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BackgroundAntigen lateral flow devices (LFDs) have been widely used to control SARS-CoV-2. Changes in LFD sensitivity and detection of infectious individuals during the pandemic with successive variants, vaccination, and changes in LFD use are incompletely understood.MethodsPaired LFD and PCR tests were collected from asymptomatic and symptomatic participants, across multiple settings in the UK between 04-November-2020 and 21-March-2022. Multivariable logistic regression was used to analyse LFD sensitivity and specificity, adjusting for viral load, LFD manufacturer, setting, age, sex, assistance, symptoms, vaccination, and variant. National contact tracing data were used to estimate the proportion of transmitting index cases (with ≥1 PCR/LFD-positive contact) potentially detectable by LFDs over time, accounting for viral load, variant, and symptom status.Findings4131/75,382 (5.5%) participants were PCR-positive. Sensitivity vs. PCR was 63.2% (95%CI 61.7-64.6%) and specificity 99.71% (99.66-99.74%). Increased viral load was independently associated with being LFD-positive. There was no evidence LFD sensitivity differed between Delta vs. Alpha/pre-Alpha infections, but Omicron infections were more likely to be LFD positive. Sensitivity was higher in symptomatic participants, 68.7% (66.9-70.4%) than in asymptomatic participants, 52.8% (50.1-55.4%). 79.4% (68.6-81.3%) of index cases resulting in probable onward transmission with were estimated to have been detectable using LFDs, this proportion was relatively stable over time/variants, but lower in asymptomatic vs. symptomatic cases.InterpretationLFDs remained able to detect most SARS-CoV-2 infections throughout vaccine roll-out and different variants. LFDs can potentially detect most infections that transmit to others and reduce risks. However, performance is lower in asymptomatic compared to symptomatic individuals.FundingUK Government.Research in contextEvidence before this studyLateral flow devices (LFDs; i.e. rapid antigen detection devices) have been widely used for SARS-CoV-2 testing. However, due to their imperfect sensitivity when compared to PCR and a lack of a widely available gold standard proxy for infectiousness, the performance and use of LFDs has been a source of debate. We conducted a literature review in PubMed and bioRxiv/medRxiv for all studies examining the performance of lateral flow devices between 01 January 2020 and 31 October 2022. We used the search terms ‘SARS-CoV-2’/’COVID-19’ and ‘antigen’/’lateral flow test’/’lateral flow device’. Multiple studies have examined the sensitivity and specificity of LFDs, including several systematic reviews. However, the majority of the studies are based on pre-Alpha infections. Large studies examining the test accuracy for different variants, including Delta and Omicron, and following vaccination are limited.Added value of this studyIn this large national LFD evaluation programme, we compared the performance of three different LFDs relative to PCR in various settings. Compared to PCR testing, sensitivity was 63.2% (95%CI 61.7-64.6%) overall, and 71.6% (95%CI 69.8-73.4%) in unselected communitybased testing. Specificity was 99.71% (99.66-99.74%). LFDs were more likely to be positive as viral loads increased. LFD sensitivity was similar during Alpha/pre-Alpha and Delta periods but increased during the Omicron period. There was no association between sensitivity and vaccination status. Sensitivity was higher in symptomatic participants, 68.7% (66.9-70.4%) than in asymptomatic participants, 52.8% (50.1-55.4%). Using national contact tracing data, we estimated that 79.4% (68.6-81.3%) of index cases resulting in probable onward transmission (i.e. with ≥1 PCR/LFD-positive contact) were detectable using LFDs. Symptomatic index cases were more likely to be detected than asymptomatic index cases due to higher viral loads and better LFD performance at a given viral load. The proportion of index cases detected remained relatively stable over time and with successive variants, with a slight increase in the proportion of asymptomatic index cases detected during Omicron.Implications of all the available evidenceOur data show that LFDs detect most SARS-CoV-2 infections, with findings broadly similar to those summarised in previous meta-analyses. We show that LFD performance has been relatively consistent throughout different variant-dominant phases of the pandemic and following the roll-out of vaccination. LFDs can detect most infections that transmit to others and can therefore be used as part of a risk reduction strategy. However, performance is lower in asymptomatic compared to symptomatic individuals and this needs to be considered when designing testing programmes.

Laboratory preparedness with quality-assured diagnostic assays is essential for controlling the current coronavirus disease (COVID-19) outbreak. We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. To analyse SARS-CoV-2 testing performance, we used an online questionnaire developed for the European Union project RECOVER to assess molecular testing capacities in clinical diagnostic laboratories.

BACKGROUND: The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies to support public health control. Early detection and evaluation of their associated risk of spreading within the population are pivotal. METHODS: Between April 2020 and February 2021, the UK Lighthouse Labs Network at Alderley Park tested more than eight million nose and throat swab samples for the presence of SARS-CoV-2, via PCR. The assay targeted three genomic regions of the virus: N, Orf1ab and S. Whole-genome next-generation sequencing was used to confirm positive PCR results. Positive results were mapped using the postal district origin of samples to allow real-time tracking of the spread of a new variant through the UK. FINDINGS: In mid-November 2020, the assay identified an increasing number of S gene negative, N and Orf1ab positive samples. Whole-genome sequencing demonstrated that the loss of S gene detection was due to the appearance of a SARS-CoV-2 lineage (B.1.1.7) designated as Variant of concern (VOC) 202012/01. By the beginning of January 2021, the new SARS-CoV-2 VOC comprised 70% of daily positive samples tested at Alderley Park and ∼98% by the end of February 2021. INTERPRETATION: The timeline view identified the rapid spread of the new SARS-CoV-2 variant across England during the first three weeks of December. Coupling high-throughput diagnostics and molecular surveillance was pivotal to the early detection of the spread of this variant. The availability of real-time tracking of an emerging variant is an important new tool to inform decision-making authorities for risk mitigation. In a respiratory pandemic, a tool for the timely response to the emergence and spread of a novel variant is vital, even more so when a variant is associated with the enhanced transmission, as has occurred with VOC 202012/01. FUNDING: None.

