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Enforcing strict protocols that prevent transmission of airborne infections in prisons is challenging. We examine a large severe acute respiratory syndrome coronavirus 2 outbreak in a Catalan penitentiary center in February-April 2021, prior to vaccination deployment. The aim was to describe the evolution of the outbreak using classical and genomic epidemiology and the containment strategy applied. The outbreak was initially detected in 1 module but spread to 4, infecting 7 staff members and 140 incarcerated individuals, 6 of whom were hospitalized (4.4%). Genomic analysis confirmed a single origin (B.1.1.7). Contact tracing identified transmission vectors between modules and prevented further viral spread. In future similar scenarios, the control strategy described here may help limit transmission of airborne infections in correctional settings., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background: Transgender women sex workers (TWSWs) and men sex workers (MSWs) are especially vulnerable to acquiring hepatitis B virus (HBV) infection. We aimed to describe HBV prevalence (hepatitis B surface antigen [HBsAg] and core antibody [HBcAb]) and associated risk factors for HBV exposure (HBcAb), to assess vaccination status and risk factors for no prior vaccination, and to compare HBV prevalence and vaccination status between TWSWs and MSWs., Methods: The SexCohort study was advertised to TWSWs and MSWs through several communication channels. At cohort entry through 2 community-based organizations in Barcelona, the study population was screened for HBV and other sexually transmitted infections, and an epidemiological questionnaire was administered (n = 271)., Results: Overall, 93.0% of participants were migrants, mostly from South and Central American countries. HBsAg prevalence was 1.9% (TWSWs, 2.4%; vs MSWs, 0.9%; P = .42), and previous exposure to HBV was 31.8% (TWSWs, 38.5%; vs MSWs, 20.8%; P = .002). Over 5 years of sex work (adjusted odds ratio [aOR], 9.35), prior exposure to Treponema pallidum (aOR, 3.49), and treatment with anxiolytic drugs (aOR, 3.23) were associated with HBV exposure. Overall, 33.7% of participants exhibited immunity from vaccination (TWSWs, 30.8%; vs MSWs, 38.61%; P < .001), while 34.4% were candidates to HBV vaccination (TWSWs, 30.8%; vs MSWs, 40.6%; P < .001). Never having been on pre-exposure prophylaxis for HIV (odds ratio [OR], 4.23) and non-Spanish origin (OR, 5.00) were associated with no prior HBV vaccination., Conclusions: There is a need to reinforce screening and vaccination programs aimed at TWSWs and MSWs as integrated services offered at the community centers commonly accessed by these populations., Competing Interests: Potential conflicts of interest. The authors have no relevant financial or nonfinancial interests to disclose related to this work., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Background: Countries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants., Materials and Methods: We used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants in Europe over a period of more than 2 years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility  ( Δ β )   between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants., Results: Our model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated Δ β between variants, revealing that: ( i ) Δ β increased progressively from the Alpha to the Omicron variant; ( i i ) Δ β showed a high degree of variability within Omicron variants; ( i i i ) a higher Δ β was associated with a later emergence of the variant within a country; ( i v ) a higher degree of immunization of the population against previous variants was associated with a higher Δ β for the Delta variant; ( v ) larger countries exhibited smaller Δ β ,  suggesting regionally diverse outbreaks within the same country; and finally ( v i ) the model reliably captures the dynamics of competing variants, even in complex scenarios., Conclusion: The use of mathematical models allows for precise and reliable estimation of daily cases of each variant. By quantifying Δ β ,  we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. Additionally, we have shown that the geographical characteristics of a country, as well as the timing of new variant entrances, can explain some of the observed differences in variant substitution dynamics across countries., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 de Rioja, Perramon-Malavez, Alonso, Andrés, Antón, Bordoy, Càmara, Cardona, Català, López, Martí, Martró, Saludes, Prats and Alvarez-Lacalle.)

