Prevalence and persistence of transmitted drug resistance mutations in the German HIV-1 Seroconverter Study Cohort

K103N, V106M and Y188L Significantly Reduce HIV-1 Subtype C Phenotypic Susceptibility to Doravirine

Doravirine (DOR) is a non-nucleoside reverse transcriptase inhibitor (NNRTI) with efficacy against some NNRTI-resistant mutants. Although DOR resistance mutations are established for HIV-1 subtype B, it is less clear for non-B subtypes. This study investigated prevalent NNRTI resistance mutations on DOR susceptibility in HIV-1 subtype C. Prevalent drug resistance mutations were identified from a South African genotypic drug resistance testing database. Mutations, single or in combination, were introduced into replication-defective pseudoviruses and assessed for DOR susceptibility in vitro. The single V106M and Y188L mutations caused high-level resistance while others did not significantly impact DOR susceptibility. We observed an agreement between our in vitro and the Stanford HIVdb predicted susceptibilities. However, the F227L mutation was predicted to cause high-level DOR resistance but was susceptible in vitro. Combinations of mutations containing K103N, V106M or Y188L caused high-level resistance, in agreement with the predictions. These mutations are frequently observed in patients failing efavirenz- or nevirapine-based first-line regimens. However, they are also observed in those failing a protease inhibitor-based second-line regimen, as we have observed in our database. Genotypic drug resistance testing is therefore vital prior to the initiation of DOR-based treatment for those previously exposed to efavirenz or nevirapine.

HIV drug resistance among patients experiencing antiretroviral therapy failure in Russia, 2019-2021

Increasing HIV drug resistance is an important public health concern. The current study aimed to assess HIV drug resistance among people who live with HIV (PLWH) experiencing virological failure. Blood samples and epidemiological characteristics were collected in four Siberian regions from PLWH experiencing ART failure. Partial pol gene sequences were obtained for the study individuals. Drug resistance mutations (DRMs) were predicted using the Stanford HIVdb Program. The association of HIV DRM with epidemiological characteristics was estimated using logistic regression analysis. Further analysis was performed for children (0-14 y old) and adults (≥15 y old) separately. In total, 815 (89.4%) patients were included in the final dataset. Overall, 501 (61.5%) patients had DRM detected. NRTI DRM was more common in children, while NRTI+NNRTI DRM was more frequent in adults (P < 0.001). Krasnoyarsk region, male sex and high viral load were positively associated with the presence of DRM in adults, while higher CD4 cell count and PI/INSTI-based ART had a negative association. No association between epidemiological characteristics and DRM was identified in children. The remaining 38.5% of patients with virological failure had no DRM detected; those patients were likely to have insufficient ART adherence. Most (55.5%) patients had HIV CRF63_02A6, followed by sub-subtype A6 (39.2%). This study revealed poor ART adherence as a main factor driving ART failure among PLWH in the Siberian region. DRM was detected in over 60% of PLWH experiencing ART failure. The current results highlight an urgent need for the introduction of special programs focusing on ART adherence improvement.

Increasing hepatitis B vaccination coverage and decreasing hepatitis B co-infection prevalence among people with HIV-1 in Germany, 1996-2019. Results from a cohort study primarily in men who have sex with men

OBJECTIVES

Viral hepatitis co-infection among people living with HIV is known to accelerate the progression of liver disease and AIDS. An increased prevalence and incidence of hepatitis B virus (HBV) infection among people living with HIV demands continuous monitoring to adapt targeted prevention strategies to reach the global goals of eliminating viral hepatitis as a public health threat.

METHODS

We determined the prevalence and incidence of HBV for the years 1996-2019 from yearly blood sample testing and questionnaire reports among people living with HIV belonging to a nationwide, multicentre observational, prospective cohort study.

RESULTS

Among this study population of 3479 participants, the majority (87%) indicated that being men who have sex with men (MSM) was their likely HIV transmission route; 51% were recruited from Berlin. HBV prevalence for acute/chronic and resolved infections decreased from 4.1% and 45% in 1996-1999 to 1.3% and 16% in 2019, respectively. Simultaneously, participants with a serological status indicating HBV vaccination increased from 25% in 1996-1999 to 69% in 2019. Among vaccinated participants with relevant information (n = 1135), 38% received their first HBV vaccination after HIV infection. The HBV incidence rate in 565 eligible participants decreased from 6.9/100 person-years in 2004-2007 to 0.45/100 person-years in 2015.

CONCLUSION

Increasing vaccination coverage because of a general HBV vaccination recommendation and catch-up vaccination efforts among risk groups decreased HBV infection prevalence over time among this study population of people living with HIV, primarily MSM and from Berlin. Despite this success, the prevalence and incidence of HBV remains higher than in the general population in Germany. This emphasizes the need for continued HBV prevention by promoting HBV vaccination and HBV screening at regular intervals based on the individual risk behaviour.

Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022

Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.

Increased prevalence of pretreatment drug resistance mutations in treatment-naïve people living with HIV-1 in Henan Province, China (2022/23)

Human deficiency virus type 1 (HIV-1) harboring drug resistance mutations (DRMs) before the initiation of antiretroviral therapy (ART) poses a serious threat to the efficacy of current ART regimens. Currently, the prevalence of pre-treatment drug resistance mutations (PDRMs) including transmitted DRMs (TDRMs) is not completely clear. Understanding this prevalence better should offer valuable data for clinical- and government-level decision-making. To closely monitor the PDRM trend in treatment-naïve people living with HIV/AIDS (PLWHA) in Henan Province, China, plasma samples from the patients seeking treatments at our hospital from January 2022 to February 2023 were collected for genotypic drug resistance testing. From the 645 patients whose samples were collected, partial pol and integrase gene sequences were obtained from 637 patients. Subtyping analysis indicated that the top-three most common subtypes, in descending order, were CRF07_BC (41.76%, 266/637), CRF01_AE (28.26%, 180/637), and B (20.41%, 130/637). PDRMs were observed in 5.18% (33/637), 6.28% (40/637), 0.31% (2/637), and 2.83% (18/637) cases for nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase strand transfer inhibitors (INSTIs), respectively; all these medications contributed to an overall PDRM prevalence of 11.93% (76/637). On analyzing individual PDRMs, we noted that the most commonly observed mutation(s) were K103S/N (3.77%, 24/637), M184I/V (3.14%, 20/637), followed by K65R (1.26%, 8/637), and V106A/M (1.10%, 7/637). PDRM prevalence in ART-naïve PLWHA of Henan Province is high and increased compared with that noted in previous years. However, evidence of cluster-linked outbreaks of PDRMs is lacking, suggesting that measures such as education about adherence and improved treatment strategies with a low incidence of failure can effectively reduce PDRM prevalence.

