MOLECULAR VIROLOGICAL ANALYSIS OF THE TRANSMISSION CLUSTERS AND RESISTANCE MUTATIONS OF HIV-1 SUBTYPE B IN BULGARIA (2012-2020)

HIV-1 infection in Bulgaria is known for its high level of genetic diversity. Previous studies have indicated that subtype B is the most common strain in Bulgaria, particularly among men who have sex with men, who are at a high risk of transmission. The primary objective of this study was to identify any transmission clusters and transmission resistance in individuals newly diagnosed with HIV-1 who have not yet received antiretroviral therapy (ART). To this end, we sequenced the HIV-1 pol gene in the samples from the study participants using either the Viroseq HIV-1 Genotyping Test (Abbott) and the Applied Biosystems 3130xl genetic analyzer or the TruGene DNA Sequencing System (Siemens Healthcare) and an OpenGene DNA sequencing system. We then subtyped the HIV-1 pol sequences, and further analyzed those that met the criteria for subtype B. The study included a total of 595 HIV-1 subtype B sequences. Our analysis revealed that the majority of those diagnosed with HIV-1 subtype B were male and lived in Sofia region. The most common transmission mode was through sexual intercourse among men who have sex with men, followed by heterosexual transmission. We also observed the presence of multiple transmission clusters , and a low percentage of transmitted drug resistance mutations (TDRMs). Overall, our study confirms that HIV-1 subtype B remains the most dominant strain in Bulgaria

Dynamic of SARS-CoV-2 spread in Bulgaria, 2020-2022

The COVID-19 pandemic is associated with high morbidity and significant mortality worldwide. The objective of this study was to track the circulation pattern of SARS-CoV-2 in Bulgaria over three consecutive years (2020-2022) and to analyze the involvement of SARS-CoV-2 in cases of co-infections. A total of 98 247 clinical samples were tested for SARS-CoV-2 using a Real-Time RT-PCR method and 25.2% of them were positive. The positive rate for SARS-CoV-2 was greater among hospitalized patients compared to outpatients (p<0.05). Approximately 48.3% of all SARS-CoV-2-positive cases were male and 51.7% were female (p<0.05). SARS-CoV-2 positivity was highest in the group of oldest adults (≥65 years) (average 40.6%), and lowest in the group of youngest children (0-5 years) (average 9.4%). Several peaks in the spread of SARS-CoV-2 infections were observed. Among the 1 463 SARS-CoV-2 positive clinical samples examined for the presence of other respiratory viruses, 109 (7.5%) cases of co-infections were found. The greatest variety of co-infections with SARS-CoV-2 and other respiratory viruses was detected during the Omicron wave. Surveillance of SARS-CoV-2 is important to continue in the future in order not to miss the emergence of new genetic variants with increased infectivity, virulence or immune escape

insights from a bio-behavioural survey in thirteen cities

Publisher Copyright: © 2020 Author(s) (or their employer(s)). No commercial re-use. See rights and permissions. Published by BMJ.Objectives: This paper aims to estimate the percentage of European men who have sex with men (MSM) who may benefit from pre-exposure prophylaxis (PrEP), applying the three most widely used HIV risk indices for MSM (MSM Risk Index, Menza score, San Diego Early Test (SDET) score) and drawing on a large-scale multisite bio-behavioural survey (Sialon II). Methods: The Sialon II study was a bio-behavioural survey among MSM implemented in 13 European cities using either time-location sampling or respondent-driven sampling. Biological and behavioural data from 4901 MSM were collected. Onlybehavioural data of HIV-negative individuals were considered. Three widely used risk indices to assess HIV acquisition risk among MSM were used to estimate individual HIV risk scores and PrEP eligibility criteria. Results: 4219 HIV-negative MSM were considered. Regardless the HIV risk score used and the city, percentages of MSM eligible for PrEP were found to range between 5.19% and 73.84%. Overall, the MSM Risk Index and the Menza score yielded broadly similar percentages, whereas the SDETIndex provided estimates constantly lower across all cities. Although all the three scores correlated positively (r>0.6), their concordance was highly variable (0.01<CCC<0.62). Conclusion: Our findings showed the impact of different scoring systems on the estimation of the percentage of MSM who may benefit from PrEP in European cities. Although our primary aim was not to compare the performance of different HIV risk scores, data show that a considerable percentage of MSM in each city should be offered PrEP in order to reduce HIV infections. As PrEP is highly effective at preventing HIV among MSM, our findings provide useful, practical guidance for stakeholders in implementingPrEP at city level to tackle HIV infections in Europe.publishersversionpublishe

Quantifying unmet prevention needs among MSM in Europe through a multi-site bio-behavioural survey

