Incidence Of Virus Research Articles

Isolation of porcine epidemic diarrhea virus strain CHCQ-2023 from Chongqing Province and analysis of S gene recombination

BackgroundIn recent years, the prevalence and incidence of porcine epidemic diarrhea virus (PEDV) infection have been on the rise. The occurrence of multiviral infections and recombination mutations has led to accelerated viral evolution and reduced vaccine efficacy. In the present study, a PEDV strain was isolated from a pig farm (Chongqing Province, China) with an outbreak of porcine diarrhea, and its S gene was found to be recombinant.ResultsThe optimal trypsin concentration for blind passage of PEDV in Vero cells was determined to be 7.5 µg/mL. Following two blind passages of the virus in Vero cells, the virus was unable to adapt to the cells. Therefore, PEDV was blindly passaged in IPEC-J2 cells using the optimal concentration of trypsin (5 µg/mL). Next, a series of characterization experiments were performed. Recombination analyses of the isolates using software revealed that the S gene of strain CHCQ-2023 was derived from the primary parent strain PEDV-1 C and secondary parent strain SQ2014, with recombination occurring at a 3152 bp breakpoint. Furthermore, a specific B-cell antigenic epitope was predicted on the S2 subunit of the S protein.ConclusionA PEDV strain was isolated and characterized, and its S gene was characterized. The findings provide a bioinformatic basis for the study of PEDV strain variation due to genetic recombination.

Seasonal Shifts in Influenza, Respiratory Syncytial Virus, and Other Respiratory Viruses After the COVID-19 Pandemic: An Eight-Year Retrospective Study in Jalisco, Mexico

The coronavirus disease 2019 (COVID-19) pandemic profoundly disrupted the epidemiology of respiratory viruses, driven primarily by widespread non-pharmaceutical interventions (NPIs) such as social distancing and masking. This eight-year retrospective study examines the seasonal patterns and incidence of influenza virus, respiratory syncytial virus (RSV), and other respiratory viruses across pre-pandemic, pandemic, and post-pandemic phases in Jalisco, Mexico. Weekly case counts were analyzed using an interrupted time series (ITS) model, segmenting the timeline into these three distinct phases. Significant reductions in respiratory virus circulation were observed during the pandemic, followed by atypical resurgences as NPIs were relaxed. Influenza displayed alternating subtype dominance, with influenza A H3 prevailing in 2022, influenza B surging in 2023, and influenza A H1N1 increasing thereafter, reflecting potential immunity gaps. RSV activity was marked by earlier onset and higher intensity post-pandemic. Other viruses, including human rhinovirus/enterovirus (HRV/HEV) and parainfluenza virus (HPIV), showed altered dynamics, with some failing to return to pre-pandemic seasonality. These findings underscore the need for adaptive surveillance systems and vaccination strategies to address evolving viral patterns. Future research should investigate the long-term public health implications, focusing on vaccination, clinical outcomes, and healthcare preparedness.

Diagnostic Challenges of Arboviral Infections and Dengue Virus Serotype Distribution in Febrile Patients in East Java, Indonesia

ObjectivesArboviruses pose significant public health threats globally, with Southeast Asia being a hotspot for these infections. This study aimed to reassess the incidence of dengue, Zika, and chikungunya viruses in patients clinically diagnosed with dengue in East Java, Indonesia in 2023. MethodsThe study included 108 patients admitted to hospitals in Jember, with blood samples collected on admission. Multiplex RT-PCR was used to detect viral RNA for dengue, Zika, and chikungunya, while dengue serotypes were identified using real-time PCR. ResultsA total of n=67/108 patients (62%) tested positive for dengue virus (DENV), one patient tested positive for chikungunya and no cases of Zika were detected. Differences in laboratory parameters between DENV RNA-negative patients and confirmed dengue cases suggest possible misdiagnosis of dengue. Serotyping of DENV-positive samples revealed DENV-3 as predominant serotype in Jember, accounting for 34% of cases (n=23/67), followed by DENV-1 and DENV-2 at 19% each (n=13/67), and 6% for DENV-4 (n=4/67), while 21% (n=14/67) remained untyped. ConclusionsThis study highlights the nature of the dengue outbreak in Jember in 2023, where all four DENV serotypes were in circulation, and underlines the need for serological or nucleic acid-based methods to improve arbovirus diagnosis in the region.