Lighthouse Labs network tests for the presence of RNA of SARS-CoV-2, the causative agent of COVID-19. The Thermofisher TaqPath assay targets three regions of SARS-CoV-2; ORF1ab, N and S-genes. The assay identified a drop in S-gene target detection among positive samples due to the circulation of a new SARS-CoV-2 Variant of Concern (VOC) designated as 202012/01. By end of December 2020, 60% of daily positive test results at Alderley Park Lighthouse Labs, were linked to the new Variant of Concern. This timeline view identifies the rapid spread of the variant across the country.

Background: The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies, in support of public health control. Early detection and evaluation of their risk of spreading within the population is pivotal. Methods: Between April 2020 and February 2021, the Lighthouse Laboratory at Alderley Park Network tested more than eight million nose and throat swab samples for the presence of SARS-CoV-2. The PCR assay used, targets three genomic regions of the virus N, Orf1ab and S. Whole genome next-generation sequencing was used to confirm PCR positive results. Positive sample results were mapped to postal code origin of samples to allow real-time tracking of the spread of the variant through the UK. Findings: In mid-November 2020 the assay identified an increasing number of S gene negative, N and Orf1ab positive samples. Whole genome sequencing demonstrated that the loss of S gene detection was due to the appearance of a SARS-CoV-2 lineage (B.1.1.7) designated as Variant of Concern (VOC) 202012/01. By the beginning of January 2021, the new SARS-CoV-2 VOC had risen to comprise 70% of daily positive samples tested at Alderley Park and ~98% by the end of February 2021. Interpretation: The timeline view identified the rapid spread of the variant across England during the first three weeks of December. Coupling high throughput diagnostics and molecular surveillance was pivotal to the early detection of the spread of this variant. The availability of real time tracking of an emerging variant is an important new tool to inform decision-making for risk mitigation. In a respiratory pandemic, a tool for the timely response to the emergence and spread of a novel variant is vital especially when a variant is associated with enhanced transmission, as has occurred with VOC 202012/01. Funding Statement: The Lighthouse laboratory network was generated using funding from DHSC. Declaration of Interests: None to declare. Ethics Approval Statement: The manuscript was reviewed by the Head of Approvals Support, NHS Health Research Authority (HRA-NHS, UK), who confirmed that the study, which used unlinked and anonymised data was health surveillance and did not require NHS Research ethics review.

To enhance global control of encephalitis and hepatitis caused by rabies-(RABV), Japanese encephalitis-(JEV), hepatitis B-virus (HBV), and enterovirus 71 (EV71) novel immunisation strategies are needed. Therefore, a multipathogen modified Vaccinia Ankara vector, expressing antigens from the above pathogens, was constructed. Two recombinants, one carrying the EV71 and JEV pathogen sequence and one the RABV-HBV pathogen sequence were generated. To ensure similar expression of the antigens, a T7-promoter was linked to the expression cassettes of all pathogen sequences. Direct regulation of this promoter was achieved through co-infection with a second T7-polymerase expressing MVA. Protein expression using this co-infection model of expression was demonstrated in vitro. To investigate the co-infection model of antigen delivery in vivo, a murine immunogenicity study was performed using the MVA-RABV-HBV recombinant. Although, serum antibodies against MVA were induced in all mice, no serum antibodies against RABV or HBV could be detected.

Introduction There are suggestions that virus co-infections may influence the clinical outcome of respiratory virus illness. We performed a systematic review of the literature to summarise the evidence. Methods MEDLINE, EMBASE, Ovid and WEB of Science databases, major organisation websites and reference lists of published studies were searched. The quality of studies was assessed using the STROBE tool (von Elm et al., 1) Individual study data was analyzed using odds ratios and 95% confidence intervals as a measure of association between exposure (co-infection), patient outcome and results summarised using forest plots and tables Results Nineteen (19) studies from all over the world were identified and included in the review. Most of the studies 73.7% (14/19) recruited children ≤6 years old. Evidence on the role of co-infection in increasing disease severity was inconclusive. In five out of eight studies, co-infection significantly increased risk of admission to general ward (OR: 2.4, 95% CI: 1.3 - 4.4, p = 0.005; OR: 2.4, 95% CI: 1.1 - 7.7, P = 0.04; OR: 3.1, 95% CI: 2.0 - 5.1, p =

Epstein–Barr virus (EBV) DNAemia in the first year posttransplantation has been studied extensively. There is a paucity of information on prevalence and sequelae of EBV infection in adult renal transplantation beyond the first year. This single-center study examines the relationship between EBV DNAemia and demographic, immunosuppressive, hematologic and infection-related parameters in 499 renal transplant recipients between 1 month and 33 years posttransplant. Participants were tested repeatedly for EBV DNAemia detection over 12 months and clinical progress followed for 3 years. Prevalence of DNAemia at recruitment increased significantly with time from transplant. In multivariate adjusted analyses, variables associated with DNAemia included EBV seronegative status at transplant (p = 0.045), non-White ethnicity (p = 0.014) and previous posttransplant lymphoproliferative disease (PTLD) diagnosis (p = 0.006), while low DNAemia rates were associated with mycophenolate mofetil use (p

Summary Background Fever with reduced consciousness is an important cause of hospital admission of children in sub-Saharan Africa, with high mortality. Cerebral malaria, diagnosed when acute Plasmodium falciparum infection and coma are recorded with no other apparent reason, is one important cause. We investigated whether viruses could also be an important cause of CNS infection in such patients, and examined the relative contribution of viral pathogens and malaria parasitaemia. Methods We did a prospective cohort study in Blantyre, Malawi. From March 1, 2002, to Aug 31, 2004, we enrolled children aged between 2 months and 15 years who were admitted to hospital with suspected non-bacterial CNS infections. Children with a cerebrospinal fluid (CSF) white cell count of less than 1000 cells per μL and negative bacterial microscopy and culture were deemed to have suspected viral CNS infection. Blood was examined for asexual forms of P falciparum. PCR was done on CSF or on post-mortem brain biopsy specimens to detect 15 viruses known to cause CNS infection. Findings Full outcome data were available for 513 children with suspected viral CNS infection, of whom 94 (18%) died. 163 children (32%) had P falciparum parasitaemia, of whom 34 (21%) died. At least one virus was detected in the CNS in 133 children (26%), of whom 43 (33%) died. 12 different viruses were detected; adenovirus was the most common, affecting 42 children; mumps, human herpes virus 6, rabies, cytomegalovirus, herpes simplex virus 1, and enterovirus were also important. 45 (9%) of the 513 children had both parasitaemia and viral infection, including 27 (35%) of 78 diagnosed clinically with cerebral malaria. Children with dual infection were more likely to have seizures than were those with parasitaemia alone, viral infection only, or neither (p

