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Background:The scale of the 2022 global mpox (formerly known as monkeypox) outbreak has been unprecedented. In less than 6 months, non-endemic countries have reported more than 67 000 cases of a disease that had previously been rare outside of Africa. Mortality has been reported as rare but hospital admission has been relatively common. We aimed to describe the clinical and laboratory characteristics and outcomes of individuals admitted to hospital with mpox and associated complications, including tecovirimat recipients. Methods:In this cohort study, we undertook retrospective review of electronic clinical records and pathology data for all individuals admitted between May 6, and Aug 3, 2022, to 16 hospitals from the Specialist and High Consequence Infectious Diseases Network for Monkeypox. The hospitals were located in ten cities in England and Northern Ireland. Inclusion criteria were clinical signs consistent with mpox and MPXV DNA detected from at least one clinical sample by PCR testing. Patients admitted solely for isolation purposes were excluded from the study. Key outcomes included admission indication, complications (including pain, secondary infection, and mortality) and use of antibiotic and anti-viral treatments. Routine biochemistry, haematology, microbiology, and virology data were also collected. Outcomes were assessed in all patients with available data. Findings:156 individuals were admitted to hospital with complicated mpox during the study period. 153 (98%) were male and three (2%) were female, with a median age of 35 years (IQR 30–44). Gender data were collected from electronic patient records, which encompassed full formal review of clincian notes. The prespecified options for data collection for gender were male, female, trans, non-binary, or unknown. 105 (71%) of 148 participants with available ethnicity data were of White ethnicity and 47 (30%) of 155 were living with HIV with a median CD4 count of 510 cells per mm3(IQR 349–828). Rectal or perianal pain (including proctitis) was the most common indication for hospital admission (44 [28%] of 156). Severe pain was reported in 89 (57%) of 156, and secondary bacterial infection in 82 (58%) of 142 individuals with available data. Median admission duration was 5 days (IQR 2–9). Ten individuals required surgery and two cases of encephalitis were reported. 38 (24%) of the 156 individuals received tecovirimat with early cessation in four cases (two owing to hepatic transaminitis, one to rapid treatment response, and one to patient choice). No deaths occurred during the study period. Interpretation:Although life-threatening mpox appears rare in hospitalised populations during the current outbreak, severe mpox and associated complications can occur in immunocompetent individuals. Analgesia and management of superimposed bacterial infection are priorities for patients admitted to hospital.

The COVID-19 pandemic has led to the rapid development of a plethora of molecular diagnostic assays with real-time polymerase chain reaction (RT-PCR) at the forefront. In this review, we will discuss the history and utility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) molecular diagnostics and the associated current and future regulatory process in Europe. We will assess the performance characteristics of a range of the most common SARS-CoV-2 molecular tests currently used in Europe with a focus on as rapid molecular platforms, stand-alone RT-PCR kits, the role of low-throughput and high-throughput end-to-end testing platforms, and the rapidly evolving field of SARS-CoV-2 variant of concern identification.

Study Objective The risks to surgeons of carrying out aerosol-generating procedures during the coronavirus disease 2019 (COVID-19) pandemic are unknown. To start to define these risks, in a systematic manner, we investigated the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in the abdominal fluid and lower genital tract of patients undergoing surgery. Design Prospective cross-sectional observational study. Setting Single, large United Kingdom hospital. Patients Total of 113 patients undergoing abdominal surgery or instrumentation of the lower genital tract. Interventions We took COVID-19 swabs from the peritoneal cavity and from the vagina from all eligible patients. Results were stratified by preoperative COVID-19 status. Measurements and Main Results In patients who were presumed COVID-19 negative at the time of surgery, SARS-CoV-2 virus RNA was detected in 0 of 102 peritoneal samples and 0 of 98 vaginal samples. Both cohorts included 4 patients who were antibody positive but nasopharyngeal swab test negative at the time of surgery. Peritoneal and vaginal swabs were also negative in 1 patient who had a positive nasopharyngeal swab immediately before surgery. Conclusion The presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed negative patients is nil or extremely low. These data will inform surgeons of the risks of restarting laparoscopic surgery at a time when COVID-19 is endemic in the population.