The highly pathogenic avian influenza H5N8 sublineage 2.3.4.4b virus: A critical analysis of genetic steadiness based on full HA gene sequencing in Egypt

The highly pathogenic avian influenza virus (HPAIV) continues to be a significant threat to the poultry industry despite the implementation of vaccination programs. The main goal of this study was to explore the incidence of avian influenza viruses (AIVs) and the stability of the hemagglutinating (HA) gene sequence. For this drive, oropharyngeal swabs (n=425) were collected from various wild and domesticated bird species from 13 provinces in Egypt from 2019 to 2021. Viral isolation in specific pathogen-free chicken embryos revealed positive HA activity in 9.88% (n=32) of the wild and 36.37% (n=64) of domesticated species. Only eight H5N8 avian influenza viruses were delivered (4/each category) in mixed infection with Newcastle disease virus (NDV). Clinically, domesticated examined birds exhibited clinical findings suggesting avian influenza, but AIVs were delivered from both apparently healthy and sick wild birds. A/chicken-cobb/Egypt/55/2019(H5N8) sequence generated in this study has been submitted to GenBank under the accession number ON724339, and its in vivo pathogenicity was evaluated in four-week-old chickens, which revealed 90% mortality and typical clinical findings of HPAIV. Based on the full HA gene sequence, the strain has a Furin-sensitive cleavage site in the HA protein, which is an HPAIV. It has been clustered in clade 2.3.4.4b within AIVs from 2016 to 2023 and coexistence of genetically stable viruses 2016-2019 with 99.8-100% similarity. The existing strain is fully identical to three strains: A/green-winged teal/Egypt/877/2016(H5N8), A/northern shoveler/Egypt/MB-D-816OP/2016(H5N8), and A/duck/Egypt/N13736E/2017 (H5N8), with the only point of mutation at position 284 (G284E). In our analysis, the majority of H5NX AIV strains detected in Egypt since 2016 possessed 156T. As a result, there is evidence suggesting that H5N8 has been introduced sequentially through the migration of European wild birds along the Black Sea–Mediterranean and East Asia–West Africa flyways. This raises the possibility of future adaptation to mammals due to spillover from avian-origin strains, especially in native aquatic birds such as geese and ducks.

Adapting COVID-19 research infrastructure to capture influenza and respiratory syncytial virus alongside SARS-CoV-2 in UK healthcare workers winter 2022/23 and beyond: protocol for a pragmatic sub-study

Introduction During the COVID-19 pandemic, extensive research was conducted on SARS-CoV-2; however, important questions about other respiratory pathogens remain unanswered. A severe influenza season in 2022–2023 with simultaneous circulation of SARS-CoV2 and respiratory syncytial virus is anticipated. This sub-study aims to determine the incidence and impact of these respiratory viruses on healthcare workers, the symptoms they experienced, the effectiveness of both COVID-19 and influenza vaccination and the burden of these infections on the National Health Service (NHS) workforce. Methods and analysis This is a longitudinal prospective cohort sub-study, utilising the population and infrastructure of the SARS-CoV-2 Immunity & Reinfection Evaluation (SIREN) study, which focuses on hospital staff in the UK. Participants undergo fortnightly nucleic acid amplification testing on a multiplex assay including SARS-CoV-2, influenza A and B and RSV, regardless of symptoms. Questionnaires are completed every two weeks, capturing symptoms, sick days, exposures, and vaccination records. Serum samples are collected monthly or quarterly from participants associated with a SIREN site. This sub-study commenced on 28/11/22 to align with the predicted influenza season and participants’ influenza vaccine status. The SIREN Participant Involvement Panel shaped the aims and methods for the study, highlighting its acceptability. UK devolved administrations were supported to develop local protocols. Analysis plans include incidence of asymptomatic and symptomatic infection, comparisons of vaccination coverage, assessment of sick day burden, and effectiveness of seasonal influenza against infection and time off work. Data are also integrated into UKHSA nosocomial modelling. Ethics and dissemination The protocol was approved by the Berkshire Research Ethics Committee (IRAS ID 284460, REC Reference 20SC0230) on 14/11/2022. Participants were informed in advance. As the frequency and method of sampling remained the same, implied consent processes were approved by the committee. Participants returning to the study give informed consent. Regular reports to advisory groups and peer-reviewed publications are planned to disseminate findings and inform decision making. Clinical trial registration number: ISRCTN11041050; registration date: 12 January 2021. Sub study included in protocol version: v8.0, and amended in v9.0