Aim To assess the role of imaging in the early management of encephalitis and the agreement on findings in a well-defined cohort of suspected encephalitis cases enrolled in the Prospective Aetiological Study of Encephalitis conducted by the Health Protection Agency (now incorporated into Public Health England). Materials and methods Eighty-five CT examinations from 68 patients and 101 MRI examinations from 80 patients with suspected encephalitis were independently rated by three neuroradiologists blinded to patient and clinical details. The level of agreement on the interpretation of images was measured using the kappa statistic. The sensitivity, specificity, and negative and positive predictive values of CT and MRI for herpes simplex virus (HSV) encephalitis and acute disseminated encephalomyelitis (ADEM) were estimated. Results The kappa value for interobserver agreement on rating the scans as normal or abnormal was good (0.65) for CT and moderate (0.59) for MRI. Agreement for HSV encephalitis was very good for CT (0.87) and MRI (0.82), but only fair for ADEM (0.32 CT; 0.31 MRI). Similarly, the overall sensitivity of imaging for HSV encephalitis was ∼80% for both CT and MRI, whereas for ADEM it was 0% for CT and 20% for MRI. MRI specificity for HSV encephalitis between 3–10 days after symptom onset was 100%. Conclusion There is a subjective component to scan interpretation that can have important implications for the clinical management of encephalitis cases. Neuroradiologists were good at diagnosing HSV encephalitis; however, agreement was worse for ADEM and other alternative aetiologies. Findings highlight the importance of a comprehensive and multidisciplinary approach to diagnosing the cause of encephalitis that takes into account individual clinical, microbiological, and radiological features of each patient., Highlights • We assessed the role of imaging in encephalitis. • We assessed the agreement between raters on scan interpretation. • Diagnosis for herpes simplex encephalitis (HSE) was good. • Agreement was worse for ADEM and other alternative aetiologies. • HSE can be dismissed if MRI normal 72 hours after neurological symptom onset (with negative CSF tests).

Merkel cell polyomavirus (MCPyV) was identified originally in association with a rare but aggressive skin cancer, Merkel cell carcinoma. The virus has since been found in the respiratory tract of some patients with respiratory disease. However, the role of MCPyV in the causation of respiratory disease has not been established. To determine the prevalence of MCPyV in 305 respiratory samples from immunocompetent and immunocompromised patients and evaluate their contribution to respiratory diseases, specimens were screened for MCPyV using single, multiplex, or real‐time PCR; co‐infection with other viruses was examined. Of the 305 samples tested, 10 (3.27%) were positive for MCPyV. The virus was found in two groups of patients: in 6 (2%) nasopharyngeal aspirate samples from children aged 26 days to 7 months who were immunocompetent; and in 4 (1.3%) of nasopharyngeal aspirate samples taken from patients aged 41 to 69 years who were severely immunosuppressed from leukemia or transplant therapy. Both groups had upper or lower respiratory tract infection. Co‐infections with other viruses were found in 30% of the MCPyV positive samples. The data present a pattern of infection similar to that seen with the polyomaviruses JC and BK in which the virus is acquired during childhood, probably by the respiratory route. The viruses then establish latency and become reactivated in the event of immunosuppression. J. Med. Virol. 83:2220–2224, 2011. © 2011 Wiley Periodicals, Inc.

The Monsall Unit, Infectious Diseases and Tropical Medicine Department, North Manchester General Hospital, Manchester, UK Enteric Virus Unit, Virus Reference Department, Centre for Infections, Health Protection Agency, Colindale, London, UK Central Manchester Foundation Trust, Department of Virology, Manchester, UK Molecular Diagnostics Department, Health Protection Agency North West, Manchester Royal Infirmary, Manchester, UK

The diagnosis of acute hepatitis C virus (HCV) infection is not straightforward; few people exhibit clinical symptoms and genome/antigen detection techniques do not indicate when infection had occurred. Here, a strategy to detect HCV RNA in the absence of antibody ('window-period') for diagnosis of acute infection is assessed. The sentinel surveillance of hepatitis testing study was used to retrospectively identify anti-HCV negative samples from high-risk individuals (2002-2003), for testing singly for HCV RNA. Additional samples were identified prospectively (2005) and tested in pools for HCV RNA. Positive samples were genotyped. Incidence and costs of adopting the pooling strategy were estimated. In the retrospective study, 8/390 (2.1%) samples were confirmed HCV RNA positive, anti-HCV negative. Prospectively, 3237 samples were tested in 325 pools. Five positive pools identified four confirmed HCV RNA positive patients (one false positive). Estimated incidence was 12.9 per 100 person-years in injecting drug users (IDUs) (retrospective study) and 3.7 per 100 person-years among drug/alcohol services and prison attendees (prospective study). Estimated costs were pound 850 per positive sample, in areas of higher risk. The yield from a window-period strategy depends upon the population tested. Pooled HCV RNA testing of anti-HCV negative samples from the current IDUs is realistic and relatively inexpensive to identify recently infected individuals.