Optimization of HIV testing services in Germany using HIV indicator diseases: study protocol of the HeLP study

BACKGROUND

Despite the potentially accompanying negative clinical, epidemiologic, and health economic effects, a large proportion of persons living with the human immunodeficiency virus (HIV) are diagnosed late. Internationally, numerous diseases are known to be HIV indicator diseases. Adequate HIV testing in the presence of HIV indicator diseases could help to diagnose unknown HIV infections earlier. The objective of the HeLP study is to validate published HIV indicator diseases for the German setting and to identify guidelines in terms of these indicator diseases in order to reduce knowledge gaps and increase HIV testing when HIV indicator diseases are diagnosed.

METHODS

A mixed methods approach is used. In a first step, published HIV indicator diseases will be identified in a systematic literature review and subsequently discussed with clinical experts regarding their relevance for the German setting. For the validation of selected indicator diseases different data sets (two cohort studies, namely HIV-1 seroconverter study & ClinSurv-HIV, and statutory health insurance routine data) will be analyzed. Sensitivity analyses using different time periods will be performed. Guidelines of HIV indicator diseases validated in the HeLP study will be reviewed for mentioning HIV and for HIV testing recommendations. In addition, semi-standardized interviews (followed by a free discussion) with guideline creators will identify reasons why HIV testing recommendations were (not) included. Subsequently, a random sample of physicians in medical practices will be surveyed to identify how familiar physicians are with HIV testing recommendations in guidelines and, if so, which barriers are seen to perform the recommended tests in everyday care.

DISCUSSION

The HeLP-study adopts the challenge to validate published HIV indicator diseases for the German setting and has the potential to close a knowledge gap regarding this objective. This has the potential to improve targeted HIV testing for patients with HIV indicator diseases and consequently lead to earlier HIV diagnosis.

TRIAL REGISTRATION

DRKS00028743.

Genetic and antiretroviral drug resistance mutations analysis of reverse transcriptase and protease gene from Pakistani people living with HIV-1

BACKGROUND

Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from intrinsic viral factors, non-compliance with drugs and/or the use of sub-optimum therapy can lead to the emergence of DRMs. In Pakistan HIV currently exists as a concentrated epidemic, however, ART coverage is very low, and drug adherence is poor. ART is selected assuming without baseline genotyping. Pakistan has recently seen a rise in treatment failures, but the country's actual burden of DRM is still unknown. In this study, we perform the genetic and drug resistance analysis of the pol gene from Pakistani HIV-positive ART-naïve and ART-experienced individuals.

METHODS

In this study, HIV-1 pol was sequenced from 146 HIV-1 positive individuals, divided into ART-naïve (n = 37) and ART-experienced (n = 109). The sequences were also used to determine HIV-1 subtypes, the prevalence of DRM, and pol genetic variability.

RESULTS

DRM analysis identified numerous DRMs against reverse transcriptase inhibitors in both ART-naïve and ART-experienced groups, including a few that are classified as rare. Additionally, the ART-experienced group showed mutations associated with resistance to protease inhibitors. Genetic analysis showed negative selection pressure in both groups, but a higher rate of evolution in the ART-naïve group.

CONCLUSION

High prevalence of DRMs, especially against previous first-line treatment in ART- naïve and the accumulation of DRMs in ART-experienced groups is concerning and warrants that a more extensive DRM survey be carried out to inform first-line and second-line ART regimen recommendations.

Transmitted drug resistance and transmission clusters among ART-naïve HIV-1-infected individuals from 2019 to 2021 in Nanjing, China

Background

Transmitted drug resistance (TDR) is an increasingly prevalent problem worldwide, which will significantly compromise the effectiveness of HIV treatments. However, in Nanjing, China, there is still a dearth of research on the prevalence and transmission of TDR among ART-naïve HIV-1-infected individuals. This study aimed to understand the prevalence and transmission of TDR in Nanjing.

Methods

A total of 1,393 participants who were newly diagnosed with HIV-1 and had not received ART between January 2019 and December 2021 were enrolled in this study. HIV-1 pol gene sequence was obtained by viral RNA extraction and nested PCR amplification. Genotypes, TDR and transmission cluster analyses were conducted using phylogenetic tree, Stanford HIV database algorithm and HIV-TRACE, respectively. Univariate and multivariate logistic regression analyses were performed to identify the factors associated with TDR.

Results

A total of 1,161 sequences were successfully sequenced, of which CRF07_BC (40.6%), CRF01_AE (38.4%) and CRF105_0107 (6.3%) were the main HIV-1 genotypes. The overall prevalence of TDR was 7.8%, with 2.0% to PIs, 1.0% to NRTIs, and 4.8% to NNRTIs. No sequence showed double-class resistance. Multivariate logistic regression analysis revealed that compared with CRF01_AE, subtype B (OR = 2.869, 95%CI: 1.093-7.420) and female (OR = 2.359, 95%CI: 1.182-4.707) were risk factors for TDR. Q58E was the most prevalent detected protease inhibitor (PI) -associated mutation, and V179E was the most frequently detected non-nucleoside reverse transcriptase inhibitor (NNRTI) -associated mutation. A total of 613 (52.8%) sequences were segregated into 137 clusters, ranging from 2 to 74 sequences. Among 44 individuals with TDR (48.4%) within 21 clusters, K103N/KN was the most frequent TDR-associated mutation (31.8%), followed by Q58E/QE (20.5%) and G190A (15.9%). Individuals with the same TDR-associated mutations were usually cross-linked in transmission clusters. Moreover, we identified 9 clusters in which there was a transmission relationship between drug-resistant individuals, and 4 clusters in which drug-resistant cases increased during the study period.

