sweden compared to other countries in the Western world. However, a near-doubled proportion of nasopharyngeal Swedish H. influenzae isolates with resistance to ß-lactams has been observed in the last decade. In the present study, the epidemiology and mechanisms of antimicrobial resistance of H. influenzae isolates from blood and cerebrospinal fluid in southern Sweden from 1997 to 2010 (n = 465) were studied. Antimicrobial susceptibility testing was performed using disk diffusion, and isolates with resistance to any tested ß-lactam were further analyzed in detail. We identified a significantly increased (P = 0.03) proportion of ß-lactam-resistant invasive H. influenzae during the study period, which was mainly attributed to a significant recent increase of ß-lactamase-negative ß-lactam-resistant isolates (P = 0.04). Furthermore, invasive ß-lactamase-negative ß-lactam-resistant H. influenzae isolates from 2007 and onwards were found in higher proportions than the corresponding proportions of nasopharyngeal isolates in a national survey. Multiple-locus sequence typing (MLST) of this group of isolates did not completely separate isolates with different resistance phenotypes. However, one cluster of ß-lactamase-negative ampicillin-resistant (BLNAR) isolates was identified, and it included isolates from all geographical areas. A truncated variant of a ß-lactamase gene with a promoter deletion, bla(TEM-1)-PΔ dominated among the ß-lactamase-positive H. influenzae isolates. Our results show that the proportions of ß-lactam-resistant invasive H. influenzae have increased in Sweden in the last decade.

Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia.

Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing countries, including Ethiopia. However, subtype-dependent polymorphic differences might influence the occurrence of HIV-drug-resistance mutations (HIVDRMs). We analyzed the prevalence of pre-treatment integrase strand transfer inhibitor (INSTI) HIVDRMs and naturally occurring polymorphisms (NOPs) of the integrase gene, using plasma samples collected as part of the national HIVDR survey in Ethiopia in 2017. We included a total of 460 HIV-1 integrase gene sequences from INSTI-naïve (n = 373 ART-naïve and n = 87 ART-experienced) patients. No dolutegravir-associated HIVDRMs were detected, regardless of previous exposure to ART. However, we found E92G in one ART-naïve patient specimen and accessory mutations in 20/460 (4.3%) of the specimens. Moreover, among the 288 integrase amino acid positions of the subtype C, 187/288 (64.9%) were conserved (<1.0% variability). Analysis of the genetic barrier showed that the Q148H/K/R dolutegravir resistance pathway was less selected in subtype C. Docking analysis of the dolutegravir showed that protease- and reverse-transcriptase-associated HIVDRMs did not affect the native structure of the HIV-1 integrase. Our results support the implementation of a wide scale-up of dolutegravir-based regimes. However, the detection of polymorphisms contributing to INSTI warrants the continuous surveillance of INSTI resistance.

Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia: Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up.

Background: Ethiopia is one of the sub-Saharan countries hit hard by the HIV epidemic. Previous studies have shown that subtype C dominates the Ethiopian HIV-1 epidemic, but the evolutionary and temporal dynamics of HIV-1 in Ethiopia have not been closely scrutinized. Understanding the evolutionary and epidemiological pattern of HIV is vital to monitor the spread, evaluate and implement HIV prevention strategies. Methods: We analyzed 1,276 Ethiopian HIV-1 subtype C polymerase (pol sequences), including 144 newly generated sequences, collected from different parts of the country from 1986 to 2017. We employed state-of-art maximum likelihood and Bayesian phylodynamic analyses to comprehensively describe the evolutionary dynamics of the HIV-1 epidemic in Ethiopia. We used Bayesian phylodynamic models to estimate the dynamics of the effective population size (Ne) and reproductive numbers (Re) through time for the HIV epidemic in Ethiopia. Results: Our analysis revealed that the Ethiopian HIV-1 epidemic originated from two independent introductions at the beginning of the 1970s and 1980s from eastern and southern African countries, respectively, followed by epidemic growth reaching its maximum in the early 1990s. We identified three large clusters with a majority of Ethiopian sequences. Phylodynamic analyses revealed that all three clusters were characterized by high transmission rates during the early epidemic, followed by a decline in HIV-1 transmissions after 1990. Re was high (4-6) during the earlier time of the epidemic but dropped significantly and remained low (Re < 1) after the mid-1990. Similarly, with an expected shift in time, the effective population size (Ne) steadily increased until the beginning of 2000, followed by a decline and stabilization until recent years. The phylodynamic analyses corroborated the modeled UNAIDS incidence and prevalence estimates. Conclusion: The rapid decline in the HIV epidemic took place a decade before introducing antiretroviral therapy in Ethiopia and coincided with early behavioral, preventive, and awareness interventions implemented in the country. Our findings highlight the importance of behavioral interventions and antiretroviral therapy scale-up to halt and maintain HIV transmissions at low levels (Re < 1). The phylodynamic analyses provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.