Post-transplant lymphoproliferative disorder (PTLD) is a rare, serious complication following solid organ transplantation, with an incidence of 2.6 cases per 1000 patient years. Optimal treatment strategies and risk stratifications specific to kidney transplantation are lacking and PTLD mortality remains high. This study investigated survival and prognosis in 89 cases of PTLD presenting over 44 years at Manchester Royal Infirmary. Patient survival following diagnosis was 72% at 6 months, 67% at 1 year and 54% at 3 years. In multivariate analysis, a poorer 3 year survival was associated with acute kidney injury at diagnosis (p = 0.0001), impaired renal function (p = 0.04), early onset (p = 0.02), T cell disease (p = 0.02) and previous treatment with anti-thymocyte globulin (p = 0.04). The inclusion of graft function adds prognostic value to risk stratification and should be explored further. Strategies to improve survival should include timing and choice of immuno-chemotherapy, preparation for dialysis and aggressive surveillance for sepsis and treatment toxicity.

PURPOSE: Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. METHODOLOGY: Published sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between co-infection and disease outcome was assessed using logistic regression. RESULTS: The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5%; 8/13) of SeasFluA/hBoV co-infections were identified in patients that were admitted either to a general ward or the intensive care unit compared to 44.3% (66/149) of single SeasFlu A virus infections (OR 2.5 95% CI 0.67-9.34, p = 0.17). In a stratified analysis, there was a trend towards higher association between FluA, hCoV and hBoV with increasing age (especially in patients aged 24-45 years and >65 year old). CONCLUSION: Our hCoV RT-PCR protocol appeared to be of adequate analytical sensitivity for diagnosis. More and larger studies are needed to confirm the role of hCoV, hBoV in causing severe disease when they co-infect with influenza A viruses.

The prevalence of concurrent multitypic hepatitis C virus (HCV) infection is uncertain. A sensitive and specific approach to identifying minority HCV genotypes in blood is presented. Following serum extraction and reverse transcription PCR to amplify cDNA originating from the viral 5′ noncoding region, the amplified product mixture was treated with genotype-specific restriction endonuclease to digest the dominant genotype. Residual amplicons were subjected to PCR cloning and then to real-time DNA sequencing using a Pyrosequencer to identify the remaining genotypes. Dilution experiments showed that minority genotypes may be detected when they represent 1:10,000 of the total population and in serum specimens with viral loads as low as 1,000 IU/ml. Of 37 patients with bleeding disorders and 44 injecting drug users, infection by more than one HCV genotype was found in 7 (19%) and 4 (9%) patients, respectively. The low rate of detection in people at high risk of repeated HCV infection suggests that multitypic HCV carriage is uncommon.

This paper describes sentinel laboratory surveillance of hepatitis C antibody testing in England. Demographic and test result data were supplemented by follow-up questionnaires sent to the requesting clinician. Between October 2002 and September 2003 almost 75000 anti-HCV tests were performed in eight sentinel centres. More males were tested than females and over half of those tested were aged 25–44 years. Overall 5·7% (3333/58144, range 2·8–7·7%) individuals tested positive. Follow-up questionnaire data showed that 82% (1043/1277) of the positives had injecting drug use reported as the main risk exposure. The majority of negative individuals were undergoing routine screening as recommended for specific patient groups. Most individuals were asymptomatic. Antibody prevalence was estimated to be 34% in current injecting drug users and 42% in former injectors. Comparing positives to routine national surveillance suggests that only 53% (1782/3333) of diagnosed cases were reported. Sentinel laboratory data can provide valuable supplementary data to national surveillance.

This study examined children with an acute encephalopathy illness for evidence of viral infection, disordered blood-brain barrier function, intrathecal immunoglobulin synthesis, and interferon (IFN) production, and related their temporal occurrence to outcome. A prospective study of 22 children (13 males, 9 females; age range 1mo to 13y, median 2y 4mo), recorded clinical details, with serum and cerebrospinal fluid (CSF) analysis near presentation and then on convalescent specimens taken up to day 39 of the neurological illness. Outcome was assessed with standard scales between 18 months and 3 years after presentation. A history consistent with viral infection was given in 17 children but laboratory evidence of viral infection was found in only 7 (7/17). In 18 out of 21 children, an elevated CSF:serum albumin ratio indicative of impairment of the blood-CSF and blood-brain barriers was detected at some stage of the illness. In 14 of the 15 children with a raised immunoglobulin G index, and in 12 of the 14 children where the CSF was positive for oligoclonal bands, this was preceded by, or was observed at the same time as, an abnormal albumin ratio. Sixteen children (16/18) had elevated IFN-alpha levels in serum, or CSF, or in both. We conclude that these findings indicate an initial disruption of the blood-brain barrier followed by intrathecal antibody production by activated lymphocytes, clonally restricted to a few antigens. This is the first in vivo study to show this as an important pathogenetic mechanism of encephalitis in children. Poor outcome was associated with young age, a deteriorating electroencephalogram pattern from grade 1 to grade 2, and the degree of blood-brain barrier impairment, particularly when prolonged, but not with Glasgow Coma Scale score. The persistence of IFN-alpha was associated with a good prognosis.

Background: There is an increasing awareness of the need for external quality control of diagnostic virology. Objectives: To assess the quality of nucleic acid amplification tests (NAT) of herpes simplex within Europe. Study design: Herpes simplex virus (HSV) proficiency panels were produced at the Swedish Institute for Infectious Disease Control on behalf of the European Union Concerted Action for Quality Control of Nucleic Acid Amplification in 1999 and 2000. Nine reference laboratories evaluated the production process. Each panel consisted of 12 coded samples with various concentrations of inactivated, freeze-dried HSV type 1 (HSV-1), and HSV type 2 (HSV-2), or negative controls. Positive samples included HSV-1 and HSV-2 in a range of concentrations (2×102 to 2×107 genome copies per ml) similar to those found in cerebrospinal fluids from patients with HSV encephalitis. Results: Sixty-six participants reported a total of 76 data sets for panel 1, and 71 reported 78 data sets for panel 2. The majority of the participants employed qualitative ‘in-house’ polymerase chain reaction (PCR) methods, either in a single, nested or semi-nested format. For panel 2, 9 laboratories reported use of ‘real-time’ PCR in contrast to 3 for panel 1. Three laboratories submitted quantitative results on both panels. Thirty percent of the data sets had correct results for the entire panel 1. In 6 data sets (8%) a total of 11 false positive results were reported. For panel 2, 28% of the data sets had correct result. Nineteen false positive results were reported in 14 data sets (18%), but most of the incorrect results reflected a lack of test sensitivity. Conclusions: The relatively high frequency of false positive results and the large number of false-negative results, albeit at low copy number, stress the need for improvement in the quality of HSV NAT and for external quality control programmes.

