Virological Samples Research Articles

Representativeness, Vaccination Uptake, and COVID-19 Clinical Outcomes 2020-2021 in the UK Oxford-Royal College of General Practitioners Research and Surveillance Network: Cohort Profile Summary

The Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) is one of Europe's oldest sentinel systems, working with the UK Health Security Agency (UKHSA) and its predecessor bodies for 55 years. Its surveillance report now runs twice weekly, supplemented by online observatories. In addition to conducting sentinel surveillance from a nationally representative group of practices, the RSC is now also providing data for syndromic surveillance. The aim of this study was to describe the cohort profile at the start of the 2021-2022 surveillance season and recent changes to our surveillance practice. The RSC's pseudonymized primary care data, linked to hospital and other data, are held in the Oxford-RCGP Clinical Informatics Digital Hub, a Trusted Research Environment. We describe the RSC's cohort profile as of September 2021, divided into a Primary Care Sentinel Cohort (PCSC)-collecting virological and serological specimens-and a larger group of syndromic surveillance general practices (SSGPs). We report changes to our sampling strategy that brings the RSC into alignment with European Centre for Disease Control guidance and then compare our cohort's sociodemographic characteristics with Office for National Statistics data. We further describe influenza and COVID-19 vaccine coverage for the 2020-2021 season (week 40 of 2020 to week 39 of 2021), with the latter differentiated by vaccine brand. Finally, we report COVID-19-related outcomes in terms of hospitalization, intensive care unit (ICU) admission, and death. As a response to COVID-19, the RSC grew from just over 500 PCSC practices in 2019 to 1879 practices in 2021 (PCSC, n=938; SSGP, n=1203). This represents 28.6% of English general practices and 30.59% (17,299,780/56,550,136) of the population. In the reporting period, the PCSC collected >8000 virology and >23,000 serology samples. The RSC population was broadly representative of the national population in terms of age, gender, ethnicity, National Health Service Region, socioeconomic status, obesity, and smoking habit. The RSC captured vaccine coverage data for influenza (n=5.4 million) and COVID-19, reporting dose one (n=11.9 million), two (n=11 million), and three (n=0.4 million) for the latter as well as brand-specific uptake data (AstraZeneca vaccine, n=11.6 million; Pfizer, n=10.8 million; and Moderna, n=0.7 million). The median (IQR) number of COVID-19 hospitalizations and ICU admissions was 1181 (559-1559) and 115 (50-174) per week, respectively. The RSC is broadly representative of the national population; its PCSC is geographically representative and its SSGPs are newly supporting UKHSA syndromic surveillance efforts. The network captures vaccine coverage and has expanded from reporting primary care attendances to providing data on onward hospital outcomes and deaths. The challenge remains to increase virological and serological sampling to monitor the effectiveness and waning of all vaccines available in a timely manner.

Exploring the drop in flu cases during the 2020–2021 season: The Italian case study

To explore the 2020-2021 influenza season by describing the case of Italy. FluNet was searched for Italian data on virological samples. French, German, and Spanish data were collected for comparison. InfluNet was used for Italian epidemiological data on influenza-like illness (ILI). Data were extracted for the period from the 42nd week of 2020 to the 16th week of 2021 and for the previous 5-year period. The Containment and Health Index were used to describe the containment measures. Among 6818 samples, 0% were positive in Italy in the 2020-2021 season (28.8% in the previous 5-year period; the percentage change in the total number of tested specimens was -51.3%). In France, Germany, and Spain, the percentage change was -23%, -7%, and -61%, respectively. The Italian ILI incidence remained below the baseline levels (mean 0.0144/100,000 inhabitants; range 0.0085-0.0204). In the previous 5-year period, the mean incidence was 0.041/100,000 inhabitants. With the increase in containment measures, a deflection of ILI incidence was described (P=.015). Despite the reduced number of collected specimens compared to previous seasons and a slight rise in influenza vaccination rates, containment measures represent the most likely factor that helped to reduce cases in the 2020-2021 influenza season in Italy.