High-resolution mapping of Blueberry scorch virus incidence using RGB and multispectral UAV images and deep learning

Blueberry scorch caused by Blueberry scorch virus (BlScV) is a destructive disease, which can result in substantial yield decline and pose a significant threat to the viability of well-established highbush blueberry fields in North America and other regions. Early detection of the disease in the field, removal of infected bushes, and control of its spread via aphids to other fields or regions are critical for managing this disease. Visual assessment of Blueberry scorch symptoms is the predominant method for identifying and estimating the disease, which, however, is labour-intensive, tedious, and inefficient. Unmanned Aerial Vehicle (UAV)-based imaging is a powerful remote sensing tool for crop monitoring with several advantages, such as flexibility to acquire images of different pixel sizes, short revisit time intervals, reduced susceptibility to cloud interference, and flexibility to equip with different sensors. This study aims to collect UAV images to detect and map BlScV-infected blueberry plants using a cutting-edge deep learning model. Images of different pixel sizes acquired by an RGB sensor, and a multispectral sensor were compared to evaluate their detection accuracies. To ensure comprehensive information dependency extraction at close-, mid-, and long-ranges, the deep learning techniques developed in this study incorporate various computer vision-based mechanisms, such as Multi-Layer Perceptron (MLP), Convolutional Neural Networks (CNNs), and Self-Attention (SA) modules. Through these innovations, the deep learning algorithm, called InceptionLSA, obtained the highest average accuracy of 76.33% and 70.00% at a 20 cm pixel size of the multispectral and RGB images, respectively.

Studies on the Detection of Viruses Infecting Capsicum Species in the Northern Zone of Cross River State, Nigeria

The objective of this study was to determine the occurrence, detection, and geographical spread of viruses that infect pepper (Capsicum spp.) in six towns spanning two local government areas (Yala and Ogoja) in the northern zone of Cross River State. A total of 348 leaf samples from symptomatic and asymptomatic pepper plants were randomly collected from farmer's fields during a survey in 2023–2024. The samples were then preliminary tested using an antigen coated plate enzyme-linked immunosorbent assay (ACP-ELISA) with seven antibodies specific for ToLCV, Cowpea aphid borne mosaic virus (CABMV), Cucumber mosaic virus (CMV), Potato virus X (PVX), Tobacco mosaic virus (TMV), and Pepper veinal mottle virus (PVMV). The findings showed that the viruses that infect pepper in Yala had a high cumulative mean incidence, accounting for 56.9% (198 infected samples). Yache in Yala had the highest virus incidence at 90%, while Bansara in Ogoja had the lowest at 40%. At different rates, ToLCV, CMV, PVY, and PVMV were found in the samples; PVX, TMV, and CABMV were not found. The CMV virus was the most commonly discovered of them. Additionally, mixed infections between the viruses—between ToLCV and PVY in Yache and between CMV and PVMV in Bansara—were found. This is the first report on account of viruses found in pepper in the northern part of Cross River State. The findings show that the viruses that cause the infections are common and might potentially be a threat to the production of pepper in that region.

Investigation of the Effect of the COVID-19 Pandemic Period on Respiratory Tract Viruses at Istanbul Medical Faculty Hospital, Turkey.

Aim: Respiratory viruses significantly impact public health, contributing to high morbidity and mortality rates in both children and adults. This study evaluates the distribution and incidence of respiratory tract viruses in our hospital from 2019 to 2022, focusing on changes post-COVID-19 pandemic. Material and Methods: Utilizing molecular methods, we analyzed nasopharyngeal swabs with the FTD Respiratory Pathogens 21 kit and the QIAStat Dx Respiratory Panel kit at Istanbul Faculty of Medicine. A total of 1186 viruses were detected in 2488 samples (47.6% of the total) examined with the FTD Respiratory Pathogens 21 kit between 2019 and 2022. Results: It was determined that the detection rates were 52.8% in 2019, 44.3% in 2020, 50.0% in 2021, and 40.0% in 2022. Notable changes in prevalence were observed for pandemic influenza A (IAV-H1N1pdm2009), parainfluenza virus (PIV)-3, rhinovirus (RV), and respiratory syncytial virus (RSV)-A/B (p < 0.05). RV consistently showed the highest detection rates across all years (17.6% to 7.9%). Additionally, 1276 viruses were detected in 1496 samples using the QIAStat DX kit, with 91.3% positivity in 2021 and 78.6% in 2022, highlighting the kit's effectiveness in rapid diagnosis. Conclusions: This study enhances understanding of respiratory virus epidemiology during and after the pandemic, emphasizing the need for ongoing surveillance and strategic public health measures to address the evolving landscape of respiratory infections.