SUMMARYRespiratory virus infections cause a significant number of hospitalization and deaths globally. This study investigated the association between single and multiple respiratory virus infections and risk of admission to a general ward, intensive care unit or death in patients aged 0–105 years (mean ± s.d. = 24·4 ± 24·1 years), from North West England, that were tested for respiratory virus infections between January 2007 and June 2012. The majority of infections were in children aged ⩽5 years. Dual or multiple infections occurred in 10·4% (1214/11 715) of patients, whereas single infection occurred in 89·6% (10 501/11 715). Rhinovirus was the most common co-infecting virus (occurring in 69·5%; 844/1214 of co-infections). In a multivariate logistic regression model, multiple infections were associated with an increased risk of admission to a general ward [odds ratio (OR) 1·43, 95% confidence interval (CI) 1·2–1·7,P P P = 0·05, respectively); admitted to an intensive-care unit or dying (OR 1·5, 95% CI 1·20–2·0,P = 0·001 and OR 1·60, 95% CI 1·02–2·40,P = 0·04, respectively). This result emphasizes the importance of RSV, hPIV and mixed infections and calls for research on vaccines, drugs and diagnostic tests targeting these respiratory viruses.

Setting: Cecilia Makiwane Hospital, Mdantsane, Eastern Cape, Republic of South Africa. Objective: To assess the role of the semi-automated Roche COBAS AMPLICORTMMycobacterium tuberculosis PCR test in the diagnosis of tuberculous meningitis (TBM). Design: Eighty-three specimens of cerebrospinal fluid (CSF) were collected prospectively from 69 patients with suspected TBM. The COBAS AMPLICOR TB PCR test was compared with the manual AMPLICORTMTB PCR test, clinical and cerebrospinal fluid (CSF) findings, direct ZN smear and radiometric TB culture. Results: CSF from 7/40 (17.5%) patients treated for TBM were positive by TB COBAS AMPLICORTM. The sensitivity of the test was not significantly different (p=0.375) from the manual TB AMPLICORTMPCR test. The comparative sensitivities of the TB COBAS AMPLICORTMPCR and the manual AMPLICOR PCR for detecting cases of definite and probable TBM from CSF collected within 9 days of commencing antituberculosis treatment were 40% and 60% respectively. All 29 patients not treated for TBM were negative by COBAS AMPLICORTM, giving a specificity of 100%. Conclusion: The COBAS AMPLICORTMTB PCR test is a rapid and highly specific diagnostic test for TBM. However, there was a non-significant trend favouring slightly greater sensitivity using the manual AMPLICORTMTB PCR test.

Glycoprotein G of HSV-2 (gG2) and a peptide, corresponding to a previously recognised immunodominant epitope spanning residues 561-578 of the protein, were compared directly for type-specific serodiagnosis of HSV-2. The protein was affinity purified and obtained in a commercially available EIA kit while the peptide, previously designated as peptide 55, was made as a multiple antigenic peptide. A panel of 100 characterised serum samples (60 HSV-2 positive, 20 HSV-1 positive and 20 HSV negative) was screened using the two antigens. The intact protein and peptide 55 showed the same sensitivity for antibodies in the serum of HSV-2 infected individuals, reacting with 96.7% (58/60) of the samples. The peptide did not react with any of the HSV-1 positive or HSV negative sera. In contrast, gG2 gave a number of false positive results, reacting with 20% (4/20) of the HSV-1 positive sera and 10% (2/20) of the HSV negative sera. The superior performance of peptide 55, together with the very much lower costs of its production, compared with gG2 suggest that the peptide will become the antigen of choice in enzyme immunoassays for type-specific serodiagnosis of HSV-2.

Evaluation was made of three enzyme-linked immunosorbent assay (ELISA) formats; varicella-zoster virus (VZV) indirect ELISA; VZV IgM capture using biotin and VZV IgM capture using peroxidase, for the detection of VZV-specific IgM antibodies in human sera. It was observed that there was no significant difference in sensitivity of detection using the three formats but there were important practical differences in the number of steps and hence time for assay completion between the three assay formats. All assays showed some cross-reactivity with sera containing anti-HSV1 antibodies.

HIV-positive patients are at increased risk of developing adenovirus infection, particularly of the gastrointestinal tract and with unusual subgenus D strains. To investigate humoral immunity to these strains of adenoviruses, the humoral immune response was examined in longitudinal samples of serum against isolates collected from a prospective study of HIV-positive patients with subgenus D adenovirus infection. Of 10 HIV-positive patients developing adenovirus infection, 3 had chronic infection (8–>27 months) with one serotype, 3 had chronic infection (≥10 months) with changing serotypes and 4 had acute and self-limiting adenovirus infection (

Subgenus identification of adenoviruses is of clinical importance and is as informative as identification by serotype in most clinical situations. A PCR-based identification of adenovirus subgenera A, B, C, D, E, and F and sometimes serotypes is described. The PCR uses nonnested primer pair ADRJC1-ADRJC2, which targets a highly conserved region of the adenovirus hexon gene, has a sensitivity of 10 to 40 copies of adenovirus type 2 (Ad2) DNA, and generates 140-bp PCR products from adenovirus serotypes representative of all the subgroups. The PCR products of all subgroups can be differentiated on the basis of the restriction fragment patterns produced by a total of five restriction endonucleases. In addition, serotypes Ad40 and Ad41 (subgroup F) and important serotypes of subgroup D (Ad8, Ad10, Ad19, and Ad37) can easily be differentiated, but serotypes within subgroups B and C cannot. The method was assessed by blind subgenus identification of 56 miscellaneous clinical isolates of adenoviruses. The identities of these isolates at the subgenus level by the PCR correlated 91% (51 of 56) with the results of serotyping by the neutralization test, and 9% (5 of 56) of clinical isolates produced discordant results.

