Seasonal distribution and upsurge of respiratory viruses among indigenous tribes with ILI and SARI in a far-flung Car Nicobar Island.

BACKGROUND: Respiratory viral illnesses among children are a prominent cause of morbidity and mortality in the developing world. The aim of this study is to understand the seasonal pattern and surge of respiratory viruses among the Nicobarese tribe. METHODS: Respiratory specimens were collected from both ARI and SARI cases attended the BJR district hospital in Car Nicobar Island, India, between 2021 and 2022. Respiratory viruses were identified from the specimens by using the qRT-PCR assay. Meteorological parameters were collected and evaluated using Microsoft Excel and SPSS 21. The significant association between the surge of respiratory viruses and each climatic parameter was evaluated. RESULTS: In this hospital-based cross-sectional study, 471 ILI cases were enrolled, and 209 of these were positive for respiratory viral infections. Of these respiratory virus infections, 201 (96.2%) were infected with a single respiratory virus infection, and 8 (3.8%) had mixed viral infections. Fever, cough, and chills were the most common symptoms of respiratory illness among this indigenous population. There was a significant link between respiratory viruses and influenza-like illness in children (below 5 years and 6 to 15 years). CONCLUSION: This prevalence study revealed that viral respiratory infections were more common in children than adults. Among these respiratory viruses, respiratory syncytial virus A (RSV) and influenza B virus were predominantly reported among tribal children up to age five years. In the year 2021, these viruses were recorded frequently during the winter season. Climate factors such as high humidity, high precipitation, moderate temperature, and moderate rainfall are found to be correlated with respiratory viral infections. This study implicates important information for preventing a further outbreak of respiratory viral infections in Car Nicobar Island.

Nowcasting methods to improve the performance of respiratory sentinel surveillance: lessons from the COVID-19 pandemic.

Respiratory diseases, including influenza and coronaviruses, pose recurrent global threats. This study delves into the respiratory surveillance systems, focusing on the effectiveness of SARI sentinel surveillance for total and severe cases incidence estimation. Leveraging data from the COVID-19 pandemic in Chile, we examined 2020-2023 data (a 159-week period) comparing census surveillance results of confirmed cases and hospitalizations, with sentinel surveillance. Our analyses revealed a consistent underestimation of total cases and an overestimation of severe cases of sentinel surveillance. To address these limitations, we introduce a nowcasting model, improving the precision and accuracy of incidence estimates. Furthermore, the integration of genomic surveillance data significantly enhances model predictions. While our findings are primarily focused on COVID-19, they have implications for respiratory virus surveillance and early detection of respiratory epidemics. The nowcasting model offers real-time insights into an outbreak for public health decision-making, using the same surveillance data that is routinely collected. This approach enhances preparedness for emerging respiratory diseases by the development of practical solutions with applications in public health.

Seroprevalence of Protective Antibodies Against Influenza and the Reduction of the Influenza Incidence Rate: An Annual Repeated Cross-Sectional Study From 2014 to 2019.

BACKGROUND: Seroepidemiological studies provide estimates of population-level immunity, prevalence/incidence of infections, and evaluation of vaccination programs. We assessed the seroprevalence of protective antibodies against influenza and evaluated the correlation of seroprevalence with the cumulative annual influenza incidence rate. METHODS: We conducted an annual repeated cross-sectional seroepidemiological survey, during June-August, from 2014 to 2019, in Portugal. A total of 4326 sera from all age groups, sex, and regions was tested by hemagglutination inhibition assay. Seroprevalence and geometric mean titers (GMT) of protective antibodies against influenza were assessed by age group, sex, and vaccine status (65+ years old). The association between summer annual seroprevalence and the difference of influenza incidence rates between one season and the previous one was measured by Pearson correlation coefficient (r). RESULTS: Significant differences in seroprevalence of protective antibodies against influenza were observed in the population. Higher seroprevalence and GMT for A(H1N1)pdm09 and A(H3N2) were observed in children (5-14); influenza B seroprevalence in adults 65+ was 1.6-4.4 times than in children (0-4). Vaccinated participants (65+) showed significant higher seroprevalence/GMT for influenza. A strong negative and significant correlation was found between seroprevalence and ILI incidence rate for A(H1N1)pdm09 in children between 5 and 14 (r = -0.84; 95% CI, -0.98 to -0.07); a weak negative correlation was observed for A(H3N2) and B/Yamagata (r ≤ -0.1). CONCLUSIONS: The study provides new insight into the anti-influenza antibodies seroprevalence measured in summer on the ILI incidence rate in the next season and the need for adjusted preventive health care measures to prevent influenza infection and transmission.

