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Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

ABSTRACT: We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.

SUBMITTER: Patino-Galindo JA

PROVIDER: S-EPMC5289541 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

Patiño-Galindo Juan Ángel JÁ Torres-Puente Manoli M Bracho María Alma MA Alastrué Ignacio I Juan Amparo A Navarro David D Galindo María José MJ Gimeno Concepción C Ortega Enrique E González-Candelas Fernando F

PloS one 20170202 2

We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). T ...[more]

PMID: 28152089

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Project description:ImportanceLimited information on the transmission and dynamics of SARS-CoV-2 at the city scale is available.ObjectiveTo describe the local spread of SARS-CoV-2 in Valencia, Spain.Design, setting, and participantsThis single-center epidemiological cohort study of patients with SARS-CoV-2 was performed at University General Hospital in Valencia (population in the hospital catchment area, 364 000), a tertiary hospital. The study included all consecutive patients with COVID-19 isolated at home from the start of the COVID-19 pandemic on February 19 until August 31, 2020.ExposuresCases of SARS-CoV-2 infection confirmed by the presence of IgM antibodies or a positive polymerase chain reaction test result on a nasopharyngeal swab were included. Cases in which patients with negative laboratory results met diagnostic and clinical criteria were also included.Main outcomes and measuresThe primary outcome was the characterization of dissemination patterns and connections among the 20 neighborhoods of Valencia during the outbreak. To recreate the transmission network, the inbound and outbound connections were studied for each region, and the relative risk of infection was estimated.ResultsIn total, 2646 patients were included in the analysis. The mean (SD) age was 45.3 (22.5) years; 1203 (46%) were male and 1442 (54%) were female (data were missing for 1); and the overall mortality was 3.7%. The incidence of SARS-CoV-2 cases was higher in neighborhoods with higher household income (β2 [for mean income per household] = 0.197; 95% CI, 0.057-0.351) and greater population density (β1 [inhabitants per km2] = 0.228; 95% CI, 0.085-0.387). Correlations with meteorological variables were not statistically significant. Neighborhood 3, where the hospital and testing facility were located, had the most outbound connections (14). A large residential complex close to the city (neighborhood 20) had the fewest connections (0 outbound and 2 inbound). Five geographically unconnected neighborhoods were of strategic importance in disrupting the transmission network.Conclusions and relevanceThis study of local dissemination of SARS-COV-2 revealed nonevident transmission patterns between geographically unconnected areas. The results suggest that tailor-made containment measures could reduce transmission and that hospitals, including testing facilities, play a crucial role in disease transmission. Consequently, the local dynamics of SARS-CoV-2 spread might inform the strategic lockdown of specific neighborhoods to stop the contagion and avoid a citywide lockdown.

Project description:BackgroundTowards the end of the 20th century, transfusion-transmitted viral infections (TTVI) represented a huge problem for public health. From the beginning of the screening of blood donations, this risk has decreased to the point that it is no longer possible to measure it directly and it is necessary to use mathematical models. Using one of these models, the aim of this study was to analyse the evolution of the residual risk of hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) transmission through blood transfusion from 2003 to 2017 in the Region of Valencia, Spain.Materials and methodsUsing data from the Blood Transfusion Centre of the Valencian Community, the incidence rate in donors and the residual risk were calculated for each agent and year by applying the most updated version of the incidence/window period model. For the set of the three viruses, these magnitudes were calculated as the algebraic sum of the specifics ones for each of them. The evolution of both magnitudes was analysed by the Mann-Kendall trend test and the Sen estimation of trend slope.ResultsThe residual risks obtained vary depending on the agent and the year. Considering the three viruses jointly, they range from 1 per 360,380 to 1 per 44,715 donations. During the study period, there was a statistically significant downward trend in the incidence rate of HBV (p<0.05, trend slope -0.88), the residual risk of HBV (p<0.0005, slope -0.98), and the joint residual risk for the three viruses (p<0.0001, slope -0.99).DiscussionThe current risk of TTVI is very low in the Region of Valencia. In the last 15 years, there has been a reduction in the donor incidence rate and in the residual risk for the case of HBV; such a reduction cannot be confirmed for HCV and HIV. Consideration of the three viruses jointly confirms a reduction in the residual risk; we are unable to establish whether the evolution of the joint incidence rate has contributed to this reduction or whether it is due only to the shortening of window periods.

Dataset Information

Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

Publications

Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

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