Hepatitis C virus (HCV) reinfection may hamper HCV elimination in prisons. We aimed to (i) determine the reinfection rate in people treated for HCV in Catalan prisons, (ii) measure reinfection in people entering prisons, and (iii) characterize the molecular epidemiology of HCV in prisons and people who inject drugs (PWID) in the community. Re-HCV was a prospective study in eight prisons (2019-2020) including two groups: (1) people cured with treatment in prison and followed-up every 6 months, and (2) people testing HCV-RNA positive at incarceration. Bio-behavioral data were collected. HCV isolates were sequenced and phylogenetically analyzed with those of PWID in the community. Reinfection follow-up after treatment was achieved in 97 individuals (103.05 person-years). Two reinfections were detected, resulting in an incidence ≤ 10/100 person-years. Among people entering prison, 2% (359/17,732) were viremic, of which 334 (93.0%) were included, and 44 (13.5%) presented with reinfection (84.7% being PWID). Frequently, HCV isolates in prisons and PWID in the community were phylogenetically related. Although HCV reinfection is low after treatment, it is common in people entering Catalan prisons. To maintain a low HCV prevalence in prisons, harm-reduction services and test-and-treat programs for PWID should be strengthened both inside and outside prisons., (© 2023. Springer Nature Limited.)

Objectives: To perform a budget impact analysis of the HepC link test-and-treat strategy in which community health agents offer hepatitis C virus (HCV) testing, diagnosis and treatment to the Pakistani population living in Catalonia compared with the current practice of the Catalan health system (without targeted screening programmes)., Methods: We estimated the population of adult Pakistani migrants registered at the primary care centres in Catalonia by means of the Information System for the Development of Research in Primary Care (n=37 972 in 2019, Barcelona health area). This cohort was followed for a time period of 10 years after HCV diagnosis (2019-2028). The statistical significance of the differences observed in the anti-HCV positivity rate between screened and non-screened was confirmed (α=0.05). The budget impact was calculated from the perspective of the Catalan Department of Health. Sensitivity analyses included different levels of participation in HepC link : pessimistic, optimistic and maximum., Results: The HepC link scenario screened a higher percentage of individuals (69.8%) compared with the current scenario of HCV care (39.7%). Viraemia was lower in the HepC link scenario compared with the current scenario (1.7% vs 2.5%, respectively). The budget impact of the HepC link scenario was €884 244.42 in 10 years., Conclusions: Scaling up the HepC link strategy to the whole Catalan territory infers a high budget impact for the Department of Health and allows increasing the detection of viraemia (+17.8%) among Pakistani migrants ≥18 years. To achieve a sustainable elimination of HCV by improving screening and treatment rates, there is room for improvement at two levels. First, taking advantage of the fact that 68.08% of the Pakistani population had visited their primary care physicians to reinforce targeted screening in primary care. Second, to use HepC link at the community level to reach individuals with reluctance to use healthcare services., Competing Interests: Competing interests: EM received lecture fees from Gilead Sciences and Abbvie, and research grants from Gilead Sciences. VS received travel sponsorship to attend scientific meetings from Gilead Sciences. MB received fees and research grants from Abbvie, Janssen and Gilead Sciences. The rest of authors have no conflict to declare., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Dried blood spots (DBS) are a reliable tool to diagnose viremic hepatitis C virus (HCV) infection. We evaluated the clinical performance of a DBS-based molecular assay for the assessment of cure and reinfection after on-site treatment at a harm reduction center (HRC). Genotyping from DBS samples was also assessed to discriminate reinfection from treatment failure. People who inject drugs (PWID) from an ongoing test-and-treat pilot at the largest HRC in Barcelona were included in the study. HCV-RNA detection from DBS collected after treatment (with follow-up at 12, 36, and 60 weeks) was compared with a molecular point-of-care test using finger-stick blood (GeneXpert). Baseline and follow-up DBS samples were genotyped by NS5B sequencing or commercial real-time PCR. Among treated patients, 193 follow-up DBS samples were tested. The DBS-based assay showed 100% specificity (129/129), and sensitivity ranged from 84.4% to 96.1% according to different viral load cut-offs (from detectable to 3000 IU/mL). Sensitivity as test of cure (follow-up 12) ranged from 85.1% to 97.4%. Among the 64 patients with recurrent viremia, 10.9% had low viral loads (≤1000 IU/mL); HCV genotyping allowed us to classify 73.5% of viremic cases either as reinfection or as treatment failure. DBS samples are useful to assess cure and differentiate reinfection from relapse after HCV antiviral treatment in the real world, facilitating decentralization of treatment and posttreatment follow-up in PWID. However, a fraction of patients presented with low viral loads, limiting viremia detection and genotyping in DBS and, therefore, repeat testing is recommended., (© 2023 The Authors. Journal of Medical Virology published by Wiley Periodicals LLC.)