Clinical profile of children with influenza like illness during pre-monsoon at coastal Karaikal, Puducherry, India.

Influenza infections in developing countries are under reported and WHO estimates that nearly 99% of influenza deaths worldwide occur in children under-five years of age in Asian and African countries. Consequently, this study aims to analyze the use of clinical profile and easily available laboratory parameters to aid identification of the possible viral etiology in the setting of pre-monsoon ILI. A cross-sectional study was carried out for three months among children with ILI attending fever clinic of a tertiary care hospital in Karaikal, South India. In the study population the prevalence of ILI was highest in the age group four to five years followed by school aged children. Adolescents were affected the least. Influenza B was most common virus causing ILI in this region, followed by covid-19 infection. Laboratory parameters depicted a significantly high ESR in COVID-19 infected ILI children. They also exhibited leucopenia and normal platelet counts. Clinical symptoms and laboratory parameters which are easily available and cheaper can be used in resource poor settings of healthcare to identify possible influenza and COVID-19 infected children amongst cases presenting with ILI.

Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from Influenza Like Illness (ILI) and Severe Acute Respiratory Illness (SARI) cases reported between July-December, 2022.

Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) cases are more prone to Influenza and SARS-CoV-2 infection. Accordingly, we genetically characterized Influenza and SARS-CoV-2 in 633 ILI and SARI cases by rRT-PCR and WGS. ILI and SARI cases showed H1N1pdm09 prevalence of 20.9% and 23.2% respectively. 135 (21.3%) H1N1pdm09 and 23 (3.6%) H3N2 and 5 coinfection (0.78%) of H1N1pdm09 and SARS-CoV-2 were detected. Phylogenetic analysis revealed H1N1pdm09 resemblance to clade 6B.1A.5a.2 and their genetic relatedness to InfA/Perth/34/2020, InfA/Victoria/88/2020 and InfA/Victoria/2570/2019. Pan 24 HA and 26 NA nonsynonymous mutations and novel HA (G6D, Y7F, Y78H, P212L, G339R, T508K and S523T) and NA (S229A) mutations were observed. S74R, N129D, N156K, S162N, K163Q and S164T alter HA Cb and Sa antibody recognizing site. Similarly, M19T, V13T substitution and multiple mutations in transmembrane and NA head domain drive antigenic drift. SARS-CoV-2 strains genetically characterized to Omicron BA.2.75 lineage containing thirty nonsynonymous spike mutations exhibited enhanced virulence and transmission rates. Coinfection although detected very minimal, the mutational changes in H1N1pdm09 and SARS-CoV-2 virus infected individuals could alter antibody receptor binding sites, allowing the viruses to escape immune response resulting in better adaptability and transmission. Thus continuous genomic surveillance is required to tackle any future outbreak.

Seasonality of influenza-like illness and short-term forecasting model in Chongqing from 2010 to 2022.

BACKGROUND: Influenza-like illness (ILI) imposes a significant burden on patients, employers and society. However, there is no analysis and prediction at the hospital level in Chongqing. We aimed to characterize the seasonality of ILI, examine age heterogeneity in visits, and predict ILI peaks and assess whether they affect hospital operations. METHODS: The multiplicative decomposition model was employed to decompose the trend and seasonality of ILI, and the Seasonal Auto-Regressive Integrated Moving Average with exogenous factors (SARIMAX) model was used for the trend and short-term prediction of ILI. We used Grid Search and Akaike information criterion (AIC) to calibrate and verify the optimal hyperparameters, and verified the residuals of the multiplicative decomposition and SARIMAX model, which are both white noise. RESULTS: During the 12-year study period, ILI showed a continuous upward trend, peaking in winter (Dec. - Jan.) and a small spike in May-June in the 2-4-year-old high-risk group for severe disease. The mean length of stay (LOS) in ILI peaked around summer (about Aug.), and the LOS in the 0-1 and ≥ 65 years old severely high-risk group was more irregular than the others. We found some anomalies in the predictive analysis of the test set, which were basically consistent with the dynamic zero-COVID policy at the time. CONCLUSION: The ILI patient visits showed a clear cyclical and seasonal pattern. ILI prevention and control activities can be conducted seasonally on an annual basis, and age heterogeneity should be considered in the health resource planning. Targeted immunization policies are essential to mitigate potential pandemic threats. The SARIMAX model has good short-term forecasting ability and accuracy. It can help explore the epidemiological characteristics of ILI and provide an early warning and decision-making basis for the allocation of medical resources related to ILI visits.