Conclusion

The overall prevalence of TDR in Nanjing was at a moderate level during the past 3 years. However, nearly half of TDR individuals were included in the transmission clusters, and some drug-resistant individuals have transmitted in the clusters. Therefore, HIV drug-resistance prevention, monitoring and response efforts should be sustained and expanded to reduce the prevalence and transmission of TDR in Nanjing.

Single-center experience evaluating and initiating people with HIV on long-acting cabotegravir/rilpivirine

OBJECTIVE

To describe our experience evaluating and initiating individuals on long-acting injectable (LAI) cabotegravir/rilpivirine (CAB/RPV) and evaluate factors associated with starting LAI CAB/RPV and reasons for not starting.

DESIGN

We conducted a retrospective single-center study at the UC San Diego Owen Clinic.

METHODS

We included all individuals who expressed interest in treatment with LAI CAB/RPV between April 2021 and June 2022 who had a definitive decision made on starting LAI CAB/RPV.

RESULTS

In total, 383 individuals were included with 201 (52.5%) initiating LAI CAB/RPV. Those who initiated LAI CAB/RPV were younger ( P  = 0.02) and were more likely to be on a two-drug regimen or first-generation integrase inhibitor regimen and less likely to be on a protease inhibitor or multiclass regimen. The most common reasons for not starting LAI CAB/RPV were inconsistent clinic attendance or difficulty being contacted and patient choice not to start. Of those who had a proviral DNA resistance test as workup for LAI CAB/RPV ( n  = 135), 18.5% had a resistance mutation identified that may have impacted the activity of LAI CAB/RPV.

CONCLUSION

Despite novel challenges over half of our cohort initiated LAI CAB/RPV. Evaluating for potential non-nucleoside reverse transcriptase inhibitor resistance is an important part of the workup for LAI CAB/RPV and proviral DNA resistance testing can be an additional tool to identify potential resistance.

Frequency of genotypic factors possibly associated with cabotegravir/rilpivirine failure in antiretroviral treatment-naïve and -experienced HIV-1- infected population

OBJECTIVES

The long-acting injectable (LAI) cabotegravir (CAB) and rilpivirine (RPV) treatment offers important advantages over oral ART (antiretroviral therapy), however baseline factors possibly contributing to the CAB/RPV treatment failure were identified. The purpose of this study was to describe the frequency of virologic factors previously influencing efficacy of this treatment, namely RPV and CAB resistance-associated mutations (RAMs) and A1/A6 subtype among naïve and treatment-experienced HIV-1-infected patients from Poland.

METHODS

The following datasets of HIV-1 sequences were analysed: 4809 protease and reverse transcriptase (PR/RT) sequences obtained from 4649 Polish Caucasian patients (4122 naive and 687 non-naïve) supplemented with integrase (PR/RT/INT) sequences in 1217 cases (942 naïve and 275 non-naïve). Sub-subtypes A were assigned by phylogenetic methods. Major and minor CAB and RPV RAMs were determined according to the IAS-USA 2019 list, while minor RAMs were additionally defined based on the Stanford database algorithm.

RESULTS

Subtype A1/A6 frequency ranged from 6.11% in ART failing cases with PR/RT sequences only, to 15.92% for the PR/RT/INT treatment-naïve dataset, while RPV RAMs were found in up to 5.89% of treatment-naïve and 14.56% of ART failing cases. Regardless treatment history, only <1% sequences had combination of two factors (RPV RAMs and A1/A6 subtype). Furthermore, CAB RAMs were found in 1.27% of treatment-naïve and 14.54% of experienced patients.

CONCLUSIONS

Despite notable frequency of subtype A1/A6 or CAB/RPV RAMs analysed separately, combination of at least two factors previously associated with failure or this treatment is rare. As subtype A1/A6 becomes more common across real-life cohorts continued subtyping and RAM screening will remain of key importance for LAI treatment implementation. Sequence data from this article have been deposited in GenBank under accession numbers: GU906860, GU906864, GU906871-GU906874, JQ305750-JQ305791, KC409134-KC409222, KM057341-KM057362, KM283892-KM284490, KT340108-KT340205, MZ468643-MZ468894, MZ671788-MZ671823, OP298017-OP302727.

High efficacy of switching to bictegravir/emtricitabine/tenofovir alafenamide in people with suppressed HIV and preexisting M184V/I

OBJECTIVE

We investigated the prevalence of preexisting M184V/I and associated risk factors among clinical trial participants with suppressed HIV and evaluated the impact of M184V/I on virologic response after switching to bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF).

DESIGN

Participant data were pooled from six clinical trials investigating the safety and efficacy of switching to B/F/TAF in virologically suppressed people with HIV.

METHODS

Preexisting drug resistance was assessed by historical genotypes and/or baseline proviral DNA genotyping. Virologic outcomes were determined by last available on-treatment HIV-1 RNA. Stepwise selection identified potential risk factors for M184V/I in a multivariate logistic regression model.

RESULTS

Altogether, 2034 participants switched treatment regimens to B/F/TAF and had follow-up HIV-1 RNA data, and 1825 of these participants had baseline genotypic data available. Preexisting M184V/I was identified in 182 (10%), mostly by baseline proviral DNA genotype ( n  = 167). Most substitutions were M184V ( n  = 161) or M184V/I mixtures ( n  = 10). Other resistance substitutions were often detected in addition to M184V/I ( n  = 147). At last on-treatment visit, 98% (179/182) with preexisting M184V/I and 99% (2012/2034) of all B/F/TAF-treated participants had HIV-1 RNA less than 50 copies/ml, with no treatment-emergent resistance to B/F/TAF. Among adult participants, factors associated with preexisting M184V/I included other resistance, black race, Hispanic/Latinx ethnicity, lower baseline CD4 + cell count, advanced HIV disease, longer duration of antiretroviral therapy, and greater number of prior third agents.