Here we describe a retrospective clinical evaluation of the QIAGEN

Highlights • MERS is an emerging infectious disease with high consequences. • PHE Manchester receives a high number of MERS surveillance samples. • Sputum samples are the optimum samples for diagnosing respiratory viruses. • Multiple samples per patient result in a 100% diagnostic yield and a confirmed end-diagnosis., Background Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in Saudi Arabia in 2012 and caused an epidemic in the Middle East. Public Health England (PHE) Manchester is one of the two PHE centres in the UK that perform testing for MERS-CoV. The results of the PHE Manchester MERS surveillance from 2012 to 2019 are presented in this report. Methods Retrospective data were collected for returning travellers from the Middle East fitting the PHE MERS case definition. Respiratory samples were tested for respiratory viruses and MERS-CoV using an in-house RT-PCR assay. Results Four hundred and twenty-six (426) samples from 264 patients were tested for MERS Co-V and respiratory viruses. No MERS-CoV infections were identified by PCR. Fifty-six percent of samples were PCR positive for viral or bacterial pathogen with Influenza A as the predominant virus (44%). Sixty-two percent of all patients had a pathogen identified with the highest positivity from sputum samples. Patients with multiple samples demonstrated a 100% diagnostic yield. Conclusions Although no cases of MERS were identified, the majority of patients had Influenza infection for which oseltamivir treatment was indicated and isolation warranted. Sputum samples were the most useful in diagnosing respiratory viruses with a 100% diagnostic yield from patients with multiple samples.

On 26th November 2021, a novel SARS-CoV-2 variant B.1.1.529 (Omicron variant) was designated as a variant of concern by the World Health Organisation. Using data from the Virology laboratory at the Manchester Medical Microbiology Partnership (MMMP, a partnership between UKHSA and the Manchester Foundation Trust), we have extracted a real-time feed of Omicron samples from hospitals across Greater Manchester, an area of the United Kingdom with a population size of approximately three million individuals. Omicron hospital samples are growing exponentially across Greater Manchester (doubling time 2.7 days (95% CI: 2.1, 3.7)). The proportion of Omicron in hospital samples follows a similar trajectory to the SGTF proportion in cases, but with a two-day offset. This is consistent with the delay from testing positive to hospital admission, implying a similar proportion of Omicron cases are converting to hospital admissions as for Delta cases. Comparing the Greater Manchester data to national hospitalisation data, similar tends are observed. Therefore, there is no signal of a substantial reduction in hospital admission risk with Omicron, and Omicron epidemics are likely to place a substantial burden on public health infrastructure.

Objectives Surveillance for Middle East respiratory syndrome (MERS) has been undertaken in the UK since September 2012. This study describes the surveillance outcomes in England from 2012 to 2018. Study Design This was a descriptive study using surveillance data. Methods Local health protection teams in England report possible MERS cases to the National Infection Service with clinical and laboratory data. Results A total of 1,301 possible MERS cases were identified in the study period. Five cases were laboratory confirmed MERS. The majority of cases had travelled to Saudi Arabia (56.7%) and United Arab Emirates (25.9%). Fifty-four percent of cases were male and 43.7% female. The majority of cases (65.1%) were aged 45 years or over. The number of tests increased in the period following Hajj each year. Laboratory confirmed alternative diagnoses were available for 513 (39.4%) cases; influenza was the most common virus detected (n=255, 52.4%). Conclusions Our study highlights the importance of differential diagnosis of influenza and other respiratory pathogens and early influenza antiviral treatment., Highlights • Routine surveillance for Middle East respiratory syndrome has been carried out. • 1,301 possible cases were identified including five laboratory confirmed cases. • Influenza was the most common pathogen detected for differential diagnosis.

Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.

