Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria

HIV-1 subtype B is the predominant strain in Bulgaria, yet little is known about the molecular epidemiology of these infections, including its origin and transmissibility. We used a phylodynamics approach by combining and analyzing 663 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1988–2018 and associated epidemiologic data to better understand this sub-epidemic in Bulgaria. Using network analyses at a 1.5% genetic distance threshold (d) we found several large phylogenetic clusters composed mostly of men who have sex with men (MSM) and male heterosexuals (HET). However, at d = 0.5%, used to identify more recent transmission, the largest clusters dissociated to become smaller in size. The majority of female HET and persons with other transmission risks were singletons or pairs in the network. Phylogenetic analysis of the Bulgarian pol sequences with publicly available global sequences showed that subtype B was likely introduced into Bulgaria from multiple countries, including Israel and several European countries. Our findings indicate that subtype B was introduced into Bulgaria multiple times since 1988 and then infections rapidly spread among MSM and non-disclosed MSM. These high-risk behaviors continue to spread subtype B infection in Bulgaria as evidenced by the large clusters at d = 0.5%. Relatively low levels of antiretroviral drug resistance were observed in our study. Prevention strategies should continue to include increased testing and linkage to care and treatment, as well as expanded outreach to the MSM communities.

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Molecular epidemiology of HIV-1 infection in immigrant population in northern Italy

Epidemiology and Infection ◽

10.1017/s0950268819002012 ◽

2020 ◽

Vol 148 ◽

Cited By ~ 3

Author(s):

Caterina Sagnelli ◽

Caterina Uberti-Foppa ◽

Sabrina Bagaglio ◽

Eleonora Cella ◽

Vittoria Scolamacchia ◽

...

Keyword(s):

Phylogenetic Tree ◽

Molecular Epidemiology ◽

Northern Italy ◽

Subtype B ◽

Immunodeficiency Virus ◽

Male Patients ◽

Sub Saharan ◽

Sex With Men ◽

Cd4 Cell ◽

Hiv 1

Abstract Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.

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Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria

Viruses ◽

10.3390/v13010116 ◽

2021 ◽

Vol 13 (1) ◽

pp. 116

Author(s):

Ivailo Alexiev ◽

Ellsworth M. Campbell ◽

Sergey Knyazev ◽

Yi Pan ◽

Lyubomira Grigorova ◽

...

Keyword(s):

Risk Groups ◽

Asian Countries ◽

Persons Who Inject Drugs ◽

Distance Threshold ◽

Epidemiological Analysis ◽

Network Analyses ◽

Recent Transmission ◽

Large Clusters ◽

Predominant Strain ◽

Hiv 1

HIV-1 subtype CRF01_AE is the second most predominant strain in Bulgaria, yet little is known about the molecular epidemiology of its origin and transmissibility. We used a phylodynamics approach to better understand this sub-epidemic by analyzing 270 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1995 and 2019. Using network analyses at a 1.5% genetic distance threshold (d), we found a large 154-member outbreak cluster composed mostly of persons who inject drugs (PWID) that were predominantly men. At d = 0.5%, which was used to identify more recent transmission, the large cluster dissociated into three clusters of 18, 12, and 7 members, respectively, five dyads, and 107 singletons. Phylogenetic analysis of the Bulgarian sequences with publicly available global sequences showed that CRF01_AE likely originated from multiple Asian countries, with Vietnam as the likely source of the outbreak cluster between 1988 and 1990. Our findings indicate that CRF01_AE was introduced into Bulgaria multiple times since 1988, and infections then rapidly spread among PWID locally with bridging to other risk groups and countries. CRF01_AE continues to spread in Bulgaria as evidenced by the more recent large clusters identified at d = 0.5%, highlighting the importance of public health prevention efforts in the PWID communities.