CONCLUSION

M184V/I was detected in 10% of virologically suppressed clinical trial participants at study baseline. Switching to B/F/TAF demonstrated durable efficacy in maintaining viral suppression, including in those with preexisting M184V/I.

Decreasing prevalence and stagnating incidence of Hepatitis C-co-infection among a cohort of HIV-1-positive patients, with a majority of men who have sex with men, in Germany, 1996-2019

Co-infection with Hepatitis C virus (HCV) among HIV-positive patients leads to accelerated progression of liver disease and AIDS. Due to increased HCV prevalence and incidence, co-infection requires monitoring trends among HIV-positive individuals. This will help target prevention strategies and support to reach the global goals of eliminating viral hepatitis as a public health threat. In this analysis HCV prevalence and incidence were determined for the years 1996-2019 from yearly blood samples and questionnaire details among HIV-1-positive patients, with a majority of men who have sex with men, belonging to a nationwide, multicentre observational, prospective cohort study. The results show that HCV prevalence for acute/chronic and resolved infection increased until 2014 to 12%. Since then, prevalence of acute/chronic HCV infection rapidly decreased and prevalence of resolved infections showed a steady increase. HCV incidence was highest in 2010 and lowest in 2017; however, no significant change in HCV incidence could be seen over the years. Therefore, the introduction of directly-acting antiviral agents for HCV treatment notably decreased prevalence and potentially incidence of acute/chronic HCV infection. Nevertheless, prevalence and incidence of HCV among these HIV-1-positive study participants remain high compared with the general population and justify the need for continuous HCV prevention and treatment efforts among HIV-positive individuals.

Prevalence and evolution of transmitted HIV drug resistance in Belgium between 2013 and 2019

Background

To assess the prevalence and evolution of transmitted drug resistance (TDR) in Belgium, a total of 3708 baseline human immunodeficiency virus (HIV)-1 polymerase sequences from patients diagnosed between 2013 and 2019 were analyzed.

Methods

Protease and reverse-transcriptase HIV-1 sequences were collected from the 7 national Aids Reference Laboratories. Subtype determination and drug resistance scoring were performed using the Stanford HIV Drug Resistance Database. Trends over time were assessed using linear regression, and the maximum likelihood approach was used for phylogenetic analysis.

Results

A total of 17.9% of the patients showed evidence of TDR resulting in at least low-level resistance to 1 drug (Stanford score  ≥15). If only the high-level mutations (Stanford score ≥60) were considered, TDR prevalence dropped to 6.3%. The majority of observed resistance mutations impacted the sensitivity for nonnucleoside reverse-transcriptase inhibitors (NNRTIs) (11.4%), followed by nucleoside reverse-transcriptase inhibitors (6.2%) and protease inhibitors (2.4%). Multiclass resistance was observed in 2.4%. Clustered onward transmission was evidenced for 257 of 635 patients (40.5%), spread over 25 phylogenetic clusters.

Conclusions

The TDR prevalence remained stable between 2013 and 2019 and is comparable to the prevalence in other Western European countries. The high frequency of NNRTI mutations requires special attention and follow-up. Phylogenetic analysis provided evidence for local clustered onward transmission of some frequently detected mutations.

HIV-1 subtype diversity, phylogenetic analysis and study of drug resistance in strains circulating in the Ural Federal District

Introduction. Ural Federal District (UFD) has been one of the most HIV-affected areas in the Russian Federation during past 20 years. The total number of people living with HIV/AIDS (PLWH) and receiving antiretroviral therapy (ART) exceeds 100,000 (61.7% of all PLWH in the UFD), which creates opportunities for the wide spread of resistant HIV strains.Research aim was to determine the distribution of HIV-1 subtypes, evaluate the genetic heterogeneity of HIV-1 strains, and analyze the prevalence of HIV-1 drug resistance mutations (DRM) and the incidence of acquired resistance to antiretroviral drugs (ARVDs) in PLWH receiving ART in the UFD.Materials and methods. 223 patients receiving ART at stage III–IV of HIV infection living in the UFD were examined. To determine the subtypes and the DRM in the HIV-1 pol gene, molecular genetic studies were performed using the AmpliSense® HIV-Resist-Seq kit by Sanger sequencing on the Applied Biosystems 3500 Genetic Analyzer. The genetic heterogeneity was evaluated by calculating the identity of the genome region of the isolated strains in comparison with the genomes of foreign HIV strains, as well as using phylogenetic analysis.Results. In the studied group of patients, 5 subtypes of HIV-1 were identified: subtype A6 prevalence was 91.03%, that of subtype B was 2.69%, 3 recombinant subtypes (CRF03_A6B, CRF02_AG, CRF63_02A6) accounted for 6.28%. Among analyzed HIV-1 strains, 43.9% had a significant genetic similarity (identity of at least 97%) with the strains isolated from patients from neighboring countries (Belarus, Kazakhstan, Kyrgyzstan, Uzbekistan, Lithuania), 35.9% were similar to the strains isolated from patients from far-abroad countries (USA, China, South Korea, Australia, Sweden, Germany). A high heterogeneity of the circulating genetic variants of HIV-1 strains in the territory of the UFD region was established, which is an unfavorable factor for the diagnosis and treatment of HIV. The most common DRMs to both nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) were detected in 81 specimens (36.3%). NRTI resistance-forming M184V DRM was more common than any other DRM with statistical significance (p = 0,0008) and was detected in 88 specimens (39.5%).Conclusion. In the subtype structure of HIV-1, the dominant subtype was subtype A6, the most common in the countries that were formerly part of the USSR. The heterogeneity of the HIV-1 strains circulating in the UFD suggests that HIV-1 infection continues to be introduced into the UFD from populations outside the Russian Federation. The findings confirm the high prevalence of DRMs (62.8%) and secondary drug resistance of HIV-1 (60.1%) among PLWH in the territory of the UFD. At the same time, high-level resistance was detected in 56.5% of patients, which requires increasing the coverage of HIV resistance testing, including the introduction of monitoring for primary resistance, in order to optimize first-line ART regimens. 

The Emergence and Transmission Dynamics of HIV-1 CRF07_BC in Mainland China

A total of 1155 partial pol gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptation, spatiotemporal and risk group dynamics, migration patterns, and protein structure of HIV-1 CRF07_BC. Due to the unequal distribution of sequences across time, location, and risk group in the complete dataset (‘full1155’), subsampling methods were used. Maximum-likelihood and Bayesian phylogenetic analysis as well as discrete trait analysis of geographical location and risk group were carried out. To study mutations of a cluster of HIV-1 CRF07_BC (CRF07-1), we performed a comparative analysis of this cluster to the other CRF07_BC sequences (‘backbone_295’) and mapped the mutations observed in the respective protein structure. Our findings showed that HIV-1 CRF07_BC most likely originated among IDU in Yunnan Province between October 1992 to July 1993 [95 per cent hightest posterior density (HPD): May 1989–August 1995] and that IDU in Yunnan Province and MSM in Guangdong Province likely served as the viral sources during the early and more recent spread in Mainland China. We also revealed that HIV-1 CRF07-1 has been spreading for roughly 20 years and continues to cause local transmission in Mainland China and worldwide. Overall, our study sheds light on the dynamics of HIV-1 CRF07_BC distribution patterns in Mainland China. Our research may also be useful in formulating public health policies aimed at controlling acquired immune deficiency syndrome in Mainland China and globally.

Pre-existing singleton E138A mutations in the reverse transcriptase gene do not affect the efficacy of first-line antiretroviral therapy regimens using rilpivirine in human immunodeficiency virus-infected patients

General consensus suggests that even singleton E138A mutations in HIV reverse transcriptase at baseline are associated with resistance to rilpivirine (RPV). We detected 11 pre-existing E138A carriers treated with RPV in the pan European EuResist database. However, all 11 patients presented with full virological efficacy for first-line RPV-based ART regimens.

Two drugs regimens for HIV

PURPOSE OF REVIEW

As the evidence for two-drug regimens (2DR) for HIV treatment accumulates and 2DR start to enter consensus guidelines, this review covers the history, rationale and current evidence for 2DR in first-line and switch settings.

RECENT FINDINGS

Until recently, most evidence for 2DR was for boosted protease inhibitor-based therapies but now we have large, randomized trials to support the use of dolutegravir (DTG)-based 2DR, both for initial therapy and suppressed switch, with high efficacy and no emergent resistance at failure.

SUMMARY

2DR will increasingly form part of the choice we are able to offer people with HIV but we must consider some of the limitations to ensure these regimens are used in the most clinically appropriate manner.

Transmitted drug resistance among HIV-1 drug-naïve patients in Greece

OBJECTIVES

Despite the success of antiretroviral treatment (ART), the persisting transmitted drug resistance (TDR) and HIV genetic heterogeneity affect the efficacy of treatment. This study explored the prevalence of TDR among ART-naïve HIV patients in Greece during the period 2016-2019.

METHODS

Genotypic resistance testing was available for 438 ART-naïve HIV patients. Multivariable Poisson regression models were fitted.

RESULTS

The majority of patients were male, and there was a slight predominance of Hellenic (26.5%) over non-Hellenic (21.9%) nationality. The prevalence of TDR was 7.8%. There was a predominance of mutations for non-nucleoside reverse-transcriptase inhibitors (5.7%) over nucleoside reverse-transcriptase inhibitors (0.2%). No mutations to protease inhibitors were detected. The prevalence of resistance was 22.1% based on all mutations identified through the HIVdb interpretation system. The most frequent resistance sites were E138A (9.6%), K103N (6.4%), and K101E (2.1%). The majority of detected mutations were confined to subtype A (52.6%), followed by B (19.6%). Non-Hellenic nationality was significantly associated with an increased risk of TDR (relative risk 1.32, 95% confidence interval 1.04-1.69).

CONCLUSIONS

Non-B HIV infections predominate in Greece, with an increasing trend in recent years. The prevalence of TDR remains stable. Ongoing surveillance of resistance testing is needed to secure the long-term success of ART.

High nonnucleoside reverse transcriptase inhibitor resistance levels in HIV-1-infected Zambian mother-infant pairs

OBJECTIVE(S)

To elucidate relationships in antiretroviral resistance between HIV-1-infected mother-infant pairs by defining the resistance profiles in the mothers and infants and quantifying drug resistance prevalence in the pairs post-Option B+ implementation.

DESIGN

Collection of dried blood spots from mother-infant pairs during routine HIV-1 screens in Lusaka, Zambia from 2015 to 2018.

METHODS

DNA was extracted from the dried blood spots, the HIV-1 pol region was amplified, and the purified proviral DNA was sequenced using Sanger sequencing. Drug resistance mutations (DRM) were identified in sequenced DNA using the Stanford HIVdb (https://hivdb.stanford.edu/).

RESULTS

DRM were detected in 45% (44/97) of samples, and these samples were found to harbor resistance to at least two antiretrovirals. The prevalence of nonnucleoside reverse transcriptase inhibitor resistance was significantly higher than that of other antiretroviral classes. DRM were detected disproportionately in infants (67%; 33/49) compared with mothers (23%; 11/48), but the magnitude of resistance did not differ when resistance was detected. The disparity in drug resistance profiles was reinforced in pairwise comparison of resistance profiles in mother-infant pairs.