Forecasting severe respiratory disease hospitalizations using machine learning algorithms

BackgroundForecasting models predicting trends in hospitalization rates have the potential to inform hospital management during seasonal epidemics of respiratory diseases and the associated surges caused by acute hospital admissions. Hospital bed requirements for elective surgery could be better planned if it were possible to foresee upcoming peaks in severe respiratory illness admissions. Forecasting models can also guide the use of intervention strategies to decrease the spread of respiratory pathogens and thus prevent local health system overload. In this study, we explore the capability of forecasting models to predict the number of hospital admissions in Auckland, New Zealand, within a three-week time horizon. Furthermore, we evaluate probabilistic forecasts and the impact on model performance when integrating laboratory data describing the circulation of respiratory viruses.MethodsThe dataset used for this exploration results from active hospital surveillance, in which the World Health Organization Severe Acute Respiratory Infection (SARI) case definition was consistently used. This research nurse-led surveillance has been implemented in two public hospitals in Auckland and provides a systematic laboratory testing of SARI patients for nine respiratory viruses, including influenza, respiratory syncytial virus, and rhinovirus. The forecasting strategies used comprise automatic machine learning, one of the most recent generative pre-trained transformers, and established artificial neural network algorithms capable of univariate and multivariate forecasting.ResultsWe found that machine learning models compute more accurate forecasts in comparison to naïve seasonal models. Furthermore, we analyzed the impact of reducing the temporal resolution of forecasts, which decreased the model error of point forecasts and made probabilistic forecasting more reliable. An additional analysis that used the laboratory data revealed strong season-to-season variations in the incidence of respiratory viruses and how this correlates with total hospitalization cases. These variations could explain why it was not possible to improve forecasts by integrating this data.ConclusionsActive SARI surveillance and consistent data collection over time enable these data to be used to predict hospital bed utilization. These findings show the potential of machine learning as support for informing systems for proactive hospital management.

Status of Invasive Species of Thrips, Thrips Parvispinus (Karny) Infesting Chilli and Investigation Studies on IPDM Package in Dharmapuri Districts, Tamil Nadu, India

Roving survey results revealed that mean population of thrips, mite population and tospovirus incidence was recorded to be 1.63, 0.68 &amp; 2.05 and 1.88, 0.74 &amp; 1.57 in Pennagaram and Palacode blocks. In the field experiments, mean population in the module I IPDM module was recorded low thrips population (1.05 nos./leaf and 0.64 nos/Sq.m2 leaves) followed by module II IPDM (1.11 Nos./leaf and 0.71nos/Sq.m2 leaves). A virus incidence of 1.0 to 2.0 % was recorded in treatment 2 module II and treatment 3 Farmers practices 2.2 to 9.5 % was observed. The per cent reduction over control of thrips and mite population is highest in T1 followed by T2 and farmer practice (81.70, 80.66 and 56.48 % &amp; 79.61,77.38 and 33.12 %). The percent reduction over control of tospovirus by thrips is highest in T1 IPDM module followed IPDM II than farmer practice (100, 88.88 and 54.40%). The yield of green chilli and BC ratio were found to be high in IPDM module (22.96 t/ha and 3.02) followed by module II IPDM (19.14 t/ha and 2.78) followed by farmer’s practice (13.88 t/ha and 1.49).

Evaluating the impact of biogenic nanoparticles and pesticide application in controlling cotton leaf curl virus disease (CLCuD) in cotton (Gossypium hirsutum L.)