Background The role of two recently identified polyomaviruses, KI and WU, in the causation of respiratory disease has not been established. Objectives To determine the prevalence of KI and WU viruses (KIV and WUV) in 371 respiratory samples and evaluate their contribution to respiratory disease. Study Design Specimens were screened for KIV and WUV using single, multiplex or real time PCR; co-infection with other respiratory viruses was evaluated. Results Of the 371 samples analysed, 10 (2.70%) were positive for KIV and 4 (1.08%) were positive for WUV yielding an overall case prevalence of KIV and WUV infection of 3.77%. KIV and WUV were identified in patients aged 45 years (3 patients) with upper respiratory tract infection. Co-infections were found in 5 (50%) and 3 (75%) of the KIV and WUV positive samples, respectively. Conclusions This study supports previous conclusions that KIV and WUV detection in the respiratory tract may be coincidental and reflect reactivation of latent or persistent infection with these viruses. The age distribution of KIV and WUV infection in this study mirrors that found for the other human polyomaviruses, BK and JC.

The Amplicor Enterovirus PCR test was compared with viral culture for the detection of enteroviruses in cerebrospinal fluid (CSF) specimens. In a multicenter study in which nine laboratories participated, a total of 476 CSF specimens were collected from patients with suspected aseptic meningitis. Sixty-eight samples were positive by PCR (14.4%), whereas 49 samples were positive by culture (10.4%), demonstrating that the Amplicor Enterovirus PCR test was significantly more sensitive than culture ( P < 0.001). After discrepancy analysis the sensitivity and specificity of the Amplicor Enterovirus PCR test obtained by using viral culture as the “gold standard” were 85.7 and 93.9%, respectively. Our results with the CSF specimens collected in different countries demonstrate that the Amplicor test is capable of detecting a large variety of enterovirus serotypes and epidemiologically unrelated isolates in CSF specimens from patients with aseptic meningitis. The Amplicor Enterovirus PCR test is a rapid assay which can be routinely performed with CSF samples and is an important improvement for the rapid diagnosis of enteroviral meningitis.

Several nucleic acid-based amplification tests are available for the detection of Mycobacterium tuberculosis , but few data are available on their use in the diagnosis of tuberculous meningitis (TBM). We performed a prospective study to assess the Roche AMPLICOR Mycobacterium tuberculosis PCR test (TB AMPLICOR) for use in the diagnosis of TBM and compared it with direct Ziehl-Neelsen staining of smears, radiometric culture for M. tuberculosis , and clinical and cerebrospinal fluid (CSF) findings. Eighty-three CSF specimens collected from 69 patients with suspected meningitis in South Africa were tested by TB AMPLICOR. On the basis of clinical and laboratory findings, 40 of these patients were treated for TBM and 29 patients were not treated for TBM. Ten CSF samples from 10 patients were positive by TB AMPLICOR. Seven of these 10 patients were classified as having definite TBM, 2 were classified as having probable TBM, and 1 was classified as having possible TBM. The sensitivity of TB AMPLICOR for detecting cases of definite and probable TBM in patients from whom CSF specimens had been collected less than 10 days into antituberculosis treatment was 60.0%. Specimens from all 29 patients not treated for TBM were negative by the TB AMPLICOR, giving a 100% specificity. TB AMPLICOR is therefore more sensitive than the combination of Ziehl-Neelsen staining of smears and radiometric culture for M. tuberculosis and is a rapid and highly specific diagnostic test for TBM.

Summary: We evaluated Cobas AmplicorTM, a highly automated polymerase chain reaction (PCR) system, to test first-void urine (FVU) and urethral swab specimens for Chlamydia trachomatis and Neisseria gonorrhoeae in men attending a sexually transmitted infection (STI) clinic. Results were compared against an inhouse radioimmune dot blot (DB) test for C. trachomatis and selective culture for N. gonorrhoeae . Three hundred and ninety sets of specimens were obtained from 378 consecutive new and returned-new patients. Gonorrhoea prevalence was 9.49%, with no significant difference in sensitivity or specificity between culture and PCR. Chlamydia prevalence was 15.4%, with sensitivities of: DB 55%, PCR of FVU 86.7%, urethral swab PCR 90%. The specificity of PCR on FVU and urethral swabs was 100%. We have shown that Cobas AmplicorTM PCR is highly sensitive and specific in the diagnosis of chlamydia and gonorrhoea in men attending an STI clinic. Further economic and scientific studies are needed to determine the costeffectiveness of this technique for screening in primary care settings.

The sensitivity and specificity of PCR of CSF for the diagnosis of progressive multifocal leuko encephalopathy is estimated at 75 and 98.5%, respectively. However, inter-laboratory and inter-technique variations have been shown to produce wide variations. A 10-fold dilution series of JC virus in cerebrospinal fluid was prepared and circulated for `blind' evaluation in laboratories participating in a European Union Concerted Action on Virus Meningitis and Encephalitis. Six of seven laboratories returned results with sensitivity of between 10 and 1 JCV DNA copy equivalents per 10 μ l of CSF, one laboratory detected 10 5 copies per 10 μ l of CSF. These results demonstrate the feasibility of using virus diluted in CSF for comparison of PCR techniques, and that the range of sensitivity of JCV PCR in proficient laboratories is between 10 and 1 copy equivalents per 10 μ l of CSF.