CONCLUSION

While Option B+ is effective in reducing mother-to-child transmission, in cases where this regimen fails, high-level nonnucleoside reverse transcriptase inhibitor resistance is frequently detected in infants. This underscores the importance of pretreatment drug resistance screening in both mothers and infants and emphasizes the necessary change to protease inhibitor-based and integrase inhibitor-based regimens for treatment of HIV-1-infected infants and mothers.

Identification of HIV-1 subtypes and drug resistance mutations among HIV-1-infected individuals residing in Pontianak, Indonesia

Introduction

The present study investigated the HIV-1 subtype classification in addition to prevalence of drug resistance mutations (DRMs) in antiretroviral therapy (ART)-experienced and ART-naïve residents of Pontianak, West Kalimantan, Indonesia.

Methods

Whole blood samples collected from 30 HIV-1-infected individuals, comprising 19 ART-experienced and 11 ART-naïve individuals, were subjected to RNA and DNA extraction, followed by HIV-1 genes amplification and sequencing analysis. HIV-1 subtyping was classified on viral pol genes encoding reverse transcriptase (RT gene) and protease (PR gene) accompanied by the env and gag genes. DRMs in the RT and PR genes were also analyzed.

Results

CRF01_AE was identified as the predominant circulating recombinant form (CRF) of HIV-1 in both ART-experienced and ART-naïve individuals. In addition, CRF02_AG, subtype B, recombinant virus expressing CRF01_AE and subtype B viral genomic fragments, also recombinant virus containing CRF01_AE and CRF02_AG genomic fragments were also identified. Acquired drug resistance (ADR) was identified in 28.5% of ART-experienced individuals, while no transmitted drug resistance was identified in ART-naïve individuals.

Conclusions

This study identified CRF01_AE as the most predominant HIV-1 CRF distributing in Pontianak, Indonesia. The prevalence of ADR is considered to be high; thus, further surveillance is needed in this region.

Evaluation of HIV Transmission Clusters among Natives and Foreigners Living in Italy

We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2–3 sequences), medium (MMTCs, 4–9 sequences) and large (LMTCs, ≥10 sequences). Among 3499 drug-naïve individuals enrolled in the Italian Cohort Naive Antiretroviral (ICONA) cohort (2804 natives; 695 migrants), 726 (20.8%; 644 natives, 82 migrants) were involved in 228 MTCs (6 LMTCs, 36 MMTCs, 186 SMTCs). Migrants contributed 14.4% to SMTCs, 7.6% to MMTCs and 7.1% to LMTCs, respectively. HIV-1 non-B subtypes were found in 51 MTCs; noteworthy was that non-B infections involved in MTCs were more commonly found in natives (n = 47) than in migrants (n = 4). Factors such as Italian origin, being men who have sex with men (MSM), younger age, more recent diagnosis and a higher CD4 count were significantly associated with MTCs. Our findings show that HIV-1 clustering transmission among newly diagnosed individuals living in Italy is prevalently driven by natives, mainly MSM, with a more recent diagnosis and frequently infected with HIV-1 non-B subtypes. These results can contribute to monitoring of the HIV epidemic and guiding the public health response to prevent new HIV infections.

A Recent Human Immunodeficiency Virus Outbreak Among People Who Inject Drugs in Munich, Germany, Is Associated With Consumption of Synthetic Cathinones

Background

Needle and syringe sharing among people who inject drugs (PWID) can result in a rapid regional spread of a human immunodeficiency virus (HIV) variant. Such outbreaks have been identified recently in several countries and have raised public health attention because of an association with new psychoactive substances (NPS).

Methods

Dried serum spots from approximately 60% of newly diagnosed HIV cases in Germany in 2013–2018 were received together with statutory notification data. Samples were sequenced in the pol-region, genotyped, and viral phylogenies were analyzed. For selected samples, the hepatitis C virus (HCV) status and the presence of NPS were determined.

Results

An outbreak of closely related 27 subtype C infections with a core of 11 cases with almost identical sequences was identified using phylogenetic analyses. The first case of the outbreak was diagnosed in 2015, and the last one was in 2018. With exception of 3 infections, all were reported from Munich, the capital of the federal state of Bavaria. Of 26 analyzed outbreak members, 24 (92.3%) had a resolved or viremic HCV coinfection. In 8 of 18 (44%) cases, α-pyrrolidinopentiothiophenone and/or the related substance α-pyrrolidinoheptiophenone was identified.

Conclusions

Despite harm reduction services in place, HIV outbreaks of considerable size can occur in PWID. The establishment of a real-time molecular surveillance is advised to rapidly identify outbreaks and target prevention measures.

GENETIC ANALYSIS OF HIV-1 IN THE ALTAI KRAY: THE FURTHER SPREAD OF THE CRF63_02A1 VARIANT IN WESTERN SIBERIA

IThe aim of this study was to characterize HIV-1 genetic strains currently circulating in Altay Kray (Western Siberia) and to analyze the HIV resistance on this territory.

Materials and methods. Blood samples were collected, with informed consent, in 2017 from 82 HIV infected persons living in Altai Kray. Sequences of pol gene fragments coding protease and part of reverse transcriptase were obtained by in house system and Sanger sequencing. Genotyping, phylogenetic and recombinant analyses were carried out by HIVdbProgram: Sequence Analysis, COMET HIV-1, REGA HIV-1 Subtyping Tool (V 3.0), MEGA 5.05, RIP and jpHMM.

Results and discussion. The results of genotype analysis revealed that the circulating recombinant form CRF63_02A1 dominated in Altay Kray (61%), subtype А was identified in 33%, the remaining subtypes, such as B, G, URF, accounted for 6%. According to phylogenetic analysis results, CRF63_02A1 sequences formed the common branch with nucleotide sequences of strains found in other regions of Siberia and Far East. All of HIV-1 variants belonging to subtype A clustered together with nucleotide sequences of A6 dominating in Russia. RIP analysis allowed to identify three unique recombinant forms (URFs), formed by CRF63_02A1 and A6. Drug resistance mutations were identified in 8 of 21 ART patients (8/21, 38%). The prevalence of drug resistance mutations in naïve patients equaled to 5,1%.

