Covid-19 Vaccine Effectiveness against the Omicron (B.1.1.529) Variant.

BACKGROUND: A rapid increase in coronavirus disease 2019 (Covid-19) cases due to the omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 in highly vaccinated populations has aroused concerns about the effectiveness of current vaccines. METHODS: We used a test-negative case-control design to estimate vaccine effectiveness against symptomatic disease caused by the omicron and delta (B.1.617.2) variants in England. Vaccine effectiveness was calculated after primary immunization with two doses of BNT162b2 (Pfizer-BioNTech), ChAdOx1 nCoV-19 (AstraZeneca), or mRNA-1273 (Moderna) vaccine and after a booster dose of BNT162b2, ChAdOx1 nCoV-19, or mRNA-1273. RESULTS: Between November 27, 2021, and January 12, 2022, a total of 886,774 eligible persons infected with the omicron variant, 204,154 eligible persons infected with the delta variant, and 1,572,621 eligible test-negative controls were identified. At all time points investigated and for all combinations of primary course and booster vaccines, vaccine effectiveness against symptomatic disease was higher for the delta variant than for the omicron variant. No effect against the omicron variant was noted from 20 weeks after two ChAdOx1 nCoV-19 doses, whereas vaccine effectiveness after two BNT162b2 doses was 65.5% (95% confidence interval [CI], 63.9 to 67.0) at 2 to 4 weeks, dropping to 8.8% (95% CI, 7.0 to 10.5) at 25 or more weeks. Among ChAdOx1 nCoV-19 primary course recipients, vaccine effectiveness increased to 62.4% (95% CI, 61.8 to 63.0) at 2 to 4 weeks after a BNT162b2 booster before decreasing to 39.6% (95% CI, 38.0 to 41.1) at 10 or more weeks. Among BNT162b2 primary course recipients, vaccine effectiveness increased to 67.2% (95% CI, 66.5 to 67.8) at 2 to 4 weeks after a BNT162b2 booster before declining to 45.7% (95% CI, 44.7 to 46.7) at 10 or more weeks. Vaccine effectiveness after a ChAdOx1 nCoV-19 primary course increased to 70.1% (95% CI, 69.5 to 70.7) at 2 to 4 weeks after an mRNA-1273 booster and decreased to 60.9% (95% CI, 59.7 to 62.1) at 5 to 9 weeks. After a BNT162b2 primary course, the mRNA-1273 booster increased vaccine effectiveness to 73.9% (95% CI, 73.1 to 74.6) at 2 to 4 weeks; vaccine effectiveness fell to 64.4% (95% CI, 62.6 to 66.1) at 5 to 9 weeks. CONCLUSIONS: Primary immunization with two doses of ChAdOx1 nCoV-19 or BNT162b2 vaccine provided limited protection against symptomatic disease caused by the omicron variant. A BNT162b2 or mRNA-1273 booster after either the ChAdOx1 nCoV-19 or BNT162b2 primary course substantially increased protection, but that protection waned over time. (Funded by the U.K. Health Security Agency.).

Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021.

When SARS-CoV-2 Omicron emerged in 2021, S gene target failure enabled differentiation between Omicron and the dominant Delta variant. In England, where S gene target surveillance (SGTS) was already established, this led to rapid identification (within ca 3 days of sample collection) of possible Omicron cases, alongside real-time surveillance and modelling of Omicron growth. SGTS was key to public health action (including case identification and incident management), and we share applied insights on how and when to use SGTS.

The spatio-temporal distribution of COVID-19 infection in England between January and June 2020.