BACKGROUND: There is little information in the literature describing the relationship between posttransplantation lymphoproliferative disorder (PTLD) incidence and presentation with both recipient Epstein-Barr virus (EBV) serostatus and EBV status of PTLD histology, particularly in the late posttransplantation period. METHODS: This study reports the largest UK single-center, single-organ analysis of PTLD to date in a retrospective cohort study of 80 cases occurring in 4189 adult renal transplant recipients. RESULTS: The incidence rate was 2.6 cases per 1000 patient-years (95% confidence interval [95% CI], 2.1-3.2) for PTLD, 1.8 (95% CI, 1.4-2.4) for non-Hodgkin's lymphoma, and 0.2 (95% CI, 0.07-4.2) for Hodgkin's lymphoma. Non-Hodgkin's lymphoma occurred at a rate 7.6 times that of the adult general population in England, whereas the rate for Hodgkin's lymphoma was 5.9 times. The incidence of PTLD was highest during the 10th to 14th posttransplantation years. Early-onset disease was associated with EBV-seronegative recipient status, EBV-positive histology, and the involvement of extranodal sites. PTLD occurring in EBV-seronegative recipients was associated with EBV nuclear antigen antibody deficiency, polymorphic disease, and the involvement of extranodal sites. EBV-negative histology occurred in 32% of cases at a median time to presentation of 109 months. PTLD involving the allograft, central nervous system, and skin was uncommon and occurred late. CONCLUSION: The incidence of PTLD is highest in the late posttransplantation period. Close clinical surveillance and education for transplant recipients is required for the duration of time while immunosuppressed. Failure to detect EBV DNA in blood should not reassure, particularly in patients with symptoms such as abdominal pain, oropharyngeal complaints, neck lumps, and B-symptoms.

Aims/background - Herpes simplex virus (HSV) may establish latent infection in the cornea and therefore be transmissible by corneal transplantation. Monitoring of donor cornea culture medium was evaluated for HSV infection. Methods - HSV was sought using virus isolation in cell culture, and its DNA was amplified to detectable levels using the polymerase chain reaction (PCR). Results - Virus isolation in cell culture was negative on neat, cell pellet, and cell free supernatant prepared from the spent culture media of 80 corneas. Three cell pellets (3.8%) were positive for HSV DNA. The PCR positive culture negative results might have reflected latent rather than active HSV infection of the cornea. Post transplant follow up of the three recipients of corneas with HSV PCR positive organ culture media revealed no evidence of HSV induced eye disease or primary graft failure. Conclusion - Screening of corneal culture medium for HSV by virus culture or for HSV DNA by PCR could not be recommended.

Five cases of apparent relapse of herpes encephalitis were investigated. All patients recovered after antiviral and corticosteroid therapy. Samples of CSF taken from the patients at intervals through the initial and subsequent encephalitic episode were examined. PCR amplification of a 351 bp sequence from the Herpesvirus simplex (HSV) thymidine kinase gene demonstrated the presence of HSV DNA in CSF taken during the initial encephalitic illness but not during the second encephalitic episode. Intrathecal synthesis of HSV antibody (HSV antibody index > 1.9) was observed in all cases following the first episode, and there appeared to be no significant increase in intrathecal antibody synthesis in the second episode. High levels of CSF myelin basic protein were found during the acute phases of both the initial and the subsequent encephalitic illnesses. These data suggest that at least in our series of five patients, relapse following HSE may not be due to active viral replication.

Adenoviruses and herpes simplex virus (HSV) can cause clinically indistinguishable episodes of acute eye disease. Adenovirus infection is associated with nosocomial outbreaks and HSV may result in episodes of recurrent ocular inflammation. In a comparison of multiplex PCR for the two viral DNAs and virus isolation in cell culture, identical results were obtained for 18 of 20 specimens (positive for adenovirus in 5, HSV in 5, and negative in 8). One specimen was falsely negative for each viral DNA. Inclusion of human beta-globin primers in the adenovirus-HSV reaction was precluded by a consequential 10--100-fold reduction in sensitivity for the two viral targets and by the failure of beta-globin DNA amplification at the annealing temperature (45 degrees C) required to ensure detection of adenoviruses of serotypes 7 and 11 with the selected adenovirus primers. A single-target beta-globin PCR gave positive results with 19 of the 20 specimens prepared by treatment with proteinase K lysis buffer, indicating the effectiveness of this simple DNA extraction procedure. Nonetheless, the availability of effective antiviral therapy for HSV made monitoring for extraction failure using human primers crucial to avoid false-negative results for HSV DNA. Adenovirus-HSV PCR has considerable potential for the rapid diagnosis of viral eye disease particularly if beta-globin primers can be included in the reaction.

Two polymerase chain reaction (RT-PCR) assays were developed to allow rapid detection of enteroviral RNA in cerebrospinal fluid samples (CSF). Primers homologous to the conserved 5′ noncoding region of the enterovirus genome were designed. The RT-PCR product size was-500 bp (479 bp for Poliovirus, 500 bp for Cox-sackievirus) and was visualized using ethidium bromide-stained gels. Assay 1 utilized Moloney Murine Leukaemia Virus Reverse Transcriptase (MMLV-RTase) for reverse transcription and Taq polymerase for subsequent PCR. Assay 2 utilized a thermoactive DNA polymerase of Thermus thermophilus (rTth enzyme) for both reverse transcription and DNA amplification. In addition, in Assay 2 reverse transcription and PCR wer eaccomplished within the same reaction tube. Both assays detected between 1 and 0.02 TCID50 of prototype strains of Polio and Coxsackie type B viruses propagated in VERO cell and spiked in a pooled preparation of CSF samples from patients with noninfective neurological disorders. However, Assay 1 was 10-fold more sensitive than Assay 2 when applied to the detection of enteroviral RNA in CSF samples from patients with etiologically well characterized acute aseptic meningitis. © Wiley-Liss, Inc.

A new, rapid, and simple method for the isolation of either RNA or DNA from cerebrospinal fluid samples for subsequent amplification by specific polymerase chain reaction (PCR) assays is described. The technique involves a single extraction with a guanidinium thiocyanate acid (GuSCN) buffer, and does not require the use of organic solvents. Applied to the recovery of enteroviral RNA, herpes simplex virus (HSV) and Varicella-zoster virus (VZV) DNAs the method has proved to be of equivalent or better efficiency than established methods of nucleic acid separation but is less laborious and time consuming. The simplicity of the procedure permits the processing of large numbers of samples and the use of a single preparative method for either RNA or DNA PCR makes it an attractive method for the routine laboratory.