Transmission characteristics, replication patterns and clinical manifestations of human monkeypox virus—an in-depth analysis of four cases from Germany

ObjectiveSince April 2022, increasing numbers of monkeypox (MPX) cases have been reported outside endemic areas as part of an international outbreak. Our study shows aspects of clinical manifestations as well as epidemiological and virological features impacting transmission, for which only scarce data are available so far. MethodsWe present a descriptive study consisting of epidemiological, clinical and virological data of four patients with confirmed MPX diagnosis. Follow-up examinations included in-depth virological investigations, including MPX virus-specific quantitative PCR and virus isolation. ResultsBetween 22 May 2022, and 21 June 2022, four patients with MPX were evaluated. The number of lesions ranged between one and more than 30, with asynchronous eruptions. The periorificial distribution of initial lesions together with the case histories strongly suggest human-to-human transmission during intimate contacts in sexual activities. None of the patients reported about memorable lesions on the skin of potential risk contacts. Virological sampling showed positive MPX virus-specific quantitative PCR results from swabs of the primary lesions (until day 22 after symptom onset), pharyngeal and anal mucosa, urine, seminal fluid, blood and samples of non-affected skin. Virus isolation was positive in 6/14 samples (lesional skin, anal and pharyngeal mucosa). One patient required inpatient treatment for bacterial superinfection; in another patient, three sexually transmitted co-infections were present. ConclusionsOur report demonstrates asynchronous multiple-site lesions of MPX with prolonged PCR positivity in mucosal swabs, swabs of non-affected skin, urine and seminal fluid. In addition, infectious virus was confirmed on lesional skin and mucosal swabs. The observed virological kinetics together with the suspected pre-symptomatic transmission may lead to effective and sustained human-to-human transmission, particularly in sexual networks. Preventive measures such as vaccination and post-exposure prophylaxis may become important for MPX control in vulnerable groups.

Prevalance of Schmallenberg orthobunyavirus (SBV) infection in sampled ruminants in Turkey's Eastern Mediterranean region between 2015 and 2017

Schmallenberg orthobunyavirus (SBV), first discovered in 2011, belongs to the Orthobunyavirus genus of the Peribunyaviridae family. SBV, which predominantly infects ruminants, can cause severe fetal malformations when pregnant animals are infected during a critical phase of gestation.In this study, 1590 blood serum samples from cattle, sheep, and goats were obtained for serological investigation and 1604 specimens for virological investigation (including 1414 whole blood with EDTA, 165 vaginal swab samples from aborting animals, and tissue samples from 25 dead and/or aborted fetuses) in private and family-type ruminant establishments in Turkey's Eastern Mediterranean region. All the blood serum samples were tested for the presence of antibodies using ELISA, which showed SBV antibodies in 29.11% (95% CI: 26.89%–31.35%). The virological samples were tested using real-time RT-PCR for SBV nucleic acid presence, which showed 3.17% (95% CI:2.32%–4.04%) were positive. Finally, 10 different Culicoides species (a total of 29,156 Culicoides, including 16,005 females and 13,151 males) were tested to identify the vectors thought to carry infections in the region. However, no SBV nucleic acid was detected in the Culicoides pools.

High-Performance Liquid Chromatography Mapping Method for the Structural Analysis of N-Glycans at the Molecular, Cellular, and Tissue Levels.

Glycans on viruses are major molecules that mediate the communication of the viruses with host cells. Investigating the structure of glycans may be important in the characterization of viruses. In this regard, the high-performance liquid chromatography (HPLC) is a widely used analytical technique. We developed a multidimensional HPLC mapping method that identifies glycan structures. This is achieved by separating and purifying glycans using three types of HPLC columns and comparing the elution time data with known data. This method enables the easy profiling of glycans at the molecular, cellular, and tissue levels and can be used to study the glycans of virological samples such as virus and their hosts. It also enables the discrimination of isomers, which is difficult via mass spectrometry. In this paper, we describe in detail the principle and method of the structural analysis of N-type glycans using the proposed method.

Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria.