Objectives SARS-CoV-2 emerged in South Asia in 2019 and has resulted in a global pandemic. Public Health England (PHE) Manchester rapidly escalated testing for SARS-CoV-2 in the highest COVID-19 incidence location in England. The results of the PHE Manchester SARS-CoV-2 surveillance during the first wave are presented. Methods Retrospective data were collected for patients fitting the PHE SARS-CoV-2 case definition from 11th February to 31st August 2020. Respiratory tract, tissue, faecal, fluid and cerebrospinal (CSF) samples were tested for SARS-CoV-2 by a semi-quantitative real-time reverse-transcription PCR. Results Of the 204,083 tests for SARS-CoV-2, 18,011 were positive demonstrating a positivity of 8.90%. Highest positivity was in nasal swabs (20.99%) followed by broncheo-alveolar lavage samples (12.50%). None of the faecal, fluid or CSF samples received were positive for SARS-CoV-2. Conclusions There was a high incidence of SARS-CoV-2 patients in the North-West of England during the first UK wave of the Covid-19 pandemic. Highest positivity rate was in nasal specimens suggesting this is the optimum sample type within this dataset for detecting SARS-CoV-2. Further studies are warranted to assess the utility of testing faecal, fluid and CSF samples. Rapid escalation of testing via multiple platforms was required to ensure prompt diagnosis and isolate infected cases to reduce transmission of the virus.

Introduction: Rapid, high throughput diagnostics are a valuable tool, allowing the detection of SARS-CoV-2 in populations, in order to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as reverse transcriptase quantitative PCR (RTqPCR), particularly throughout the first months of the pandemic. We investigated the use of LamPORE, where loop mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS CoV 2 in symptomatic and asymptomatic populations. Methods: In an asymptomatic prospective cohort; health care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self swabbed with nasopharyngeal swabs weekly for three weeks and supplied a saliva specimen daily. These samples were tested for SARS CoV 2 RNA using the Oxford Nanopore LamPORE system and a reference RTqPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza like illness from March 2020 to June 2020, were similarly tested from nasopharyngeal swabs. Results: In the asymptomatic cohort a total of 1200 participants supplied 23,427 samples (3,966 swab, 19,461 saliva) over a three-week period. The incidence of SARS CoV 2 was 0.95% using LamPORE. Diagnostic sensitivity and specificity was > 99.5% in both swab and saliva asymptomatic samples as compared to the reference RTqPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%. Conclusions: LamPORE is a highly accurate methodology for the detection of SARS CoV 2 in both the symptomatic and asymptomatic population settings and can be used as an alternative to RTqPCR.

Introduction The risks to surgeons of carrying out aerosol generating procedures during the COVID pandemic are unknown To define these risks in a systematic manner we investigated the presence of SARS-CoV-2 virus in the peritoneal fluid and lower genital tract of patients undergoing surgery at a time when COVID infection remained steady in the population Methods We carried out a prospective cross sectional observational study of patients undergoing abdominal surgery or instrumentation of the lower genital tract at a single large institution in the UK We took COVID swabs from the peritoneal cavity and from the vagina from all eligible patients All patients underwent preoperative nasopharyngeal testing and results were stratified by pre operative COVID status Results To date we have recruited 74 patients undergoing surgery The commonest procedure undertaken was caesarean section but patients undergoing laparotomy and cancer surgery were also included No patients had faecal or amniotic contamination of the abdomen or vagina at the time of sampling All patients had negative nasopharyngeal COVID swabs within 48 hours of recruitment although 4/74 (5%) had the presence of antibodies suggesting previous infection SARS-CoV-2 virus RNA was detected in 0/63 peritoneal samples and 0/68 lower genital tract samples Conclusions The presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed COVID negative patients is nil or extremely low These data will inform surgeons of the risks of restarting laparoscopic and gynaecologic surgery at a time when COVID19 is endemic in the population

BackgroundDried blood spot samples (DBS) provide an alternative sample type to venous blood samples for antibody testing. DBS are used by NHS for diagnosing HCV and by PHE for large scale HIV and Hepatitis C serosurveillance; the applicability of DBS based approaches to SARS-CoV-2 antibody detection is uncertain.ObjectiveTo compare antibody detection in dried blood spot eluates using the Roche Elecsys ® immunoassay (index test) with antibody detection in paired plasma samples, using the same assay (reference test).SettingOne Police and one Fire & Rescue facility in England.Participants195 participants within a larger sample COVID-19 serodiagnostics study of keyworkers, EDSAB-HOME.Outcome MeasuresSensitivity and specificity of DBS (the index test) relative to plasma (the reference test), at an experimental cut-off; quality of DBS sample collected; estimates of relative sensitivity of DBS vs. plasma immunoassay in a larger population.Results18/195 (9.2%) participants tested positive using plasma samples. DBS sample quality varied markedly by phlebotomist, and low sample volume significantly reduced immunoassay signals. Using a cut-off of ten median absolute deviations above the immunoassay result with negative samples, sensitivity and specificity of DBS were 89.0% (95% CI 67.2, 96.9%) and 100.0% (95% CI 97.9, 100%) respectively compared with using plasma. The limit of detection for DBS is about 30 times higher than for plasma.ConclusionDBS use for SARS-CoV-2 serology, though feasible, is insensitive relative to immunoassays on plasma. Sample quality impacts on assay performance. Alternatives, including the collection of capillary blood samples, should be considered for screening programs.