Intra-Patient Evolution of HIV-2 Molecular Properties.

Limited data are available on the pathogenesis of HIV-2, and the evolution of Env molecular properties during disease progression is not fully elucidated. We investigated the intra-patient evolution of molecular properties of HIV-2 Env regions (V1-C3) during the asymptomatic, treatment-naïve phase of the infection in 16 study participants, stratified into faster or slower progressors. Most notably, the rate of change in the number of potential N-linked glycosylation sites (PNGS) within the Env (V1-C3) regions differed between progressor groups. With declining CD4+ T-cell levels, slower progressors showed, on average, a decrease in the number of PNGSs, while faster progressors showed no significant change. Furthermore, diversity increased significantly with time in faster progressors, whereas no such change was observed in slower progressors. No differences were identified between the progressor groups in the evolution of length or charge of the analyzed Env regions. Predicted virus CXCR4 use was rare and did not emerge as a dominating viral population during the studied disease course (median 7.9 years, interquartile range [IQR]: 5.2-14.0) in either progressor groups. Further work building on our observations may explain molecular hallmarks of HIV-2 disease progression and differences in pathogenesis between HIV-1 and HIV-2.

High Level of HIV Drug Resistance and Virologic Nonsuppression Among Female Sex Workers in Ethiopia: A Nationwide Cross-Sectional Study.

OBJECTIVE: To determine viral load (VL) nonsuppression (VLN) rates, HIV drug resistance (HIVDR) prevalence, and associated factors among female sex workers (FSWs) in Ethiopia. METHODS: A cross-sectional biobehavioral survey was conducted among FSWs in 11 cities in Ethiopia in 2014. Whole blood was collected, and HIVDR genotyping was performed. Logistic regression analysis was performed to identify factors associated with VLN and HIVDR. RESULTS: Among 4900 participants, 1172 (23.9%) were HIV-positive and 1154 (98.5%) had a VL result. Participants were categorized into antiretroviral therapy (ART) (n = 239) and ART-naive (n = 915) groups based on self-report. From the 521 specimens (ART, 59; ART-naive, 462) with VL ≥1000 copies/mL, genotyping was successful for 420 (80.6%) and 92 (21.9%) had drug resistance mutations (DRMs). Pretreatment drug resistance (PDR) was detected in 16.5% (63/381) of the ART-naive participants. Nucleoside reverse transcriptase inhibitor (NRTI), non-NRTIs (NNRTIs), and dual-class DRMs were detected in 40 (10.5%), 55 (14.4%), and 35 (9.2%) of the participants, respectively. Among 239 participants on ART, 59 (24.7%) had VLN. Genotyping was successfully performed for 39 (66.1%). DRMs were detected in 29 (74.4%). All 29 had NNRTI, 23 (79.3%) had NRTI or dual-class DRMs. VLN was associated with age 35 years or older, CD4+ T-cell count <350 cells/mm3, and being forced into selling sex. PDR and acquired drug resistance were associated with CD4+ T-cell count <350 cells/mm3 (P < 0.001). CONCLUSIONS: The high VLN and HIVDR rates among FSWs underscore the need for targeted interventions to improve ART access and virologic monitoring to maximize the benefit of ART and limit the spread of HIV and HIVDR.

Hierarchical Clustering and Trajectory Analyses Reveal Viremia-Independent B-Cell Perturbations in HIV-2 Infection.

Time to AIDS in HIV-2 infection is approximately twice as long compared to in HIV-1 infection. Despite reduced viremia, HIV-2-infected individuals display signs of chronic immune activation. In HIV-1-infected individuals, B-cell hyperactivation is driven by continuous antigen exposure. However, the contribution of viremia to B-cell perturbations in HIV-2-infected individuals remains largely unexplored. Here, we used polychromatic flow cytometry, consensus hierarchical clustering and pseudotime trajectory inference to characterize B-cells in HIV-1- or HIV-2-infected and in HIV seronegative individuals. We observed increased frequencies of clusters containing hyperactivated T-bethighCD95highCD27int and proliferating T-bet+CD95highCD27+CD71+ memory B-cells in viremic HIV-1 (p < 0.001 and p < 0.001, respectively), viremic HIV-2 (p < 0.001 and p = 0.014, respectively) and in treatment-naïve aviremic HIV-2 (p = 0.004 and p = 0.020, respectively)-infected individuals, compared to seronegative individuals. In contrast, these expansions were not observed in successfully treated HIV-1-infected individuals. Finally, pseudotime trajectory inference showed that T-bet-expressing hyperactivated and proliferating memory B-cell populations were located at the terminal end of two trajectories, in both HIV-1 and HIV-2 infections. As the treatment-naïve aviremic HIV-2-infected individuals, but not the successfully ART-treated HIV-1-infected individuals, showed B-cell perturbations, our data suggest that aviremic HIV-2-infected individuals would also benefit from antiretroviral treatment.