BackgroundDeep sequencing could improve understanding of HIV treatment failure and viral population dynamics. However, this tool is often inaccessible in low- and middle-income countries.ObjectivesTo determine the genetic patterns of resistance emerging in West African HIV-1 subtypes during first-line virological failure, and the implications for future antiretroviral options.Patients and methodsParticipants were selected from a Nigerian cohort of people living with HIV who had failed first-line ART and subsequently switched to second-line therapy. Whole HIV-1 genome sequences were generated from first-line virological failure samples with Illumina MiSeq. Mutations detected at ≥2% frequency were analysed and compared by subtype.ResultsHIV-1 sequences were obtained from 101 participants (65% female, median age 30 years, median 32.9 months of nevirapine- or efavirenz-based ART). Thymidine analogue mutations (TAMs) were detected in 61%, other core NRTI mutations in 92% and NNRTI mutations in 99%. Minority variants (<20% frequency) comprised 18% of all mutations. K65R was more prevalent in CRF02_AG than G subtypes (33% versus 7%; P = 0.002), and ≥3 TAMs were more common in G than CRF02_AG (52% versus 24%; P = 0.004). Subtype G viruses also contained more RT cleavage site mutations. Cross-resistance to at least one of the newer NNRTIs, doravirine, etravirine or rilpivirine, was predicted in 81% of participants.ConclusionsExtensive drug resistance had accumulated in people with West African HIV-1 subtypes, prior to second-line ART. Deep sequencing significantly increased the detection of resistance-associated mutations. Caution should be used if considering newer-generation NNRTI agents in this setting.

Italian flu season 2020-2021: reasons for the drop and insights for the future

BackgroundHaving seen the trend of 2020 flu season in the Southern hemisphere, the objectives of this study were to describe the trend of 2020-21 flu season in Italy, relating it with containment measures undertaken due to COVID-19, and to provide insights for next flu seasons and prevention of airborne diseases.MethodsWe collected data on Italian influenza virological samples on FluNet. We also collected French, German and Spanish data as a comparison. Data on Italian ILI (influenza-like illness) surveillance system were assessed with InfluNet. We used the Containment and Health Index of the Oxford COVID-19 Government Response Tracker (OxCGRT) to evaluate the impact of containment measures on Italian ILI incidence (Spearman's correlation).ResultsNo sample out of 6818 tested positive to influenza virus in Italy in 2020-21 flu season; 21.6% of the samples tested positive to SARS-CoV-2. France, Germany and Spain registered a maximum of 0.10% of positive samples to influenza virus. In Italy the mean of positive samples to influenza virus in seasons from 2015-16 to 2019-20 was 28.8%; the mean number of processed samples in those seasons was 14008. ILI incidence in Italy remained at interseasonal levels during all flu season (mean 1.44/1000; range 0.85-2.04). According to the Containment and Health Index, with increasing containment measures a deflection of ILI incidence in Italy was described (p = 0.015).ConclusionsContainment measures, along with rise of seasonal flu vaccination, are the most likely factors to explain the drop in cases in Italian 2020-21 flu season. The reduction of cases in neighbouring countries lower the role of the downsizing of Italian surveillance system seen in 2020-21 compared to seasons from 2015-16 to 2019-20. Rules and conducts may perpetrate the benefit on the decreased disease activity seen in 2020-21 flu season.Key messages Containment measures and flu vaccinations are the most impacting factors on the drop of influenza cases in 2020-21 in Italy.Though the Italian surveillance system was downsized in 2020-21, the experience of neighbouring countries suggests that the decreased flu activity was factual.

Prospective Clinical, Virologic, and Immunologic Assessment of COVID-19 in Transplant Recipients.