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022 A heterosexual outbreak in Doncaster involving subtype B of HIV-1: molecular epidemiology as a supplement to contact tracing

HIV Medicine ◽

10.1046/j.1468-1293.2000.00024-43.x ◽

2000 ◽

Vol 1 (3) ◽

pp. 172-172

Author(s):

A Hayman ◽

T Moss ◽

C Arnold ◽

l Naylor-Adamson ◽

J Hawkswell ◽

...

Keyword(s):

Molecular Epidemiology ◽

Contact Tracing ◽

Subtype B ◽

Hiv 1

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Identification of an HIV-1 and Neurosyphilis Cluster in Vermont

Clinical Infectious Diseases ◽

10.1093/cid/ciaa1834 ◽

2020 ◽

Author(s):

Devika Singh ◽

William M Switzer ◽

Roy Belcher ◽

Daniel Daltry ◽

Jennifer S Read

Keyword(s):

Newly Diagnosed ◽

Viral Loads ◽

Network Analyses ◽

Intervention Specialists ◽

Cell Counts ◽

Cd4 Cell Counts ◽

Sex With Men ◽

Cd4 Cell ◽

Hiv 1 ◽

Sexual Networking

Abstract Background Rates of syphilis in the U.S. have more than doubled over the last several decades, largely among men who have sex with men (MSM). Our study characterizes a cluster of neurosyphilis cases among HIV-1-infected individuals in Vermont in 2017-2018. Methods Vermont Department of Health disease intervention specialists conduct interviews with all newly diagnosed HIV-1 cases and pursued sexual networking analyses. Phylogenetic and network analyses of available Vermont HIV-1 polymerase (pol) sequences identified clusters of infection. Fishers-exact and independent t-tests were used to compare HIV-1-infected individuals within or outside an identified cluster. Results Between January 1, 2017 and December 31, 2018, 38 Vermont residents were newly diagnosed with HIV-1 infection. The mean age was 35.5 years, 79% were male and 82% were white. Risk factors for HIV-1 acquisition included MSM status (79%) and methamphetamine use (21%). Eighteen cases (49%) had HIV-1 viral loads (VLs) >100,000 copies/mL and 47% had CD4 cell counts <200/mm 3. Eleven of the 38 (29%) cases had positive syphilis serology, including four (36%) with neurosyphilis. Sexual networking analysis revealed a ten-person cluster with higher VLs at diagnosis (90% with VLs > 100,000 copies/mL vs. 33%, p=0.015). Phylogenetic analysis of pol sequences showed a cluster of 14 cases with sequences that shared 98-100% HIV-1 nucleotide identity. Conclusions This investigation of newly infected HIV-1 cases in Vermont led to identification of a cluster that appeared more likely to have advanced HIV-1 disease and neurosyphilis. Identification of a cluster was strongly supported by both phylogenetic and network analyses of HIV-1 pol sequences.

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New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men Who Have Sex With Men

JAIDS Journal of Acquired Immune Deficiency Syndromes ◽

10.1097/qai.0000000000002076 ◽

2019 ◽

Vol 81 (5) ◽

pp. 578-584 ◽

Cited By ~ 1

Author(s):

Erik Billings ◽

Gustavo H. Kijak ◽

Eric Sanders-Buell ◽

Nicaise Ndembi ◽

Anne Marie OʼSullivan ◽

...

Keyword(s):

Sub Saharan Africa ◽

Subtype B ◽

Nigerian Men ◽

Sub Saharan ◽

Sex With Men ◽

Hiv 1

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Molecular Epidemiology of HIV-1 Infected Migrants Followed Up in Portugal: Trends between 2001–2017

Viruses ◽

10.3390/v12030268 ◽

2020 ◽

Vol 12 (3) ◽

pp. 268 ◽

Cited By ~ 2

Author(s):

Victor Pimentel ◽

Marta Pingarilho ◽

Daniela Alves ◽

Isabel Diogo ◽

Sandra Fernandes ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Molecular Epidemiology ◽