BackgroundCotton leaf curl virus disease (CLCuD) is one of the major concerns for cotton growers. The traditional approach to managing CLCuD involves the control of the vector (whitefly) population through the use of pesticides. This study compares the efficacy of zinc oxide, iron oxide, copper and silver nanoparticles with conventional pesticides. Nanoparticles dose was optimized by evaluating their phytotoxic threshold in our previous study. In this study, optimized doses of nanoparticles such as zinc oxide (100 ppm), iron oxide (50 ppm), copper (50 ppm) and silver nanoparticles (25 ppm) were applied in a field trial of cotton against cotton leaf curl virus disease (CLCuD). Morphological parameters (height of stem, monopodial branches, sympodial branches, staple length, boll weight and number of bolls), yield parameters (seed cotton yield and ginning outturn), chlorophyll content (chlorophyll a, chlorophyll b, carotenoids and total chlorophyll), biochemical parameters (superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), catalase (CAT), hydrogen peroxide (H2O2) and electrolyte leakage) and disease parameters (reduction infection, disease severity and disease incidence) were determined in this study.ResultsThe incidence of cotton leaf curl virus was confirmed by triple antibody sandwich–enzyme-linked immunosorbent assay (TAS-ELISA). The pesticide Imidacloprid significantly reduced the infection by 79.3%. However, in comparison to pesticide, application of nanoparticles also reduced the infection. ZnO NPs reduced the infection by 42.33%, FeO NPs by 41%, Cu NPs by 34.7%, and Ag NPs by 44.8%. Moreover, these nanoparticles also improved the plant growth parameters as compared to control treatment. ZnO NPs enhanced morphological, yield parameters, and chlorophyll content by 36%, 22%, and 29%, respectively. FeO NPs showed improvements by 38%, 21%, and 29%; Cu NPs 39%, 25%, and 29%; and Ag NPs 31%, 19%, and 18%, respectively.ConclusionAlthough treatment pesticide showed the least disease incidence compared to nanoparticles, nanoparticles are eco-friendly and safe as compared to pesticides. Farmers can apply these nanoparticles at their optimal thresholds through foliar application as an alternative to traditional pesticides. It is concluded that nanocomposites and hybrid modes may be used for managing CLCuD efficiently in the future.Graphical abstract

Introduction of nirsevimab in Catalonia, Spain: description of the incidence of bronchiolitis and respiratory syncytial virus in the 2023/2024 season.

Respiratory syncytial virus (RSV) causes most of the cases of bronchiolitis and thousands of deaths annually, particularly in infants less than 6months old. In Catalonia (Spain), infants born between April 2023 and March 2024 aged 0-6months during their first RSV season have been candidates to receive nirsevimab, the novel monoclonal antibody against RSV, since October 2023. We aimed to analyse the dynamics of all-causes bronchiolitis diagnoses and RSV community infections in the current season and compare them to pre-nirsevimab epidemics. We collected epidemiological data from the Information System for Surveillance of Infections in Catalonia (SIVIC) on daily all-causes bronchiolitis clinical diagnoses and RSV-confirmed cases provided by rapid antigen tests in primary care practices. We calculated the rate ratio (RR) for the incidence of all-causes bronchiolitis for children aged 0-11m-old with respect to 12-35m-old between September 2014 and January 2024. We analysed the RR of the incidence of RSV-confirmed infection for 0-11m-old and 12-35m-old with respect to the > 35m-old, from January 2021 to January 2024. We then computed the relative difference of the RR, designated as percentage of reduction of risk, between season 2023/2024 and former epidemics. With a global coverage recorded rate for nirsevimab of 82.2% in January 2024, the age-specific 0-11m-old RR (95% CI) of RSV infection incidence for > 35m-old was 1.7 (1.5-2.0) in season 2023/2024. The RR (95% CI) had been 7.4 (5.6-9.9), 8.8 (6.9-11.3), and 7.1 (5.7-8.9) in 2020/2021, 2021/2022, and 2022/2023, respectively. Regarding the incidence of all-causes bronchiolitis for the 0-11m-old group compared to the 12-35m-old, the pre-pandemic (2014/2015-2019/2020) and 2022/2023 RR (95% CI) were 9.4 (9.2-9.6) and 6.0 (5.7-6.2), respectively, significantly higher than the RR of 3.6 (3.4-3.8) for the most recent season, 2023/2024. Conclusion: Concurring with the introduction of nirsevimab, the risk of RSV infection for infants aged 0-11m-old compared to > 35m-old has been reduced by 75.6% (73.4-77.5) in last season, and the risk for all-causes bronchiolitis for 12-35m-old by 61.9% (60.9-62.9) from the pre-pandemic period and by 39.8% (39.3-40.2) from the 2022/2023 epidemic, despite high RSV community transmission, especially in older infants What is Known: • RSV is responsible for approximately 70% of bronchiolitis cases and causes severe disease, particularly in infants < 6months of age. • Nirsevimab effectiveness against RSV-associated disease, particularly hospitalisations, was expected to be around 80%; other Spanish regions, such as Galicia and Valencia, and European countries including Luxembourg and Germany, have already reported good results in implementing nirsevimab to prevent RSV-associated hospitalisations and PICU stays. What is New: • We provide insight into the community incidence of RSV and all-causes bronchiolitis for season 2023/2024, when nirsevimab has been introduced to the Catalan population, using. primary healthcare data, which enabled us to assess the burden of RSV infections and bronchiolitis in the commonly seasonally saturated primary healthcare practices. • Our study reveals that the risk of all-causes bronchiolitis for infants aged 0-11m-old compared to older infants was reduced by 40% compared to the previous season and 62% compared to pre-pandemic standards, and for RSV infection it was reduced by 76%.