Several studies have described the clinical features of COVID-19 in solid-organ transplant recipients. However, many have been retrospective or limited to more severe cases (hospitalized) and have not routinely included serial virological sampling (especially in outpatients) and immunologic assessment. Transplant patients diagnosed with COVID-19 based on a respiratory sample PCR were prospectively followed up to 90 d. Patients provided consent for convalescent serum samples and serial nasopharyngeal swabs for SARS-CoV-2 antibody (antinucleoprotein and anti-RBD) and viral load, respectively. In the 161 SOT recipients diagnosed with COVID-19, the spectrum of disease ranged from asymptomatic infection (4.3%) to hospitalization (60.6%), supplemental oxygen requirement (43.1%), mechanical ventilation (22.7%), and death (15.6%). Increasing age (OR, 1.031; 95% CI, 1.001-1.062; P = 0.046) and ≥2 comorbid conditions (OR, 3.690; 95% CI, 1.418-9.615; P = 0.007) were associated with the need for supplemental oxygen. Allograft rejection was uncommon (3.7%) despite immunosuppression modification. Antibody response at ≥14 d postsymptoms onset was present in 90% (anti-RBD) and 76.7% (anti-NP) with waning of anti-NP titers and stability of anti-RBD over time. Median duration of nasopharyngeal positivity was 10.0 d (IQR, 5.5-18.0) and shedding beyond 30 d was observed in 6.7% of patients. The development of antibody did not have an impact on viral shedding. This study demonstrates the spectrum of COVID-19 illness in transplant patients. Risk factors for severe disease are identified. The majority form antibody by 2 wk with differential stability over time. Prolonged viral shedding was observed in a minority of patients. Reduction of immunosuppression was a safe strategy.

Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021

BackgroundIn Japan, a part of confirmed patients’ samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. The present study aimed to estimate the actual number of cases with variant alpha and reconstruct the epidemiological dynamics.MethodsThe number of cases with variant alpha out of all PCR confirmed cases was estimated, employing a hypergeometric distribution. An exponential growth model was fitted to the growth data of variant alpha cases over fourteen weeks in Tokyo.ResultsThe weekly incidence with variant alpha from 18–24 January 2021 was estimated at 4.2 (95% confidence interval (CI): 0.7, 44.0) cases. The expected incidence in early May ranged from 420–1120 cases per week, and the reproduction number of variant alpha was on the order of 1.5 even under the restriction of contact from January-March, 2021, Tokyo.ConclusionsThe variant alpha was predicted to swiftly dominate COVID-19 cases in Tokyo, and this has actually occurred by May 2021. Devising the proposed method, any country or location can interpret the virological sampling data.

Influenza and Respiratory Virus Surveillance, Vaccine Uptake, and Effectiveness at a Time of Cocirculating COVID-19: Protocol for the English Primary Care Sentinel System for 2020-2021.

BackgroundThe Oxford–Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) and Public Health England (PHE) are commencing their 54th season of collaboration at a time when SARS-CoV-2 infections are likely to be cocirculating with the usual winter infections.ObjectiveThe aim of this study is to conduct surveillance of influenza and other monitored respiratory conditions and to report on vaccine uptake and effectiveness using nationally representative surveillance data extracted from primary care computerized medical records systems. We also aim to have general practices collect virology and serology specimens and to participate in trials and other interventional research.MethodsThe RCGP RSC network comprises over 1700 general practices in England and Wales. We will extract pseudonymized data twice weekly and are migrating to a system of daily extracts. First, we will collect pseudonymized, routine, coded clinical data for the surveillance of monitored and unexpected conditions; data on vaccine exposure and adverse events of interest; and data on approved research study outcomes. Second, we will provide dashboards to give general practices feedback about levels of care and data quality, as compared to other network practices. We will focus on collecting data on influenza-like illness, upper and lower respiratory tract infections, and suspected COVID-19. Third, approximately 300 practices will participate in the 2020-2021 virology and serology surveillance; this will include responsive surveillance and long-term follow-up of previous SARS-CoV-2 infections. Fourth, member practices will be able to recruit volunteer patients to trials, including early interventions to improve COVID-19 outcomes and point-of-care testing. Lastly, the legal basis for our surveillance with PHE is Regulation 3 of the Health Service (Control of Patient Information) Regulations 2002; other studies require appropriate ethical approval.ResultsThe RCGP RSC network has tripled in size; there were previously 100 virology practices and 500 practices overall in the network and we now have 322 and 1724, respectively. The Oxford–RCGP Clinical Informatics Digital Hub (ORCHID) secure networks enable the daily analysis of the extended network; currently, 1076 practices are uploaded. We are implementing a central swab distribution system for patients self-swabbing at home in addition to in-practice sampling. We have converted all our primary care coding to Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) coding. Throughout spring and summer 2020, the network has continued to collect specimens in preparation for the winter or for any second wave of COVID-19 cases. We have collected 5404 swabs and detected 623 cases of COVID-19 through extended virological sampling, and 19,341 samples have been collected for serology. This shows our preparedness for the winter season.ConclusionsThe COVID-19 pandemic has been associated with a groundswell of general practices joining our network. It has also created a permissive environment in which we have developed the capacity and capability of the national primary care surveillance systems and our unique public health institute, the RCGP and University of Oxford collaboration.