 Conclusion. Currently, the process of changing the dominant strain to CRF63_02A1 is ongoing in the Altai Kray, where 13 years ago the main variant was HIV sub-subtype A6 (IDU-A).

COVID-19 in people living with human immunodeficiency virus: a case series of 33 patients

Introduction

Data on people living with human immunodeficiency virus (PLWH) in the current SARS-CoV-2 pandemic are still scarce. This case series of 33 PLWH patients with COVID-19 reveals symptoms and outcome in this special population.

Methods

Retrospective analysis of anonymized data including age, gender, HIV-associated parameters, symptoms, and outcome.

Results

Three out of 32 patients with documented outcomes died (9%). 91% of the patients recovered and 76% have been classified as mild cases. All patients were on antiretroviral treatment, of them 22 on tenofovir-containing regimen and 4 on the protease inhibitor darunavir.

Conclusions

This preliminary case series does not support excess morbidity and mortality among symptomatic COVID-19 PLWH and with viral suppression on ART. SARS-CoV-2 infections may occur during boosted darunavir-based and/or on tenofovir-containing ART.

Characterization of HIV-1 subtypes and drug resistance mutations in Henan Province, China (2017-2019)

Human immunodeficiency virus type 1 (HIV-1) infection remains a severe public health problem worldwide. In this study, we investigated the distribution of HIV-1 subtypes and the prevalence of drug resistance mutations (DRMs) among patients with HIV-1 infection in Henan Province, China. HIV-1 strains in blood samples taken from inpatients and outpatients visiting the Sixth People’s Hospital of Zhengzhou from August 2017 to July 2019 with a viral load (VL) greater than 1000 copies/ml were subjected to subtype and DRMs analysis. Out of a total of 769 samples, subtype and DRM data were obtained from 657 (85.43%) samples. Phylogenetic analysis based on partial pol gene sequences indicated that the most commonly found genotype was subtype B (45.51%, 299/657), followed by CRF01_AE (28.61%, 188/657), CRF07_BC (15.68%, 103/657), CRF08_BC (0.76%, 5/657), C (0.61%, 4/657), A (0.30%, 2/657), and others (8.52%, 56/657). Circulating recombinant forms (CRFs) were most commonly found in patients who were naïve to antiretroviral treatment (ART) (68.67%, 160/233). The percentage of patients with one or more major drug-resistance mutations was 50.99% (335/657), and it was 6.44% (15/233) in ART-naive patients that were primarily infected with subtype B (17.74%). Resistance mutations were most common at codons 65, 103, 106, 184, and 190 of the reverse transcriptase gene and codon 46 of the protease gene. Our study provides detailed information about the distribution of HIV-1 subtypes and the incidence of drug resistance mutations of different subtypes in ART-experienced and naïve patients. This can guide policymakers in making decisions about treatment strategies against HIV-1.

Transmitted HIV drug resistance among individuals with newly diagnosed HIV infection: a multicenter observational study

OBJECTIVES

Fifteen years after the roll-out of antiretroviral treatment (ART) in China, there is limited information available on transmitted HIV drug resistance (TDR). This study aimed to characterize the epidemiology of TDR in China.

DESIGN

We conducted a prospective cross-sectional observational study.

METHODS

We analyzed the demographic, clinical, and virological data of individuals with newly diagnosed HIV infection using data from the Beijing HIV laboratory network collected between 2001 and 2017. We did population-based sequencing of the pol gene on plasma specimens and identified TDR mutations using the WHO list for surveillance of TDR mutations.

RESULTS

Data on TDR were available for 91% of the 10 115 individuals with newly diagnosed HIV infection tested, of whom 19.2% were from rural areas. The overall prevalence of TDR was 4.1% [95% confidence interval (CI): 3.7-4.5%], with a declining trend over the period 2001-2017. In the multivariable analysis, the risk of TDR differed significantly according to sex [odds ratio (OR) for women vs. men: 0.41, 95% CI: 0.22-0.69, P = 0.002]; infection type (OR for CRF07_BC vs. CRF01_AE: 0.24, 95% CI: 0.16-0.36, P < 0.001); and sampling period (OR for 2009-2012 vs. 2001-2008: 0.57, 95% CI: 0.41-0.79; P = 0.01), and was significantly higher among individuals from Hebei province than in those from Beijing (OR: 1.43, 95% CI: 1.05-1.96; P = 0.02).

CONCLUSION

In China, the prevalence of TDR among individuals with newly diagnosed HIV infection is relatively low. Trends in TDR should be assessed in other countries with a high TDR burden.

Establishment of an anti-hepatitis C virus IgG avidity test for dried serum/plasma spots

Monitoring recency of infection helps to identify current transmission in vulnerable populations for effective disease control. We have established an in-house avidity based hepatitis C virus (HCV) recency assay based on the Monolisa Anti-HCV PLUS Version 3 ELISA kit for use of dried serum/plasma spots (DS/PS) in order to distinguish recent and long-term infections. A first panel of DS/PS (n = 218; genotype 1 n = 170 and non-genotype 1 n = 48) consisting of primary and at least one follow up sample was used to analyze the temporal changes of the Avidity Index (AI) over time. Sub-panels of longitudinal DS/PS (n = 66) and acute cases (<26 weeks; n = 34) were taken to calculate the Mean Duration of Recent Infection (MDRI) and the False Long-term Rate (FLTR), respectively. A second panel of DS/PS >104 weeks (n = 132) and a third panel of DS/PS prepared from resolved infections (≥180 days since last positive; n = 32) were used to calculate the False Recent Rate (FRR). For all genotypes, the optimal AI cut-off was determined to be 40% resulting in an MDRI of 364 days (95% CI: 223-485). FLTR was 5.9% (95% CI: 0.7-19.7), 8.3% (95% CI: 1-27), and 0% (-) and FRR was 13.6% (95% CI: 8.3-20.7), 11.7% (95% CI: 6.6-19), and 30.6% (95% CI: 9.1-61.4) for all genotypes, genotype 1, and non-genotype 1 infections, respectively. For resolved infections, the FRR was 53.1% (95% CI: 35.8-70.4). Thus, this assay performs particularly well for genotype 1 reaching a high rate of correct discriminations between infections acquired less than a year before diagnosis and those acquired earlier by applying an AI cut-off of 40%. Due to a rapid decline in avidity post resolution of an HCV infection this assay is not recommended to be used in HCV RNA negative patients.