Incidence of Respiratory Syncytial Virus in Community-Dwelling Adults Aged 18-64 Years Over 2 Seasons, 2022-2024, in a North American Community.

The incidence of respiratory syncytial virus (RSV)-acute respiratory infection (ARI) in community-dwelling adults after the Omicron variant of the COVID-19 pandemic is unknown. Our aim was to assess the incidence of RSV-ARI in adults aged 18 to 64 years over 2 consecutive RSV seasons (October-April 2022-2024) in 4 US states. This community-based prospective cohort study comprised 7501 participants in Minnesota, Wisconsin, Florida, and Arizona. We calculated RSV-ARI and RSV-lower respiratory tract disease (LRTD) incidence and attack rates. We reported unadjusted incidence by age group, gender, race and ethnicity, Charlson Comorbidity Index, socioeconomic status, residential state, and rural/urban setting. Seasons 1 and 2 had 2250 and 2377 ARI episodes, respectively, with an RSV-ARI positivity rate of 5.5% for season 1 and 5.8% for season 2 among those tested. In season 1, the overall incidence of RSV-ARI was 27.71 (95% CI, 22.82-33.34) per 1000 person-years (1.49% attack rate). Almost half (49.0%) had RSV-LRTD, with an incidence of 13.53 (95% CI, 10.19-17.61) per 1000 person-years (0.73% attack rate). In season 2, the RSV-ARI and RSV-LRTD incidence rates were 26.39 (95% CI, 21.73-31.75) per 1000 person-years (1.51% attack rate) and 12.43 (95% CI, 9.31-16.26) per 1000 person-years (0.72% attack rate). RSV-ARI incidence peaked in November 2022 and December 2023. Our observations suggest that RSV-ARI incidence and seasonal pattern are shifting to prepandemic RSV epidemiology.

Respiratory viral infections in bone marrow transplant patients: insights from a tertiary care hospital in Rawalpindi, Pakistan.

To determine the incidence of respiratory viral infections in bone marrow transplant patients. The prospective, descriptive, cross-sectional study was conducted at a tertiary care hospital in Rawalpindi, Pakistan, from September 2019 to August 2020, and comprised respiratory specimens from recipients of haematopoietic stem cell transplant. The specimens were collected in viral transport medium, and were then taken to the Department of Virology. Multiplex polymerase chain reaction was performed on the specimens to ascertain the incidence and prevalence of respiratory viruses. Data was analysed using SPSS 24. Of the 85 subjects, 53(62.35%) were males and 32(37.65%) were females. The overall median age was 20.0 years (interquartile range: 11.0-32.0 years). Respiratory viral infections were detected in 31(36.4%) specimens. Among them, human rhinovirus was detected in 12(38.7%) cases, respiratory syncytial virus in 5(16.1%), influenza A/H3 in 4(13%), human parainfluenza virus-1 in 3(9.7%), adenovirus in 2(6.4%), human parainfluenza virus-3 in 1(3.2%), human parainfluenza virus-4 in 1(3.2%) and human metapneumovirus in 1(3.2%) case. There were 2(6.4%) cases of co-infection. More than one-third recipients of haematopoietic stem cell transplant were found to have respiratory viral infections, highlighting the importance of employing multiplex respiratory polymerase chain reaction in early diagnosis and treatment of such infections.

A Model-Based Estimation of RSV-Attributable Incidence of Hospitalizations and Deaths in Italy Between 2015 and 2019.