Biodistribution and serologic response in SARS-CoV-2 induced ARDS: A cohort study.

BackgroundThe viral load and tissue distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain important questions. The current study investigated SARS-CoV-2 viral load, biodistribution and anti-SARS-CoV-2 antibody formation in patients suffering from severe corona virus disease 2019 (COVID-19) induced acute respiratory distress syndrome (ARDS).MethodsThis is a retrospective single-center study in 23 patients with COVID-19-induced ARDS. Data were collected within routine intensive care. SARS-CoV-2 viral load was assessed via reverse transcription quantitative polymerase chain reaction (RT-qPCR). Overall, 478 virology samples were taken. Anti-SARS-CoV-2-Spike-receptor binding domain (RBD) antibody detection of blood samples was performed with an enzyme-linked immunosorbent assay.ResultsMost patients (91%) suffered from severe ARDS during ICU treatment with a 30-day mortality of 30%. None of the patients received antiviral treatment. Tracheal aspirates tested positive for SARS-CoV-2 in 100% of the cases, oropharyngeal swabs only in 77%. Blood samples were positive in 26% of the patients. No difference of viral load was found in tracheal or blood samples with regard to 30-day survival or disease severity. SARS-CoV-2 was never found in dialysate. Serologic testing revealed significantly lower concentrations of SARS-CoV-2 neutralizing IgM and IgA antibodies in survivors compared to non-survivors (p = 0.009).ConclusionsCOVID-19 induced ARDS is accompanied by a high viral load of SARS-CoV-2 in tracheal aspirates, which remained detectable in the majority throughout intensive care treatment. Remarkably, SARS-CoV-2 RNA was never detected in dialysate even in patients with RNAemia. Viral load or the buildup of neutralizing antibodies was not associated with 30-day survival or disease severity.

Replication of Influenza D Viruses of Bovine and Swine Origin in Ovine Respiratory Explants and Their Attachment to the Respiratory Tract of Bovine, Sheep, Goat, Horse, and Swine.

Bovine is considered the main reservoir of influenza D virus (IDV), however, low levels of seropositivity in other farmed species suggest a wide range of potential hosts. Nevertheless, it is not clear whether this scenario is the result of rare spillover events upon contact with bovines, or a lack of adaptation of IDV to these hosts. Among these species, sheep represents a crucial component of the rural economy in many developing countries, but little is known about its role in the ecology of the disease. To evaluate the susceptibility of sheep to IDV viruses of different origin, we used ovine respiratory tissues as an ex vivo model and investigated the infective phenotype of two IDV strains isolated from either bovine (IDV-BOV) or swine (IDV-SW). For translatability purposes, we included a parainfluenza type 3 virus, as positive control, given its known respiratory tropism in sheep. We performed a timed evaluation of the viral infectivity, cell tropism and the associated histopathology, by means of tissue culture infectious dose assays on supernatants and histological/immunohistochemical analyses on explanted tissues, respectively. To further investigate differences in the phenotype of these two strains and to identify the potential targets of replication in the most commonly land-based farmed mammalian species, we carried out virus binding assays on histological sections of the respiratory tract of bovine, caprine, ovine, horse and swine. Our results demonstrated that IDV successfully replicates in nasal, tracheal and lung ovine tissues, suggesting a moderate susceptibility of this species to IDV infection. Interestingly, despite the high genetic identity of these strains, IDV- BOV consistently replicated to higher titers than IDV-SW in all respiratory tracts, suggesting IDV viruses might display considerable levels of variability in their phenotype when crossing the species barrier. Virus binding assays confirmed a superior affinity of the IDV viruses for the bovine upper respiratory tract, and a preference for the pharyngeal epithelium of small ruminants, indicating possible targets to improve the sensitivity of virological sampling for diagnostic and post-mortem purposes. Further pathogenesis and cross-species transmission studies will be necessary to elucidate the ecology of IDV and eventually allow the design of cost-effective surveillance strategies.