HIV-1 subtype diversity, drug resistance, and genetic transmission networks in men who have sex with men with virologic failure in antiretroviral therapy in Sichuan, China, 2011 to 2017

This study sought to examine the human immunodeficiency virus type 1 (HIV-1) genetic diversity on drug resistance among men who have sex with men (MSM) with virologic failure in antiretroviral therapy (ART), and investigate linking-associated factors for genetic transmission networks.Seven hundred and thirty-four HIV-positive MSM with virologic failure in ART were recruited into our study from 2011 to 2017. HIV-1 pol gene sequences were used for phylogenetic and genotypic drug resistance analyses. The drug resistance mutations were determined using the Stanford University HIV Drug Resistance Database. The genetic transmission networks were analyzed for CRF01_AE and CRF07_BC sequences by the genetic distance-based method.Of 734 subjects, 372 (50.68%) showed drug resistance, in which CRF01_AE and CRF07_BC were the predominating subtypes. Drug resistance more frequently occurred in non-nucleoside reverse transcriptase inhibitors (NNRTIs) treatment (48.64%), and followed by nucleoside reverse transcriptase inhibitors (NRTIs) (36.51%) and PIs (4.03%). The most common drug resistance-associated mutations in protease inhibitors (PIs), NRTIs and NNRTIs were K20I/R, M184V/I and K103N/KN, respectively. For 283CRF01_AE sequences, 64 (22.61%) fell into clusters at a genetic distance of 0.011, resulting in 17 clusters ranging in size from 2 to 16 individuals. For 230 CRF07_BC sequences, 66 (28.69%) were connected to at least one other sequence with 0.005 genetic distances, resulting in 8 clusters ranging in size from 2 to 52 individuals. Individuals who showed drug resistance to ART were less likely to fall into clusters than those who did not. The genetic linkage was robust by the exclusion of sites associated with drug resistance.CRF01_AE and CRF07_BC were the main strains among MSM with virologic failure in ART, and the drug resistance more frequently occurred in NNRTIs, followed by NRTIs and PIs. Genetic transmission networks revealed a complexity of transmission pattern, suggesting early-diagnosis and in-time intervention among MSM.

Surveillance of transmitted HIV drug resistance among newly diagnosed, treatment-naive individuals at a county HIV clinic in Santa Clara County

Introduction

To our knowledge, HIV transmitted drug resistance (TDR) patterns have not been characterized specifically in Santa Clara County (SCC), California, one of the largest counties by population in the United States. Understanding TDR here will help improve antiretroviral therapy outcomes and prevent future transmission events.

Material and methods

This is a retrospective analysis of TDR among patients establishing care at a county HIV clinic at the Santa Clara Valley Health and Hospital System. We identified 206 treatment-naive individuals who were newly diagnosed with HIV between 2006-2013. Using these individuals, we assessed the prevalence and temporal trends of total TDR and TDR to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase strand transfer inhibitors (INSTIs).

Results

We identified a total TDR prevalence of 17.5% during 2006–2013 (7.3% NNRTI, 6.8% NRTI, 2.4% PI, 2.9% INSTI) with 1.9% exhibiting dual-class resistance. Total TDR prevalence initially ranged between 19.0-22.7% during 2006–2008 and decreased to within 10.5–16.2% during 2011–2013, though this decrease was not significant (p = 0.42). NRTI TDR decreased from 22.7% in 2006 to 5.3% in 2013 (p = 0.02), and NNRTI TDR appeared to fluctuate between 2.7-13.5% (p = 0.96). PI and INSTI TDR remained low, with noted E138A prevalence of 2.9%.

Conclusions

The prevalence of TDR was substantial among newly diagnosed, treatment-naive individuals establishing care at a SCC-based county HIV clinic from 2006 to 2013. This, along with the presence of transmitted mutations associated with INSTI resistance, warrants continued surveillance of TDR in SCC and use of baseline genotyping prior to antiretroviral therapy initiation.

Evaluation of a BioRad Avidity assay for identification of recent HIV-1 infections using dried serum or plasma spots

Serological methods to differentiate between recently acquired and established HIV-1 infections are a useful tool in the HIV-surveillance to characterize the epidemic, identify groups at risk and assess HIV-preventive interventions. Therefore, an avidity-based, modified BioRad Genscreen™ HIV-1/2 assay (BRA_EUR) was evaluated according to the avidity-based, modified BioRad HIV-1/2 Plus O protocol (BRA_USA). Overall, 692 well defined samples (82.5% B and 17.5% non-B subtypes) from recent (<180 days, n = 239), intermediate (181-364 days, n = 35) or long term infections (≥365 days, n = 419) were used to determine a 'mean duration of recent infection' (MDRI), a 'median DRI' (MdDRI), the false recent rate (FRR), and concordance between the BRAs and the Sedia BED HIV-1 Capture enzyme immunoassay (BED). The optimal avidity index cut-off was determined to be 70% resulting in an MDRI of 233 days (95% IQR: 174-351) and an MdDRI of 171 days (95% IQR: 142-212). Concordance with the BRA_USA was high with 96.4%. The FRR of 6.0% as well as the MdDRI are similar to the BED (8.4%; 170 (139-214) days). Therefore, the BRA_EUR is a suitable alternative to replace the BED and trend analysis will be feasible after minimal adjustments for the MdDRI and the MDRI.