Respiratory syncytial virus (RSV) incidence is known to be underestimated in adults due to its infrequent diagnostic testing and lower sensitivity of single nasal/nasopharyngeal swab PCR testing outside of the early childhood period. RSV can trigger acute cardiac events as well as cause respiratory disease. Consequently, we used a model-based study to estimate RSV-attributable hospitalization and mortality incidence among adults in Italy between 2015 and 2019. Through a database predisposed by CREA Sanità, by extracting monthly data from the Italian hospitalization collection data of the Ministry of Health and the Italian National Institute of Statistics (ISTAT) data (mortality), we estimated yearly RSV-attributable incidence of events for different cardiorespiratory outcomes. We used a quasi-Poisson regression model, which accounted for periodic and aperiodic time trends and viral activity proxies. The yearly RSV-attributable cardiorespiratory hospitalization incidence increased with age and was highest among adults aged≥75 years (1064-1527 cases per 100,000 person-years). Similarly, the RSV-attributable cardiorespiratory mortality rate was highest among persons aged≥75 years (59-85 deaths per 100,000 person-years). Incidence rates for RSV-attributable hospitalizations and RSV-attributable mortality were on average 2-3 times higher for cardiorespiratory than respiratory disease alone. Incidence rate based on RSV-specific ICD codes only were 405-1729 times lower than modeled estimates accounting for untested events. RSV causes a substantial disease burden among adults in Italy and contributes to both respiratory and cardiovascular conditions. Our results emphasize the need for effective RSV prevention strategies, particularly among older adults.

The relationship between Zoster serology, vaccination uptake and infection rates: a single-centre cross-sectional study.

This study aimed to assess the prevalence of Varicella-Zoster Virus (VZV) immunity, vaccination uptake and incidence of VZV-related events in inflammatory arthritis (IA) patients initiating biologic or targeted synthetic disease-modifying antirheumatic drugs. An observational study was conducted in a single hospital between March 2019 and December 2020. Ninety-three IA patients were included. Data were collected from electronic health records and analysed using the chi-squared test. The majority of patients (91.4%) were seropositive for VZV, reaffirming the necessity for vaccination. In total, 8.6% of the cohort received the Zostavax vaccine, despite a small yet significant number of patients (4.3%) experiencing Herpes Zoster after initiating treatment. Multiple factors contributed to low vaccine uptake, including limited vaccine availability, discrepancies between the British Society for Rheumatology and Joint Committee on Vaccination and Immunisation guidelines, vaccine hesitancy and concerns regarding vaccine efficacy and risks. Significant VZV immunity exists among patients prior to targeted therapy commencement. Risk factors for VZV-related events include Janus kinase inhibition, increasing age and long-term steroid use. VZV-related events occurred exclusively in patients with prior viral immunity. Despite most patients having serological evidence of prior VZV exposure, our study exposes critical gaps between current clinical guidelines and practice, particularly in VZV vaccine uptake. Barriers to vaccination include inconsistent guidelines, limited vaccine availability and patient-level hesitancy. This is concerning as our cohort demonstrated small but significant rates of zoster, mostly among patients on long-term steroids.

Irrigation increases and stabilizes mosquito populations and increases West Nile virus incidence

Humans have greatly altered earth’s terrestrial water cycle with the majority of fresh water being used for agriculture. Irrigation changes spatial and temporal water availability and alters mosquito abundance and phenology. Previous studies evaluating the effect of irrigation on mosquito abundance and mosquito-borne disease have shown inconsistent results and little is known about the effect of irrigation on variability in mosquito abundance. We examined the effect of irrigation, climate and land cover on mosquito abundance and human West Nile virus (WNV) disease cases across California. Irrigation made up nearly a third of total water inputs, and exceeded precipitation in some regions. Abundance of two key vectors of several arboviruses, including WNV, Culex tarsalis and the Culex pipiens complex, increased 17–21-fold with irrigation. Irrigation reduced seasonal variability in C. tarsalis abundance by 36.1%. Human WNV incidence increased with irrigation, which explained more than a third (34.2%) of the variation in WNV incidence among California counties. These results suggest that irrigation can increase and decouple mosquito populations from natural precipitation variability, resulting in sustained and increased disease burdens. Shifts in precipitation due to climate change are likely to result in increased irrigation in many arid regions which could increase mosquito populations and disease.