Human T lymphotropic virus antibodies seroprevalence among healthy blood donors and high risk groups at Riyadh regional laboratory in Riyadh, Saudi Arabia

Aims: Transmission of human T lymphotropic viruses (HTLV) testing performed as routine pretransfusion screening. In Riyadh city the prevalence of HTLV1/2 among healthy volunteers in Riyadh city more than two decades. In addition, no information available related to the HTLV1/2 infections in HIV/AIDS patients. This study first aims to determine the prevalence of HTLV1/2 infections among healthy volunteers in Riyadh city. Second, as HTLV1/2 transmission similar as HIV routes, we assess rates of HTLV1/2 coinfection among patients infected with HIV. Materials and Methods: A retrospective study depends on the data obtained from Riyadh Regional Laboratory (RRL) for 3 years, 2017–2019. The samples enrolled in study consist of 114638 healthy blood donors and 243 patient samples referred to RRL virology samples. In addition, 474 HIV-infected patients were included. All serum samples tested to detect infection with HTLV1/2 by commercial CMIA or enzyme-linked immunosorbent assay kits and any positive results confirmed and differentiated by western blot. Results: Among of 114638 blood donations were tested, only two confirmed HTLV1 positive found from two (0.002%) donors, one of them is Saudi female and the second donor was expatriates. None was positive for anti-HTLV2. The overall HTLV1 prevalence was 1.7/100,000 donations during the 3 years tested. In addition, none of the referred sample was positive for anti-HTLV1/2. In addition, a large number of HIV-positive individual population enrolled none tested positive for HTLV1/2. Conclusions: HTLV seroprevalence is very low among healthy blood donors population in Riyadh city, which reflects the situation in the general population. However, screening for HTLV1/2 blood donors for the first donation from endemic countries donors would keep safe blood donation in Saudi Arabia.

Evaluation of the inactivation of Venezuelan equine encephalitis virus by several common methods

Working with virological samples requires validated inactivation protocols for safe handling and disposal. Although many techniques exist to inactivate samples containing viruses, not all procedures have been properly validated or are compatible with subsequent assays. To aid in the development of inactivation protocols for Alphaviruses, and specifically Venezuelan equine encephalitis virus (VEEV), a variety of methods were evaluated for their ability to completely inactivate a high titer sample of the vaccine strain VEEV TC-83. The methods evaluated include reagents used in RNA extraction, fixation, treatment with a detergent, and heat inactivation. Most methods were successful at inactivating the sample; however, treatment with only Buffer AVL, SDS, and heat inactivation at 58 °C for one hour were not capable of complete inactivation of the virus in the sample. These results provide a substantial framework for identifying techniques that are safe for complete inactivation of Alphaviruses and to advise protocol implementation.

Avian influenza epidemiology in semi-intensive free ranging duck flocks of the Moyingyi Wetland in Bago East District, Myanmar.

Highly pathogenic avian influenza virus subtype H5N1 first entered Myanmar in 2006 in the Mandalay District. Several H5N1 outbreaks followed and the one of Bago East District (2007) required post outbreak surveillance in the at-risk domestic duck population of the Moyingyi Wetland. A field epidemiological study based on a randomised prospective stratified study with five surveys provided the serological evidence that the avian influenza H5 subtype circulates in the domestic duck population and spreads to almost all the newly housed (and negative) flocks in the time span of a seasonal production cycle. Virological investigation was negative. The survival analysis showed that the probability of seroconversion increased rapidly over the study period, without significant difference among different agro-ecosystems. The analysis suggests that viral spread in the new cycle could be limited if control measures were adopted at the time new flocks are housed. The study recommends that future surveillance schemes for ducks are designed in a way to get as much information as possible from serological results which should drive virological sampling to determined farms.

Influenza virus infections among patients attending emergency department according to main reason to presenting to ED: A 3-year prospective observational study during seasonal epidemic periods.

ObjectiveThe role of influenza virus in patients presenting at ED during seasonal-epidemic periods has not previously been specified. Our objective was to determine its frequency according to clinical presentation.MethodsThis is a prospective observational study conducted during three-consecutive seasonal Influenza epidemics (2013–2015), including patients presenting i) community-acquired pneumonia (CAP); ii) severe acute symptoms (SAS): respiratory failure (RF), hemodynamic failure (HF), cardiac failure (CF), and miscellaneous symptoms (M); iii) symptoms suggesting influenza (PSSI). Patients were tested for influenza using specific PCR on naso-pharyngeal swabs.ResultsOf 1,239 patients, virological samples were taken from 784 (63.3%), 213 (27.2%) of whom were positive for the influenza virus: CAP 52/177 (29.4%), SAS 115/447 (25.7%) and PSSI 46/160 (28.8%) (p = 0.6). In the SAS group positivity rates were: RF 76/263 (28.9%), HF 5/29 (17.2%), CF 15/68 (22.1%), and M 19/87 (21.8%) (p = 0.3). Among the major diagnostic categories, the influenza virus positivity rates were: asthma 60/231 (26%), acute exacerbation of chronic obstructive pulmonary disease 18/86 (20.9%), HIV 5/21 (23.8%) and cardiac failure 33/131 (25.2%). The positivity of the samples has not been associated (p>0.1) nor the presence of signs of severity or admission rate in medical ward nor intensive care unit.ConclusionsOur results indicate that during seasonal influenza epidemics, Influenza virus-positivity rate is similar in patients attending ED for influenza-compatible clinical features, patients with acute symptoms including pneumonia, respiratory, hemodynamic and cardiac distress, and patients presenting for acute decompensation of chronic respiratory and cardiac diseases.

Respiratory Infections and Antibiotic Usage in Common Variable Immunodeficiency

BackgroundPatients with common variable immunodeficiency (CVID) suffer frequent respiratory tract infections despite immunoglobulin replacement and are prescribed significant quantities of antibiotics. The clinical and microbiological nature of these exacerbations, the symptomatic triggers to take antibiotics, and the response to treatment have not been previously investigated.ObjectivesTo describe the nature, frequency, treatment, and clinical course of respiratory tract exacerbations in patients with CVID and to describe pathogens isolated during respiratory tract exacerbations.MethodsWe performed a prospective diary card exercise in 69 patients with CVID recruited from a primary immunodeficiency clinic in the United Kingdom, generating 6210 days of symptom data. We collected microbiology (sputum microscopy and culture, atypical bacterial PCR, and mycobacterial culture) and virology (nasopharyngeal swab multiplex PCR) samples from symptomatic patients with CVID.ResultsThere were 170 symptomatic exacerbations and 76 exacerbations treated by antibiotics. The strongest symptomatic predictors for commencing antibiotics were cough, shortness of breath, and purulent sputum. There was a median delay of 5 days from the onset of symptoms to commencing antibiotics. Episodes characterized by purulent sputum responded more quickly to antibiotics, whereas sore throat and upper respiratory tract symptoms responded less quickly. A pathogenic virus was isolated in 56% of respiratory exacerbations and a potentially pathogenic bacteria in 33%.ConclusionsPatients with CVID delay and avoid treatment of symptomatic respiratory exacerbations, which could result in structural lung damage. However, viruses are commonly represented and illnesses dominated by upper respiratory tract symptoms respond poorly to antibiotics, suggesting that antibiotic usage could be better targeted.

Evaluation of the Influenza Sentinel Surveillance System in Singapore 2011-2012

We evaluated the Singapore Ministry of Health's sentinel surveillance system for influenza virus, which included the monitoring of virological samples from patients with influenza-like illness seen at government primary care clinics and private general practitoner clinics in 2011-12. Using a systematic approach, we analysed weekly data collected for the full two year period from 2011-12. Criteria applied for evaluation were based on the US Centers for Disease Control's Guidelines for Evaluating Public Health Surveillance Systems, and included quality of the data, acceptability and geographic representativeness. The current surveillance system is satisfactory but could be enhanced by focusing on strategies to improve its acceptability and representativeness. We recommend enhancing quality of the data submitted through further engagement and information sharing with stakeholders involved.

Virological and molecular epidemiological investigations into the role of wild birds in the epidemiology of influenza A/H5N1 in central Thailand

A serological and virological surveillance program to investigate the HPAI H5N1 virus in wild bird populations was undertaken from February 2007 to October 2008. The purpose of the survey was to investigate the infection status in free ranging wild birds in Banglane district, Nakhon Pathom province, central Thailand. Samples from wild birds were collected every two months. Choanal and cloacal swabs, serum and tissue samples were collected from 421 birds comprising 44 species. Sero-prevalence of the virus tested by H5N1 serum neutralization test (using a H5N1 virus clade 1; A/chicken/Thailand/vsmu-3-BKK/2004) was 2.1% (8 out of 385 samples; 95% CI 0.7, 3.5). Species that were antibody positive included rock pigeons ( Columba livia), Asian pied starling ( Gracupica contra), spotted dove ( Streptopelia chinensis), oriental magpie robin ( Copsychus saularis), blue-tailed bee-eater ( Merops philippinus), myna ( Acridotheres spp.), and pond heron ( Ardeola spp.). Prevalence by H5N1 virus isolation was 0.5% (2 out of 421 samples; 95% CI 0.0, 1.1); the two H5N1 virus-positive samples were from Asian pied starling ( Gracupica contra) and white vented myna ( Acridotheres grandis). Positive virological samples were collected in June 2007 while all positive serology samples were collected between May and August except for one sample collected in December 2007. No positive samples were collected in 2008. Molecular studies revealed that the wild bird H5N1 viruses were closely related to poultry viruses isolated in other parts of Thailand. However, there was no poultry H5N1 prevalence study performed in the study site during the time of this wild bird survey. Interpretation of source of virus isolates would include spill-over of H5N1 viruses from contaminated sources due to movement of domestic poultry and/or fomites from other areas; or infection of wild birds within the outbreak locations and then translocation by wild bird movement and interaction with wild birds inhabiting distant locations.

Impétigo streptococcique apparu sur les sites d’application du tacrolimus chez une jeune atopique

We report a case of staphylococcal impetigo in a girl treated with tacrolimus ointment (Protopic) for atopic dermatitis.A 15 year-old girl was receiving treatment with tacrolimus 0.03% (Protopic) for an episode of atopic dermatitis. On reduction of applications of tacrolimus, a vesicular-pustular rash appeared and was treated with pristinamycin and valaciclovir. At the end of antibiotic and antiviral therapy, the vesicular-pustular rash recurred while the goal was receiving treatment once more with tacrolimus ointment 0.1%. The bacteriological and virological skin samples revealed B-haemolytic streptococcus group A. The negative results for cutaneous virological samples ruled out Kaposi-Juliusberg syndrome and a diagnosis of staphylococcal impetigo was made. The intrinsic imputability of tacrolimus was I3 (C3 S2).The most obvious specific feature of this impetigo was its limitation to areas of eczema treated by application of tacrolimus. In prospective studies in large patient cohorts, tacrolimus ointment has been associated with two types of adverse effect: local irritations and skin infections chiefly caused by Staphylococcus aureus. To date, there have been no reports in the literature of impetigo due to haemolytic B streptococcus following application of tacrolimus. Because of its immunodepressant effect, tacrolimus ointment may result in increased incidence of skin infections even though a number of studies have shown a reduction in such infections.