The spatio-temporal dynamics of an outbreak provide important insights to help direct public health resources intended to control transmission. They also provide a focus for detailed epidemiological studies and allow the timing and impact of interventions to be assessed.A common approach is to aggregate case data to administrative regions. Whilst providing a good visual impression of change over space, this method masks spatial variation and assumes that disease risk is constant across space. Risk factors for COVID-19 (e.g. population density, deprivation and ethnicity) vary from place to place across England so it follows that risk will also vary spatially. Kernel density estimation compares the spatial distribution of cases relative to the underlying population, unfettered by arbitrary geographical boundaries, to produce a continuous estimate of spatially varying risk.Using test results from healthcare settings in England (Pillar 1 of the UK Government testing strategy) and freely available methods and software, we estimated the spatial and spatio-temporal risk of COVID-19 infection across England for the first 6 months of 2020. Widespread transmission was underway when partial lockdown measures were introduced on 23 March 2020 and the greatest risk erred towards large urban areas. The rapid growth phase of the outbreak coincided with multiple introductions to England from the European mainland. The spatio-temporal risk was highly labile throughout.In terms of controlling transmission, the most important practical application of our results is the accurate identification of areas within regions that may require tailored intervention strategies. We recommend that this approach is absorbed into routine surveillance outputs in England. Further risk characterisation using widespread community testing (Pillar 2) data is needed as is the increased use of predictive spatial models at fine spatial scales.

Pathways to, and use of, sexual healthcare among Black Caribbean sexual health clinic attendees in England: evidence from cross-sectional bio-behavioural surveys.

BACKGROUND: In England, people of Black Caribbean (BC) ethnicity are disproportionately affected by sexually transmitted infections (STI). We examined whether differences in sexual healthcare behaviours contribute to these inequalities. METHODS: We purposively selected 16 sexual health clinics across England with high proportions of attendees of BC ethnicity. During May-September 2016, attendees at these clinics (of all ethnicities) completed an online survey that collected data on health service use and sexual behaviour. We individually linked these data to routinely-collected surveillance data. We then used multivariable logistic regression to compare reported behaviours among BC and White British/Irish (WBI) attendees (n = 627, n = 1411 respectively) separately for women and men, and to make comparisons by gender within these ethnic groups. RESULTS: BC women's sexual health clinic attendances were more commonly related to recent bacterial STI diagnoses, compared to WBI women's attendances (adjusted odds ratio, AOR 3.54, 95% CI 1.45-8.64, p = 0.009; no gender difference among BC attendees), while BC men were more likely than WBI men (and BC women) to report attending because of a partner's symptoms or diagnosis (AOR 1.82, 95% CI 1.14-2.90; AOR BC men compared with BC women: 4.36, 95% CI 1.42-13.34, p = 0.014). Among symptomatic attendees, BC women were less likely than WBI women to report care-seeking elsewhere before attending the sexual health clinic (AOR 0.60, 95% CI 0.38-0.97, p = 0.039). No ethnic differences, or gender differences among BC attendees, were observed in symptom duration, or reporting sex whilst symptomatic. Among those reporting previous diagnoses with or treatment for bacterial STI, no differences were observed in partner notification. CONCLUSIONS: Differences in STI diagnosis rates observed between BC and WBI ethnic groups were not explained by the few ethnic differences which we identified in sexual healthcare-seeking and use. As changes take place in service delivery, prompt clinic access must be maintained - and indeed facilitated - for those at greatest risk of STI, regardless of ethnicity.

Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: A cross-sectional study at the UK's largest sexual health service.

OBJECTIVES: Outbreaks of bacterial enteric pathogens (BEPs) in men who have sex with men (MSM) associated with antimicrobial resistance are a public health concern. We investigated the prevalence and risk factors of BEPs in MSM to inform infection control. METHODS: We conducted a cross-sectional study at a London sexual health clinic between 20/12/2017 and 06/02/2018. Residual rectal swabs from MSM attending for sexually transmitted infection (STI) testing were anonymously tested for a range of BEPs using real-time PCR. A sub-set of samples were tested for the mphA gene (a marker of azithromycin resistance). Results were linked to electronic health records. RESULTS: BEPs were detected in 207 of 2116 participants, giving an overall prevalence of 9.8% (95% CI 8.5%-11.1%) ranging from 0.8% (0.4%-1.2%) for Shigella to 4.9% (4.0%-5.9%) for Enteroaggregative E. coli. MSM with BEPs were more likely to have a history of bacterial STIs (p = 0.010), to report more sexual partners (p<0.001), and among HIV-negative MSM, to report current HIV pre-exposure prophylaxis use (p<0.001). Gastrointestinal symptoms were rare (1.7%) and not associated with BEPs. 41.3% of MSM with BEPs and 14.1% of those without BEPs carried mphA (p<0.001). Among the former, this was associated with a history of bacterial STIs (51.5% vs 31.1%, p = 0.003). CONCLUSIONS: One in ten MSM had a BEP detected and most did not report symptoms. MphA carriage was common, particularly among those with BEPs. Bacterial STI treatment might contribute to selection of resistant gut organisms, emphasising the need for better antimicrobial stewardship.

Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID-19 cases treated with sotrovimab in the community in England.

There are concerns that sotrovimab has reduced efficacy at reducing hospitalisation risk against the BA.2 sub-lineage of the Omicron SARS-CoV-2 variant. We performed a retrospective cohort (n = 8850) study of individuals treated with sotrovimab in the community, with the objective of assessing whether there were any differences in risk of hospitalisation of BA.2 cases compared with BA.1. We estimated that the hazard ratio of hospital admission with a length of stay of 2 days or more was 1.17 for BA.2 compared with BA.1 (95%CI 0.74-1.86). These results suggest that the risk of hospital admission was similar between the two sub-lineages.

Correction: Sera selected from national STI surveillance system shows Chlamydia trachomatis PgP3 antibody correlates with time since infection and number of previous infections.

[This corrects the article DOI: 10.1371/journal.pone.0208652.].

Understanding the burden of bacterial sexually transmitted infections and Trichomonas vaginalis among black Caribbeans in the United Kingdom: Findings from a systematic review.

BACKGROUND: In the UK, people of black Caribbean (BC) ethnicity continue to be disproportionately affected by bacterial sexually transmitted infections (STIs) and Trichomonas vaginalis (TV). We systematically reviewed evidence on the association between bacterial STIs/TV and ethnicity (BC compared to white/white British (WB)) accounting for other risk factors; and differences between these two ethnic groups in the prevalence of risk factors associated with these STIs, sexual healthcare seeking behaviours, and contextual factors influencing STI risk. METHODS: Studies presenting relevant evidence for participants aged ≥14 years and living in the UK were eligible for inclusion. A pre-defined search strategy informed by the inclusion criteria was developed. Eleven electronic databases were searched from the start date to September-October 2016. Two researchers independently screened articles, extracted data using a standardised proforma and resolved discrepancies in discussion with a third researcher. Descriptive summaries of evidence are presented. Meta-analyses were not conducted due to variation in study designs. Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed. RESULTS: Of 3815 abstracts identified, 15 articles reporting quantitative data were eligible and included in the review. No qualitative studies examining contextual drivers of STI risk among people of BC ethnicity were identified. Compared to the white/WB ethnic group, the greater STI/TV risk among BCs was partially explained by variations in socio-demographic factors, sexual behaviours, and recreational drug use. The prevalence of reporting early sexual debut (<16 years), concurrency, and multiple partners was higher among BC men compared to white/WB men; however, no such differences were observed for women. People of BC ethnicity were more likely to access sexual health services than those of white/WB ethnicity. CONCLUSIONS: Further research is needed to explore other drivers of the sustained higher STI/TV prevalence among people of BC ethnicity. Developing holistic, tailored interventions that address STI risk and target people of BC ethnicity, especially men, could enhance STI prevention.

The Acceptability and Feasibility of Implementing a Bio-Behavioral Enhanced Surveillance Tool for Sexually Transmitted Infections in England: Mixed-Methods Study.