Introduction: The HIV epidemic represents an important public health issue in Europe particularly among men who have sex with men (MSM). Global AIDS Monitoring indicators (GAM) have been widely and jointly promoted as a set of crucial standardised items to be adopted for monitoring and responding to the epidemic. Methods: The Sialon II study, implemented in 13 European cities (2013-14), was a complex multicentre integrated bio-behavioural cross sectional survey targeted at MSM, with a concomitant collection of behavioural and biological (oral fluid or blood specimens) data. Rigorous sampling approaches for hard-to-reach populations were used (time-location sampling and respondent-driven sampling) and GAM indicators were calculated; sampling frames were adapted to allow weighted estimates of GAM indicators. Results: 4,901 MSM were enrolled. HIV prevalence estimates ranged from 2.4% in Stockholm to 18.0% in Bucharest. When exploring city-level correlations between GAM indicators, prevention campaigns significantly correlated with levels of condom use and level of HIV testing among MSM. Conclusion: The Sialon II project has made an important contribution to the monitoring and evaluation of the HIV epidemic across Europe, integrating the use of GAM indicators within a second generation HIV surveillance systems approach and in participatory collaboration with MSM communities. It influenced the harmonisation of European data collection procedures and indicators via GAM country reporting and contributed essential knowledge informing the development and implementation of strategic, evidence-based HIV prevention campaigns for MSM.publishersversionpublishe

Earlier initiation of antiretroviral treatment coincides with an initial control of the HIV-1 sub-subtype F1 outbreak among men-having-sex-with-men in Flanders, Belgium

Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59-74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23-12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0-75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000-2004) and birth-death models suggested that its extensive growth had been controlled (Re < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention.publishersversionpublishe

Quantifying Unmet Prevention Needs Among MSM in Europe Through a Multi-site Bio-behavioural Survey

The HIV epidemic represents an important public health issue in Europe particularly among men who have sex with men (MSM). Global AIDS Monitoring indicators (GAM) have been widely and jointly promoted as a set of crucial standardised items to be adopted for monitoring and responding to the epidemic. Methods: The Sialon II study, implemented in 13 European cities (2013-14), was a complex multicentre integrated bio-behavioural cross-sectional survey targeted at MSM, with a concomitant collection of behavioural and biological (oral fluid or blood specimens) data. Rigorous sampling approaches for hard-to-reach populations were used (time-location sampling and respondent-driven sampling) and GAM indicators were calculated; sampling frames were adapted to allow weighted estimates of GAM indicators. Results: 4,901 MSM were enrolled. HIV prevalence estimates ranged from 2.4% in Stockholm to 18.0% in Bucharest. When exploring city-level correlations between GAM indicators, prevention campaigns significantly correlated with levels of condom use and level of HIV testing among MSM. Conclusion: The Sialon II project has made an important contribution to the monitoring and evaluation of the HIV epidemic across Europe, integrating the use of GAM indicators within a second generation HIV surveillance systems approach and in participatory collaboration with MSM communities. It influenced the harmonisation of European data collection procedures and indicators via GAM country reporting and contributed essential knowledge informing the development and implementation of strategic, evidence-based HIV prevention campaigns for MSM

Quantifying unmet prevention needs among MSM in Europe through a multi-site bio-behavioural survey

Introduction The HIV epidemic represents an important public health issue in Europe particularly among men who have sex with men (MSM). Global AIDS Monitoring indicators (GAM) have been widely and jointly promoted as a set of crucial standardised items to be adopted for monitoring and responding to the epidemic. Methods The Sialon II study, implemented in 13 European cities (2013-14), was a complex multi-centre integrated bio-behavioural cross-sectional survey targeted at MSM, with a concomitant collection of behavioural and biological (oral fluid or blood specimens) data. Rigorous sampling approaches for hard-to-reach populations were used (time-location sampling and respondent-driven sampling) and GAM indicators were calculated; sampling frames were adapted to allow weighted estimates of GAM indicators. Results 4,901 MSM were enrolled. HIV prevalence estimates ranged from 2.4% in Stockholm to 18.0% in Bucharest. When exploring city-level correlations between GAM indicators, prevention campaigns significantly correlated with levels of condom use and level of HIV testing among MSM. Conclusion The Sialon II project has made an important contribution to the monitoring and evaluation of the HIV epidemic across Europe, integrating the use of GAM indicators within a second generation HIV surveillance systems approach and in participatory collaboration with MSM communities. It influenced the harmonisation of European data collection procedures and indicators via GAM country reporting and contributed essential knowledge informing the development and implementation of strategic, evidence-based HIV prevention campaigns for MSM.Peer Reviewe

Global disparities in SARS-CoV-2 genomic surveillance

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity

Global disparities in SARS-CoV-2 genomic surveillance

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity