Respiratory syncytial virus incidence and typing in the last six seasons in the north of Spain (Asturias). Genetic characterization during the SARS-CoV-2 pandemic.

Respiratory syncytial virus is associated with lower respiratory tract infections. As several types and genotypes can circulate at the same time, genomic characterization is important for timely epidemiological control and treatment measures. In the last 6 seasons (2017-2023), 191 236 nasopharyngeal swabs were processed for respiratory viruses to determine the etiology of acute respiratory infections, describe the incidence and distribution of RSV types and enrich the data of epidemiological molecular studies on RSV in Spain. The incidence of RSV reached 7% in the pre-pandemic season. RSV was most frequent in children under 5 years of age (12.6%), but was also significant in those over 70 years of age (5.63%). The measures taken to control SARS-CoV-2 infection were useful for RSV control and the incidence decreased to 1.8%, but caused a change in the types. Pre-pandemic, the majority circulating types were RSV-B/RSV-B/RSV-A and in the pandemic it was RSV-B/RSV-B. In the last season, RSV-B and RSV-A were detected in the same proportion. Genetic characterization showed three new clades. This has been taken into account to understand the epidemiology as well as the development of therapeutic and preventive strategies.

Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain.

Mutational analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can quantify the relative importance of variants over time, enable dominant mutations to be identified, and facilitate near real-time detection, comparison and tracking of evolving variants. SARS-CoV-2 in Asturias, an autonomous community of Spain with a large ageing population, and high levels of migration and tourism, was monitored and tracked from the beginning of the pandemic in February 2020 until its decline and stabilization in August 2021, and samples were characterized using whole genomic sequencing and single nucleotide polymorphisms. Data held in the GISAID database were analysed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1 % of the population with SARS-CoV-2 were found, identifying ten major variants worldwide (seven arose before January 2021), 19 regional and one local. In Asturias only 17 different variants were found. After vaccination, no further regional major variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures such as rapid diagnosis, isolation and vaccination were efficient.

Transfusion-transmission of hepatitis E virus through red blood cell transfusion but not through platelet concentrates: A case report from Spain.

BACKGROUND: Few cases of transfusion-transmitted hepatitis E virus (HEV) have been published in Spain. Here, we describe a well-characterized lookback investigation of a transfusion-transmitted HEV case at the Community Centre for Blood and Tissues of Asturias (Spain). CASE REPORT: A female patient with chronic myeloid leukemia underwent an allogeneic bone marrow transplant in March 2019 and showed alterations in liver function shortly afterwards. This patient received blood components from 30 different donors in the 3 months before the transplant. Frozen plasma samples from these donations were investigated for the presence of HEV-RNA. One frequent donor was identified as asymptomatic HEV RNA-positive at the time of his whole blood donation. The investigation revealed that this donor's plasma unit, originally intended for the fractionation industry, had a viral RNA concentration of 1.9 × 104 copies/mL. HEV RNA was detected initially in the index patient who received the red cell concentrate from this donor 25 days after the transfusion. HEV RNA isolated from both donor and recipient were identified as subtype 3f. The recipient of platelet concentrate (PC), treated with a riboflavin-based pathogen reduction technology (PRT) was not infected, being negative for the presence of HEV IgM, IgG, and HEV RNA before and after the transfusion. CONCLUSION: This case study shows that HEV was transmitted through red cell transfusion to a recipient, while the patient who received riboflavin/UV light treated PC did not develop signs of infection. A causal relationship between PRT treatment of the PC and the non-transmission of HEV remains to be established.

Comparison of in-house SARS-CoV-2 genome extraction procedures. A need for COVID-19 pandemic.

Among the methods used to diagnose COVID-19, those based on genomic detection by q(RT)-PCR are the most sensitive. To perform these assays, a previous genome extraction of the sample is required. The dramatic increase in the number of SARS-CoV-2 detection assays has increased the demand for extraction reagents hindering the supply of commercial reagents. Homemade reagents and procedures could be an alternative. Nasopharyngeal samples were extracted by seven different methods as well as the automatic method MagNaPure96, to detect SARS-CoV-2. All protocols show sensitivity higher than 87 %, in comparison with reference method, for detecting SARS-CoV-2 as well as human ß- globin. Our results support that these procedures, using common and cheap reagents, are effective to extract RNA (from SARS-CoV-2) or DNA (from human ß-globin) genome from nasopharyngeal swabs. Furthermore, these procedures could be easily adopted by routine diagnostic laboratories to implement detection methods to help to fight against COVID-19 pandemic.

SARS-CoV-2 analysis on environmental surfaces collected in an intensive care unit: keeping Ernest Shackleton's spirit.

BACKGROUND: Intensive care unit workers are at high risk of acquiring COVID-19 infection, especially when performing invasive techniques and certain procedures that generate aerosols (< 5 µm). Therefore, one of the objectives of the health systems should implement safety practices to minimize the risk of contagion among these health professionals. Monitoring environmental contamination of SARS-CoV-2 may help to determine the potential of the environment as a transmission medium in an area highly exposed to SARS-CoV-2, such as an intensive care unit. The objective of the study was to analyze the environmental contamination by SARS-CoV-2 on surfaces collected in an intensive care unit, which is dedicated exclusively to the care of patients with COVID-19 and equipped with negative pressure of - 10 Pa and an air change rate of 20 cycles per hour. Furthermore, all ICU workers were tested for COVID-19 by quantitative RT-PCR and ELISA methods. RESULTS: A total of 102 samples (72 collected with pre-moistened swabs used for collection of nasopharyngeal exudates and 30 with moistened wipes used in the environmental microbiological control of the food industry) were obtained from ventilators, monitors, perfusion pumps, bed rails, lab benches, containers of personal protective equipment, computer keyboards and mice, telephones, workers' shoes, floor, and other areas of close contact with COVID-19 patients and healthcare professionals who cared for them. The analysis by quantitative RT-PCR showed no detection of SARS-CoV-2 genome in environmental samples collected by any of the two methods described. Furthermore, none of the 237 ICU workers was infected by the virus. CONCLUSIONS: Presence of SARS-CoV-2 on the ICU surfaces could not be determined supporting that a strict cleaning protocol with sodium hypochlorite, a high air change rate, and a negative pressure in the ICU are effective in preventing environmental contamination. These facts together with the protection measures used could also explain the absence of contagion among staff inside ICUs.

Hemicorporal paresthesias in a parvovirus infection / Parestesias hemicorporales en una infección por parvovirus

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Neuroinvasion of influenza A/H3N2: a fatal case in an immunocompetent adult.

Acute necrotizing encephalopathy (ANE) is a severe neurologic complication caused by influenza virus that has been infrequently reported in adult population. The diagnosis is made on epidemiological, clinical, and neuroimaging suspicion, but is rarely confirmed by microbiological findings in samples from the central nervous system (CNS), thus making it difficult to define the mechanism of pathogenesis of influenza-associated encephalitis/encephalopathies (IAE). We report a microbiologically documented case of ANE caused by influenza A/H3N2, in a previously healthy adult patient infected during a flu epidemic in Asturias (Spain). Direct viral invasion of the CNS was demonstrated with the isolation of the virus in a brain biopsy.

Levels of anti-CMV antibodies are modulated by the frequency and intensity of virus reactivations in kidney transplant patients.

Anti-CMV (cytomegalovirus) antibody titers are related to immune alterations and increased risk of mortality. To test whether they represent a marker of infection history, we analyzed the effect of viral reactivations on the production of specific antibodies in kidney transplant patients. We quantified CMV-DNAemia and antibody titers in 58 kidney transplant patients before transplantation and during a follow-up of 315 days (standard deviation, SD: 134.5 days). In order to calculate the intensity of the infection, we plotted the follow-up time of the infection on the x-axis and the number of DNA-CMV copies on the y-axis and calculated the area under the curve (CMV-AUC). The degree of T-lymphocyte differentiation was analyzed with flow cytometry, the cells were labelled with different monoclonal antibodies in order to distinguish their differentiation state, from naive T-cells to senescent T-cells. Peak viremia was significantly higher in patients experiencing a primary infection (VI) compared to patients experiencing viral reactivation (VR). Our data indicate that the overall CMV viral load over the course of a primary infection is significantly higher than in a reactivation of a previously established infection. Whereas patients who experienced an episode of CMV reactivation during the course of our observation showed increased levels of CMV-specific antibodies, patients who did not experience CMV reactivation (WVR) showed a drop in CMV antibody levels that corresponds to an overall drop in antibody levels, probably due to the continuing immunosuppression after the renal transplant. We found a positive correlation between the CMV viremia over the course of the infection or reactivation and the CMV-specific antibody titers in the examined patients. We also observed a positive correlation between anti-CMV titers and T-cell differentiation. In conclusion, our data show that anti-CMV antibody titers are related to the course of CMV infection in kidney transplant patients.

Diagnóstico molecular de la infección por ParapoXVIrus / Molecular diagnosis of ParapoXVIrus infection

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Quantification of human papilloma virus (HPV) DNA using the Cobas 4800 system in women with and without pathological alterations attributable to the virus.

BACKGROUND AND PURPOSE: Surrogate markers such as viral load are necessary to follow the evolution of disease resulting from infection with Human Papilloma virus (HPV), especially in this era of vaccination. As such, this paper uses the automated system Cobas-4800-HPV to define viral load as number of HPV copies/cell and apply the results to clinical samples. STUDY DESIGN: A curve to determine viral load per cell was constructed from HPV plasmid and cell concentrations using the Cobas-4800-HPV system. According to these curves, HPV viral load was determined in 309 positive endocervical swabs (58 from patients with previous HPV-infection, 118 with current lesions and 133 symptom-free patients presenting for screening) from women attending gynaecology consultations from January to June 2013. RESULTS: In curves with r(2)≥0.95 the Cobas-4800-HPV system has a detection limit of 150 (2.18 log) viral copies, and the limit for ß-globin corresponds to that of a single cell. In women reporting for screening, viral load was under 10(4) (4 log) copies/10(3) cells. For women with lesions or previous HPV infection loads were significantly higher particularly in the 30-45 year group (p=0.038). Elevated viral loads were especially noticeable in non-HPV 16/HPV 18. CONCLUSIONS: Automated system Cobas-4800-HPV is suitable for define viral load of HPV. Correlation between viral load and number of cells established. Higher viral load in women with disease, and those between 30 and 45 years. Increased viral load of non-16/18 high-risk HPV genotypes detected in patients with lesions compared to screening patients. A difference not observed for HPV 16/18, or in coinfections.

Human papillomavirus infection in a male population attending a sexually transmitted infection service.

OBJECTIVE: Human Papillomavirus (HPV) infection in men may produce cancer and other major disorders. Men play an important role in the transmission of the virus and act as a reservoir. The aim of this study was to determine the HPV-genotypes and their prevalence in a group of men attending a Sexually Transmitted Infection service. PATIENTS AND SAMPLES: Between July 2002 and June 2011, 1392 balanopreputial, 435 urethral, 123 anal, and 67 condyloma lesions from 1551 men with a mean age of 35.8±11.3 years old (range: 17-87) were collected for HPV-DNA testing. METHODS: A fragment of the L1-gene and a fragment of the E6/E7-genes were amplified by PCR. Positive samples were typed by hybridization. RESULTS: The HPV genome was detected in 36.9% (486/1318) balanopreputial and in 24.9% (101/405) urethral (p<0.0001) swabs from 38.1% (538) of 1469 men. Co-infections were present in 5.4% (80/1469) of cases. HPV was found in 43.9% (373/850) of men younger than 35 vs. 31.7% (187/589) of men aged >35. HPV was found in 59.4% (104) of 165 men with lesions (macroscopic or positive peniscopy), and in 22.8% (61/267) without clinical alterations. HPV was also detected in 71.4% (40/56) men with condylomata and in 58.7% (64/109) of men with positive peniscopy. CONCLUSIONS: HPV prevalence in men was high and decreased with age. HPV was found more frequently in balanopreputial than in urethral swabs. There was a low rate of co-infections. Low-risk HPV vaccine genotypes were the most recurrent especially in younger. Although HPV has been associated with clinical alterations, it was also found in men without any clinical presentation. Inclusion of men in the national HPV vaccination program may reduce their burden of HPV-related disease and reduce transmission of the virus to non-vaccinated women.

Noroviruses as cause of gastroenteritis in elderly patients.

BACKGROUND AND AIMS: Gastroenteritis is one of the infections which are particularly important in elderly people. Knowledge of the main pathogens causing gastroenteritis in this group of patients, whose number will dramatically increase in coming decades, is essential. The contribution of group A rotavirus, adenovirus types 41 and 42, norovirus and astrovirus as causes of gastroenteritis among patients of all ages, especially those with over 65 was evaluated over an extended time period. METHODS: A total of 4024 fecal samples, collected during seven seasons (October 2000 to September 2007), were tested with a commercial immunoassay (rotavirus) and an "in house" nested RT-PCR (adenovirus, norovirus and astrovirus). RESULTS: Although norovirus was the second most common cause of gastroenteritis (7.9%) in the total population, it was predominant in the age group over the age of 6, causing 7.2% of gastroenteritis in the 6-16-year-old group, 8.6% in the 16-64-year-old group, and 11.1% in the >65-year group (p=0.001). In the last age group, norovirus was the most frequently detected (11.1%), followed by adenovirus (7.4%), astrovirus (3.6%) and rotavirus (3.3%) (p<0.0001). In addition, norovirus was rarely found in association with other viruses. CONCLUSIONS: Our data suggest that the elderly are highly vulnerable to certain infections, and indicate the need to introduce simple tests for an early identification of norovirus in cases of gastroenteritis affecting elderly patients, improving patient care by reducing unnecessary treatments and hospital stays.