BACKGROUND: Sexually transmitted infection (STI) surveillance is vital for tracking the scale and pattern of epidemics; however, it often lacks data on the underlying drivers of STIs. OBJECTIVE: This study aimed to assess the acceptability and feasibility of implementing a bio-behavioral enhanced surveillance tool, comprising a self-administered Web-based survey among sexual health clinic attendees, as well as linking this to their electronic health records (EHR) held in England's national STI surveillance system. METHODS: Staff from 19 purposively selected sexual health clinics across England and men who have sex with men and black Caribbeans, because of high STI burden among these groups, were interviewed to assess the acceptability of the proposed bio-behavioral enhanced surveillance tool. Subsequently, sexual health clinic staff invited all attendees to complete a Web-based survey on drivers of STI risk using a study tablet or participants' own digital device. They recorded the number of attendees invited and participants' clinic numbers, which were used to link survey data to the EHR. Participants' online consent was obtained, separately for survey participation and linkage. In postimplementation phase, sexual health clinic staff were reinterviewed to assess the feasibility of implementing the bio-behavioral enhanced surveillance tool. Acceptability and feasibility of implementing the bio-behavioral enhanced surveillance tool were assessed by analyzing these qualitative and quantitative data. RESULTS: Prior to implementation of the bio-behavioral enhanced surveillance tool, sexual health clinic staff and attendees emphasized the importance of free internet/Wi-Fi access, confidentiality, and anonymity for increasing the acceptability of the bio-behavioral enhanced surveillance tool among attendees. Implementation of the bio-behavioral enhanced surveillance tool across sexual health clinics varied considerably and was influenced by sexual health clinics' culture of prioritization of research and innovation and availability of resources for implementing the surveys. Of the 7367 attendees invited, 85.28% (6283) agreed to participate. Of these, 72.97% (4585/6283) consented to participate in the survey, and 70.62% (4437/6283) were eligible and completed it. Of these, 91.19% (4046/4437) consented to EHR linkage, which did not differ by age or gender but was higher among gay/bisexual men than heterosexual men (95.50%, 722/756 vs 88.31%, 1073/1215; P<.003) and lower among black Caribbeans than white participants (87.25%, 568/651 vs 93.89%, 2181/2323; P<.002). Linkage was achieved for 88.88% (3596/4046) of consenting participants. CONCLUSIONS: Implementing a bio-behavioral enhanced surveillance tool in sexual health clinics was feasible and acceptable to staff and groups at STI risk; however, ensuring participants' confidentiality and anonymity and availability of resources is vital. Bio-behavioral enhanced surveillance tools could enable timely collection of detailed behavioral data for effective commissioning of sexual health services.

Sera selected from national STI surveillance system shows Chlamydia trachomatis PgP3 antibody correlates with time since infection and number of previous infections.

BACKGROUND: Seroprevalence surveys of Chlamydia trachomatis (CT) antibodies are promising for estimating age-specific CT cumulative incidence, however accurate estimates require improved understanding of antibody response to CT infection. METHODS: We used GUMCAD, England's national sexually transmitted infection (STI) surveillance system, to select sera taken from female STI clinic attendees on the day of or after a chlamydia diagnosis. Serum specimens were collected from laboratories and tested anonymously on an indirect and a double-antigen ELISA, both of which are based on the CT-specific Pgp3 antigen. We used cross-sectional and longitudinal descriptive analyses to explore the relationship between seropositivity and a) cumulative number of chlamydia diagnoses and b) time since most recent chlamydia diagnosis. RESULTS: 919 samples were obtained from visits when chlamydia was diagnosed and 812 during subsequent follow-up visits. Pgp3 seropositivity using the indirect ELISA increased from 57.1% (95% confidence interval: 53.2-60.7) on the day of a first-recorded chlamydia diagnosis to 89.6% (95%CI: 79.3-95.0) on the day of a third or higher documented diagnosis. With the double-antigen ELISA, the increase was from 61.1% (95%CI: 53.2-60.7) to 97.0% (95%CI: 88.5-99.3). Seropositivity decreased with time since CT diagnosis on only the indirect assay, to 49.3% (95%CI: 40.9-57.7) two or more years after a first diagnosis and 51.9% (95%CI: 33.2-70.0) after a repeat diagnosis. CONCLUSION: Seropositivity increased with cumulative number of infections, and decreased over time after diagnosis on the indirect ELISA, but not on the double-antigen ELISA. This is the first study to demonstrate the combined impact of number of chlamydia diagnoses, time since diagnosis, and specific ELISA on Pgp3 seropositivity. Our findings are being used to inform models estimating age-specific chlamydia incidence over time using serial population-representative serum sample collections, to enable accurate public health monitoring of chlamydia.