Limiting outbreaks in long-term care facilities (LTCFs) is a cornerstone strategy to avoid an excess of COVID-19-related morbidity and mortality and to reduce its burden on the health system. We studied a large outbreak that occurred at an LTCF, combining methods of classical and genomic epidemiology analysis. The outbreak lasted for 31 days among residents, with an attack rate of 98% and 57% among residents and staff, respectively. The case fatality rate among residents was 16% ( n  = 15). Phylogenetic analysis of 59 SARS-CoV-2 isolates revealed the presence of two closely related viral variants in all cases (B.1.177 lineage), revealing a far more complex outbreak than initially thought and suggesting an initial spread driven by staff members. In turn, our results suggest that resident relocations to mitigate viral spread might have increased the risk of infection for staff members, creating secondary chains of transmission that were responsible for prolonging the outbreak. Our results highlight the importance of considering unnoticed chains of transmission early during an outbreak and making an adequate use and interpretation of diagnostic tests. Outbreak containment measures should be carefully tailored to each LTCF. IMPORTANCE The impact of COVID-19 on long-term care facilities (LTCFs) has been disproportionately large due to the high frailty of the residents. Here, we report epidemiological and genomic findings of a large outbreak that occurred at an LTCF, which ultimately affected almost all residents and nearly half of staff members. We found that the outbreak was initially driven by staff members; however, later resident relocation to limit the outbreak resulted in transmission from residents to staff members, evidencing the complexity and different phases of the outbreak. The phylogenetic analysis of SARS-CoV-2 isolates indicated that two closely related variants were responsible for the large outbreak. Our study highlights the importance of combining methods of classical and genomic epidemiology to take appropriate outbreak containment measures in LTCFs.

Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCt NR ) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCt NR correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCt NR , prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics., (© 2022. The Author(s).)

We performed a prospective, cross-sectional study of household contacts of symptomatic index case-patients with SARS-CoV-2 infection during the shift from Delta- to Omicron-dominant variants in Spain. We included 466 household contacts from 227 index cases. The secondary attack rate was 58.2% (95% CI 49.1%-62.6%) during the Delta-dominant period and 80.9% (95% CI 75.0%-86.9%) during the Omicron-dominant period. During the Delta-dominant period, unvaccinated contacts had higher probability of infection than vaccinated contacts (odds ratio 5.42, 95% CI 1.6-18.6), but this effect disappeared at ≈20 weeks after vaccination. Contacts showed a higher relative risk of infection (9.16, 95% CI 3.4-25.0) in the Omicron-dominant than Delta-dominant period when vaccinated within the previous 20 weeks. Our data suggest vaccine evasion might be a cause of rapid spread of the Omicron variant. We recommend a focus on developing vaccines with long-lasting protection against severe disease, rather than only against infectivity.

Background: The aim of this study was to describe the socio-demographics, and the sexual and health-seeking behaviours of cisgender men and transgender women sex workers (M & TWSW) attending community-based organisations (CBOs) in Barcelona, Spain, as well as to estimate the prevalence of HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), Chlamydia Trachomatis (CT) and Neisseria gonorrhoeae (NG) among them at different anatomical sites., Methods: The Sweetie Project was a community-based cross-sectional study of 147 M & TWSW recruited in two CBOs in Barcelona between 2017 and 2018. A nurse collected biological samples from rectum, pharynx and urethra from the subjects at each CBO and the participants self-completed an epidemiological questionnaire., Results: The highest prevalence observed was for HIV infection (25.3%) followed by bacterial STIs (NG 19.2% and CT 10.3%). The most prevalent anatomical site was pharyngeal (17.7%) followed by rectal (13.8%). More than half of participants who had a pharyngeal infection presented an isolated pharyngeal infection (57.7%) and half of those who had a rectal or urethral infection presented an isolated infection respectively. The seroprevalence of HCV and HBV was 2.4% and 34.2% respectively. There was a poor but statistically significant correlation between HIV and rectal CT infection ( r = 0.31), previous exposure to HCV ( r = 0.27) or self-reported STI ( r = 0.23), as well as between previous exposure to HCV and rectal CT ( r = 0.21) or self-reported STI ( r = 0.20)., Discussion: The Sweetie Project confirms the high burden of HIV and bacterial STIs among a sample of M&TWSW recruited in CBOs and reinforces the need to routinely screen them at all exposed anatomical sites.