SUMMARYSurveillance of acute hepatitis B in England is necessary to estimate incidence, determine routes of transmission and inform public health actions. Here we describe an automated process to extract information on testing for markers of hepatitis B infection in English sentinel laboratories between 2002 and 2008. The resulting data were used to identify individuals with acute infections, describe their characteristics and estimate the incidence of infection. Two-thirds of acute infections were in males. Heterosexual exposure and injecting drug use were the main risks reported. Annual incidence was estimated at 1·3/100 000 person-years overall (1·7 and 0·6 for males and females, respectively) and declined each year. Automated extraction of hepatitis B markers, including quantitative results where available, can help to classify HBV status more accurately for surveillance. HBV incidence in England is at its lowest level in recent years.

Electron microscopy (EM), real-time polymerase chain reaction (PCR) and conventional PCR were used to identify viruses associated with infection in 2 transplantation patients. An autologous haematopoietic stem cell, liver and renal transplant recipient was found to be positive for simian virus 40 (SV40). Dual BK virus and SV40 infection was found in a heart and renal transplantation patient. SV40 infection can occur in immunocompromised patients. © 2011 Informa Healthcare.

A competitive enzyme-linked immunosorbent assay (ELISA) for determining HSV antibody status was developed and evaluated in a study to investigate the prevalence of HSV antibodies in blood donors. When compared with the radioimmunosorbent assay (RIA) and the complement fixation test (CFT) the competitive ELISA was less sensitive than the RIA but more sensitive than the CFT. A total of 224 251 (89.24%) samples gave concordant results in the RIA and ELISA compared with 209 251 (83.26%) in the CFT and RIA. HSV antibody was found in 40% of blood donors 60 years old. A further 37 samples collected from 37 prospective bone marrow transplant recipients were tested in the competitive ELISA and the CFT. Thirty (81%) gave concordant results; 63% were antibody-positive. The discordant samples were tested in the RIA. All seven samples were antibody-positive in the ELISA and RIA but four were antibody-negative in the CFT. The remaining three samples were anticomplementary. A total of nine of the 26 (34.6%) patients with serological evidence of HSV infection before transplantation had evidence of HSV infection post-transplant. By contrast, not one of the HSV antibody-negative transplant recipients had evidence of HSV infection post-transplant.

We investigated the cost-effectiveness of strategies for screening pregnant women for herpes simplex virus (HSV) genital infection. The cost of performing tests for HSV-1 antibody and for HSV-2 antibody on each serum was likely to average approximately 10 pounds sterling per sample and the total cost of screening 37,500 pregnancies in Manchester would be between 0.4 pounds sterling and 0.5 pounds sterling million per year. This estimated cost might prevent the development of neonatal herpes due to a primary HSV infection. However, initial HSV-2 infection is also associated with neonatal herpes and therefore the above cost-estimates might be a gross underestimate.

OBJECTIVES: To assess the feasibility and utility of sentinel laboratory surveillance of HIV testing as a tool for understanding patterns and trends in HIV testing in a range of healthcare services. METHODS: Data on all anti-HIV antibody tests carried out by the Leeds Teaching Hospital Trust laboratory over a 12-month period were collated and analysed by demographic information and place of test. Individuals who tested positive were matched to the national database of HIV diagnoses to identify the proportion newly diagnosed with HIV. RESULTS: 41,013 individuals over 1 year of age were tested at least once for HIV during the study period, of whom 0.8% (n=312) were positive. The majority of individuals (77%) were tested in a genitourinary medicine (GUM) clinic or as part of antenatal care, while routine testing of people undergoing haemodialysis, fertility treatment or occupational health screening accounted for a further 13% of those tested. Few individuals (

Objectives To describe testing for hepatitis C virus (HCV) in sexual health services in England between 2002 and 2007, using data from a sentinel surveillance study of hepatitis testing. Methods Data on all anti-HCV tests carried out between 2002 and 2007 were collected from 20 participating laboratories. Test requests originating in sexual health services were identified, allowing analysis of the demographic and clinical characteristics of individuals tested in this setting. KC60 statutory returns data were used to estimate the proportion of new genitourinary medicine clinic attendees tested for hepatitis C each year. Results 90 424 individuals were tested for anti-HCV in 100 sexual health clinics; 3.2% (n=2858) were found to be positive. Multivariable analysis showed anti-HCV status to be associated with male sex and a reported history of injecting drug use. In those clinics for which data on trends were available, testing for anti-HCV increased over the study period and the percentage testing positive decreased. KC60 data suggested that most clinics tested less than 20% of new patients for anti-HCV, although the proportion of patients tested increased over time. Conclusions Sexual health services have become increasingly important locations for hepatitis C testing in England, although the proportion of patients testing positive is low compared with other settings. We suggest that testing in this setting could be better targeted to those most at risk of infection by thorough investigation of risk factors among service users.

Herpes simplex virus (HSV) glycoprotein G (gG2) has been used as the basis of many serological assays for the detection of HSV type 2 (HSV-2)-specific antibodies. In the present study, an enzyme-linked immunosorbent assay (ELISA), the Pathozyme Viro HSV-2 immunoglobulin G (IgG) ELISA (Omega Diagnostics, Alva, United Kingdom), based on an immunodominant epitope of gG2 presented in a branched-chain format (peptide 55), was compared with two commercially available gG2-specific assays, the Bioelisa HSV-2 IgG assay (Biokit, S.A., Barcelona, Spain) and the HerpesSelect HSV-2 IgG assay (Focus Diagnostics, Cypress, CA). A panel of 218 well-characterized serum samples was tested. Thirty-one samples were determined to be HSV-2 IgG antibody positive and 164 samples were determined to be negative with all three kits. The levels of concordance between the tests were 95.9% between the Omega and HerpeSelect assays, 90.8% between the Omega and Bioelisa assays, and 94.5% between the HerpeSelect and Bioelisa assays. Twenty-three samples gave discordant results. Western blot results showed that of these, the results for 77% were correctly identified by the Omega assay, the results for 68% were correctly identified by the HerpeSelect assay, and the results for 13.6% were correctly identified by the Bioelisa assay. Although there was a high level of agreement between the results obtained by the three assays and no false-positive results were detected by any of the three kits, confirmation of the results for samples with discordant results by Western blotting suggested that the peptide 55-based Omega assay is the most sensitive and specific assay among the assays evaluated.