RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: a design and retrospective evaluation study.

BACKGROUND: Whole-genome sequencing (WGS) is the gold standard diagnostic tool to identify and genetically characterise emerging pathogen mutations (variants), but cost, capacity, and timeliness limit its use when large populations need rapidly assessing. We assessed the potential of genotyping assays to provide accurate and timely variant information at scale by retrospectively examining surveillance for SARS-CoV-2 variants in England between March and September, 2021, when genotyping assays were used widely for variant detection. METHODS: We chose a panel of four RT-PCR genotyping assays to detect circulating variants of SARS-COV-2 in England and developed a decision algorithm to assign a probable SARS-CoV-2 variant to samples using the assay results. We extracted surveillance data from the UK Health Security Agency databases for 115 934 SARS-CoV-2-positive samples (March 1-Sept 6, 2021) when variant information was available from both genotyping and WGS. By comparing the genotyping and WGS variant result, we calculated accuracy metrics (ie, sensitivity, specificity, and positive predictive value [PPV]) and the time difference between the sample collection date and the availability of variant information. We assessed the number of samples with a variant assigned from genotyping or WGS, or both, over time. FINDINGS: Genotyping and an initial decision algorithm (April 10-May 11, 2021 data) were accurate for key variant assignment: sensitivities and PPVs were 0·99 (95% CI 0·99-0·99) for the alpha, 1·00 (1·00-1·00) for the beta, and 0·91 (0·80-1·00) for the gamma variants; specificities were 0·97 (0·96-0·98), 1·00 (1·00-1·00), and 1·00 (1·00-1·00), respectively. A subsequent decision algorithm over a longer time period (May 27-Sept 6, 2021 data) remained accurate for key variant assignment: sensitivities were 0·91 (95% CI 0·74-1·00) for the beta, 0·98 (0·98-0·99) for the delta, and 0·93 (0·81-1·00) for the gamma variants; specificities were 1·00 (1·00-1·00), 0·96 (0·96-0·97), and 1·00 (1·00-1·00), respectively; and PPVs were 0·83 (0·62-1·00), 1·00 (1·00-1·00), and 0·78 (0·59-0·97), respectively. Genotyping produced variant information a median of 3 days (IQR 2-4) after the sample collection date, which was faster than with WGS (9 days [8-11]). The flexibility of genotyping enabled a nine-times increase in the quantity of samples tested for variants by this method (from 5000 to 45 000). INTERPRETATION: RT-PCR genotyping assays are suitable for high-throughput variant surveillance and could complement WGS, enabling larger scale testing for known variants and timelier results, with important implications for effective public health responses and disease control globally, especially in settings with low WGS capacity. However, the choice of panels of RT-PCR assays is highly dependent on database information on circulating variants generated by WGS, which could limit the use of genotyping assays when new variants are emerging and spreading rapidly. FUNDING: UK Health Security Agency and National Institute for Health Research Health Protection Research Unit in Emergency Preparedness and Response.

Did anonymity in self-administered questionnaires improve disclosure of sensitive information during the 2022 mpox outbreak in England? An observational study.

BACKGROUND: Between May 6, 2022, and Jan 16, 2023, 3555 mpox cases were reported in England, predominantly in gay, bisexual, and other men who have sex with men. Initially, the UK Health Security agency administered questionnaires to laboratory-detected cases via telephone calls. From June, 2022, cases were requested by text or email to complete the questionnaire online, with optional anonymous completion. To inform future approaches, we assess whether anonymity improved disclosure of sensitive information. METHODS: In this observational study we analysed questionnaire data completed by people with a laboratory-detected case of mpox. We included questionnaires that were completed from May 25, 2022, to Jan 16, 2023, and restricted them to anonymous or identifiable self-completed responses. Questionnaires with forename, surname, and birth date, or an ID emailed to participants, which therefore could link to laboratory data, were considered identifiable. Questionnaires without any personal identifiable information were considered anonymous. We compared the responses to seven sensitive risk factor or exposure questions using Pearson's χ2. FINDINGS: All 3555 people diagnosed with mpox infection in England were invited to complete the questionnaire through either phone call or web link.We obtained 1075 (30%) completed questionnaires, with a response rate decreasing from 45% in May to 20% in July 2022. We included 531 self-completed questionnaires in this analysis, of which 259 (49%) were anonymous and 272 (51%) were identifiable. The median age of participants was 39 years, with 514 (97%) men, 12 (2%) women, and five (1%) other. The largest ethnic groups were white (79%; n=422) and mixed or multiple ethnic groups (9%; n=47). Results of all seven questions were similar: 98% (n=254/259) of anonymous and 97% (n=265/272) of identifiable cases answered all seven questions, 49% (n=127) and 54% (n=147) reported a sexually transmitted infection diagnosis in the past 12 months (p=0·2), 24% (n=63) and 27% (n=73) reported ten or more sexual partners in the past 3 months (p=0·8), and 15% (n=38) and 18% (n=50) reported knowing another person with mpox infection (p=0·5), respectively. INTERPRETATION: Transitioning to self-completed questionnaires resulted in reduced uptake, although optional anonymity possibly prevented a steeper drop. Anonymity did not appear to affect reporting of sensitive information, specifically of sexual behaviours or history associated with mpox risk, which reinforces results of previous literature. Our interpretation is limited, however, by relatively low questionnaire uptake, and by only analysing reported rather than true risk. The decision to implement anonymous questionnaires should therefore weigh the potential benefits of increased uptake against the disadvantage of restricted data linkage. FUNDING: None.

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.