IntroductionThe risks to surgeons of carrying out aerosol generating procedures during the COVID pandemic are unknown. To start to define these risks, in a systematic manner, we investigated the presence of SARS-CoV-2 virus in the abdominal fluid and lower genital tract of patients undergoing surgery.MethodsWe carried out a prospective cross sectional observational study of 113 patients undergoing abdominal surgery or instrumentation of the lower genital tract. We took COVID swabs from the peritoneal cavity and from the vagina from all eligible patients. Results were stratified by pre operative COVID status.ResultsIn patients who were presumed COVID negative at the time of surgery SARS-CoV-2 virus RNA was detected in 0/102 peritoneal samples and 0/98 vaginal samples. Peritoneal and vaginal swabs were also negative in one patient who had a positive nasopharyngeal swab immediately prior to surgery.ConclusionsThe presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed negative patients is nil or extremely low. These data will inform surgeons of the risks of restarting laparoscopic surgery at a time when COVID19 is endemic in the population.

Background: Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. Infection control is challenging in these environments due to regular contact between healthcare workers (HCWs) and patients. This is amplified by increased frequency of severe adverse responses to SARS-CoV-2 in patients with underlying health conditions. Methods: We sequenced SARS-CoV-2 genomes for patients and HCWs across multiple geographically distinct UK hospitals. All hospitals were actively enforcing zoning approaches (SARS-CoV-2 negative and SARS-CoV-2 positive areas) as an infection control measure. We integrated patient movement and staff location data into the analysis of viral genome data in order to understand geographical and temporal dynamics of SARS-CoV-2 transmission. Findings: We obtained 173 high-quality SARS-CoV-2 genomes from patients ( n =134) and HCWs ( n =39). The median number of genomic variants per sample of 11 (range=0-16), with a 61.5% average pairwise similarity in the variants (range=0-100%). Integration of patient movement identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples ( p

Objectives Rapid, high throughput diagnostics are a valuable tool, allowing the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations so as to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as quantitative RT-PCR (RT-qPCR), particularly throughout the first months of the coronavirus disease 2019 pandemic. We investigated the use of LamPORE, where loop-mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS-CoV-2 in symptomatic and asymptomatic populations. Methods In an asymptomatic prospective cohort, for 3 weeks in September 2020, health-care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self-swabbed with nasopharyngeal swabs weekly and supplied a saliva specimen daily. These samples were tested for SARS-CoV-2 RNA using the Oxford Nanopore LamPORE system and a reference RT-qPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza-like illness from March 2020 to June 2020 were similarly tested from nasopharyngeal swabs. Results In the asymptomatic cohort a total of 1200 participants supplied 23 427 samples (3966 swab, 19 461 saliva) over a 3-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (decreasing to approximately 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared with the reference RT-qPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%. Conclusions LamPORE is a highly accurate methodology for the detection of SARS-CoV-2 in both symptomatic and asymptomatic population settings and can be used as an alternative to RT-qPCR.

Aim: A prospective study was undertaken to establish the prevalence of enterovirus D68 (EV-D68) in the northwest of England. Patients & samples: In the period 24 October through 31 December 2014, respiratory samples were screened by a specific real-time PCR and EV-D68 was identified by nucleotide sequence-based typing. Results: Enterovirus was detected in 7.4% of samples and EV-D68 was confirmed in 32 cases. Phylogenetic analysis showed that EV-D68 strains corresponded to clades A and B. Clinical presentation of cases ranged from mild to severe respiratory infection. The majority of cases had comorbidities that might predispose to severe infection. Conclusion: EV-D68 was circulating in our region during late 2014 and has the potential to cause severe disease.