Nucleoside Reverse Transcriptase Inhibitor ◽

Country Of Origin ◽

Transcriptase Inhibitor ◽

Subtype B ◽

Reverse Transcriptase Inhibitor ◽

Hiv 1 ◽

Over Time

Migration is associated with HIV-1 vulnerability. Objectives: To identify long-term trends in HIV-1 molecular epidemiology and antiretroviral drug resistance (ARV) among migrants followed up in Portugal Methods: 5177 patients were included between 2001 and 2017. Rega, Scuel, Comet, and jPHMM algorithms were used for subtyping. Transmitted drug resistance (TDR) and Acquired drug resistance (ADR) were defined as the presence of surveillance drug resistance mutations (SDRMs) and as mutations of the IAS-USA 2015 algorithm, respectively. Statistical analyses were performed. Results: HIV-1 subtypes infecting migrants were consistent with the ones prevailing in their countries of origin. Over time, overall TDR significantly increased and specifically for Non-nucleoside reverse transcriptase inhibitor (NNRTIs) and Nucleoside reverse transcriptase inhibitor (NRTIs). TDR was higher in patients from Mozambique. Country of origin Mozambique and subtype B were independently associated with TDR. Overall, ADR significantly decreased over time and specifically for NRTIs and Protease Inhibitors (PIs). Age, subtype B, and viral load were independently associated with ADR. Conclusions: HIV-1 molecular epidemiology in migrants suggests high levels of connectivity with their country of origin. The increasing levels of TDR in migrants could indicate an increase also in their countries of origin, where more efficient surveillance should occur.

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1280. Geospatial Spread of HIV in the Cologne-Bonn Region, Germany: From 2001 to 2016

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.1113 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S390-S390

Author(s):

Melanie Stecher ◽

Martin Hoenigl ◽

Anna-Maria Eis-Huebinger ◽

Clara Lehmann ◽

Gerd Fätkenheuer ◽

...

Keyword(s):

Gene Flow ◽

Hiv Transmission ◽

Viral Gene ◽

Network Analyses ◽

Hiv Intervention ◽

Subtype B ◽

Geospatial Analyses ◽

The Impact ◽

Zip Code ◽

Hiv 1

Abstract Background Geographical targeting of interventions of hotspots of HIV transmission increases the impact of HIV intervention. We combined molecular epidemiology and geospatial analyses to provide insights into the drivers of HIV transmission and the contribution of geographical hot spots to the rapidly evolving local HIV epidemic of Cologne-Bonn. Methods We included 714 HIV-1-infected ART naïve individuals, followed at the University Hospitals Cologne and Bonn between 2001 and 2016. Phylogenetic and network analyses were performed to infer putative relationships. Assortativity index (AI, i.e., shared attributes) and characteristics of genetically linked individuals were analyzed. The geospatial diffusion of the local epidemic (i.e., viral gene flow) was evaluated using a Slatkin-Maddison approach. Geospatial dispersal of local HIV transmission was determined by calculating the average distance between genetically linked individuals (centroids of 3-digit zip code of residency, ArcGIS®). Results Of 714 sequences, 217 (30.4%) had a putative linkage with at least one other sequence, forming 77 clusters (size range: 2–8). Genetically linked individuals were significantly more likely to live in suburban areas (P = 0.035), <30 years of age (P = 0.013), infected with HIV-1 subtype B (P = 0.002). AI for concurrent area of residency showed that individuals were nonassortative in the network (−0.0026, P = 0.046), indicating that clustering individuals tended to cluster with individuals living in a different zip code. Geospatial analyses revealed that the median distance between genetically linked individuals was 23.4 km, significantly lower than expected (median 39.68 km; P < 0.001) (Figure 1A). Slatkin Maddison analyses revealed increased gene flow originating from Central Cologne toward the surrounding areas (P < 0.001, Figure 1B). Conclusion Phylogeographic analysis suggests that central Cologne may be a significant driver of the regional epidemic. While clustering individuals lived closer than unlinked individuals, they were less likely to be linked to others from their same zip code. This may reflect individuals reaching out of their neighborhoods and social circles to meet new partners. Disclosures All authors: No reported disclosures.

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