Infection of South American coatis (Nasua nasua) with highly pathogenic avian influenza H5N1 virus displaying mammalian adaptive mutations

Deadly outbreaks among poultry, wild birds, and carnivorous mammals by the highly pathogenic H5N1 virus of the clade 2.3.4.4b have been reported in South America. The increasing virus incidence in various mammal species poses a severe zoonotic and pandemic threat. In Uruguay, the clade 2.3.4.4b viruses were first detected in February 2023, affecting wild birds and backyard poultry. Three months after the first reported case in Uruguay, the disease affected a population of 23 coatis (Nasua) in an ecological park. Most animals became infected, likely directly or indirectly from wild birds in the park, and experienced sudden death. Five animals from the colony survived, and four of them developed antibodies. The genomes of the H5N1 strains infecting coatis belonged to the B3.2 genotype of the clade 2.3.4.4b. Genomes from coatis were closely associated with those infecting backyard poultry, but transmission likely occurred through wild birds. Notable, two genomes have a 627K substitution in the RNA polymerase PB2 subunit, a hallmark amino acid linked to mammalian adaptation. Our findings support the ability of the avian influenza virus of the 2.3.4.4b clade to infect and transmit among terrestrial mammals with high pathogenicity and undergo rapid adaptive changes. It also highlights the coatis' ability to develop immunity and naturally clear the infection.

Improvement in the 95-95-95 Targets Is Accompanied by a Reduction in Both the Human Immunodeficiency Virus Transmission Rate and Incidence in China.

In 2016, China has implemented the World Health Organization's "treat all" policy. We aimed to assess the impact of significant improvements in the 95-95-95 targets on population-level human immunodeficiency virus (HIV) transmission dynamics and incidence. We focused on 3 steps of the HIV care continuum: diagnosed, on antiretroviral therapy, and achieving viral suppression. The molecular transmission clusters were inferred using HIV-TRACE. New HIV infections were estimated using the incidence method in the European Centre for Disease Prevention and Control HIV Modelling Tool. Between 2004 and 2023, the national HIV epidemiology database recorded 2.99 billion person-times of HIV tests and identified 1 976 878 new diagnoses. We noted a roughly "inverted-V" curve in the clustering frequency, with the peak recorded in 2014 (67.1% [95% confidence interval, 63.7%-70.5%]), concurrent with a significant improvement in the 95-95-95 targets from 10-13-<71 in 2005 to 84-93-97 in 2022. Furthermore, we observed a parabolic curve for a new infection with the vertex occurring in 2010. In general, it was suggested that the improvements in the 95-95-95 targets were accompanied by a reduction in both the population-level HIV transmission rate and incidence. Thus, China should allocate more effort to the first "95" target to achieve a balanced 95-95-95 target.

Respiratory Viral Infections from 2015 to 2022 in the HIVE Cohort of American Households: Incidence, illness characteristics, and seasonality.

Viral respiratory illnesses are the most common acute illnesses experienced and generally follow a predicted pattern over time. The SARS-CoV-2 pandemic interrupted that pattern. The HIVE (Household Influenza Vaccine Evaluation) study was established in 2010 to follow a cohort of Southeast Michigan households over time. Initially focused on influenza, surveillance was expanded to include other major respiratory pathogens, and, starting in 2015, the population was followed year-round. Symptoms of acute illness were reported, and respiratory specimens were collected and tested to identify viral infections. Based on the known population being followed, virus-specific incidence was calculated. From 2015 to 2022, 1755 participants were followed in HIVE for 7785 person-years with 7833 illnesses documented. Before the pandemic, rhinovirus (RV) and common cold human coronaviruses (HCoVs) were the viruses most frequently identified, and incidence decreased with increasing age. Type A influenza was next but with comparable incidence by age. Parainfluenza and respiratory syncytial viruses were less frequent overall, followed by human metapneumoviruses. Incidence was highest in young children, but infections were frequently documented in all age groups. Seasonality followed patterns established decades ago. The SARS-CoV-2 pandemic disrupted these patterns, except for RV and, to a lesser extent, HCoVs. In the first two years of the pandemic, RV incidence far exceeded that of SARS-CoV-2. Longitudinal cohort studies are important in comparing the incidence, seasonality, and characteristics of different respiratory viral infections. Studies documented the differential effect of the pandemic on the incidence of respiratory viruses in addition to SARS-CoV-2.