Real-time investigation of an influenza A(H3N2) virus outbreak in a refugee community, November 2022.

OBJECTIVES: To report epidemiological and virological results of an outbreak investigation of influenza-like illness (ILI) among refugees in Northern Italy. STUDY DESIGN: Outbreak investigation of ILI cases observed among nearly 100 refugees in Northern Italy unvaccinated for influenza. METHODS: An epidemiological investigation matched with a differential diagnosis was carried out for each sample collected from ILI cases to identify 10 viral pathogens (SARS-CoV-2, influenza virus type A and B, respiratory syncytial virus, metapneumovirus, parainfluenza viruses, rhinovirus, enterovirus, parechovirus, and adenovirus) by using specific real-time PCR assays according to the Centers for Disease Control and Prevention (CDC) protocols. In cases where the influenza virus type was identified, complete hemagglutinin (HA) gene sequencing and the related phylogenetic analysis were conducted. RESULTS: The outbreak was caused by influenza A(H3N2): the attack rate was 83.3% in children aged 9-14 years, 84.6% in those aged 15-24 years, and 28.6% in adults ≥25 years. Phylogenetic analyses uncovered that A(H3N2) strains were closely related since they segregated in the same cluster, showing both a high mean nucleotide identity (100%), all belonging to the genetic sub-group 3C.2a1b.2a.2, as those mainly circulating into the general population in the same period. CONCLUSIONS: The fact that influenza outbreak strains as well as the community strains were genetically related to the seasonal vaccine strain suggests that if an influenza prevention by vaccination strategy had been implemented, a lower attack rate of A(H3N2) and ILI cases might have been achieved.

Prevalence of respiratory syncytial virus infection and associated factors in children aged under five years with severe acute respiratory illness and influenza-like illness in Ethiopia.

Objectives: Acute respiratory infections because of respiratory syncytial viruses (RSVs) are among the major leading causes of morbidity and mortality in children worldwide. RSV prevalence and its contributing factors among children aged under 5 years in Ethiopia are not well studied. To assess the prevalence and associated factors of RSV infection in children aged under 5 years using influenza sentinel surveillance sites in Ethiopia. Methods: A cross-sectional study design was used utilizing influenza-like illness/sever acute respiratory illness surveillance data from January 2021 to December 2022 at the Ethiopian Public Health Institute. Results: In total, 2234 cases were included, with an overall RSV positivity rate of 16.2%. The RSV positivity rate was high in children aged under 1 year (22.8%) and during fall season (24.8%). The RSV positivity rate was significantly associated with ages under 1 year (adjusted odds ratio [AOR] 2.8, 95% confidence interval [CI]: 1.89-4.15) and 1-2 years (AOR 1.9, 95% CI: 1.26-2.73) and the fall season (AOR 1.67, 95% CI: 1.17-2.38). Conclusion: The study revealed that a considerably high RSV positivity rate was detected in children aged under 5 years. The age of children and season have a significant association with RSV positivity rate. Further studies of RSV viral genotype, clinical characteristics, and disease outcome need to be conducted for a better understanding of the virus and disease outcome.

Application of the Time Derivative (TD) Method for Early Alert of Influenza Epidemics.

BACKGROUND: In order to minimize the spread of seasonal influenza epidemic to communities worldwide, the Korea Disease Control and Prevention Agency has issued an influenza epidemic alert using the influenza epidemic threshold formula based on the results of the influenza-like illness (ILI) rate. However, unusual changes have occurred in the pattern of respiratory infectious diseases, including seasonal influenza, after the coronavirus disease 2019 (COVID-19) pandemic. As a result, the importance of detecting the onset of an epidemic earlier than the existing epidemic alert system is increasing. Accordingly, in this study, the Time Derivative (TD) method was suggested as a supplementary approach to the existing influenza alert system for the early detection of seasonal influenza epidemics. METHODS: The usefulness of the TD method as an early epidemic alert system was evaluated by applying the ILI rate for each week during past seasons when seasonal influenza epidemics occurred, ranging from the 2013-2014 season to the 2022-2023 season to compare it with the issued time of the actual influenza epidemic alert. RESULTS: As a result of applying the TD method, except for the two seasons (2020-2021 season and 2021-2022 season) that had no influenza epidemic, an influenza early epidemic alert was suggested during the remaining seasons, excluding the 2017-2018 and 2022-2023 seasons. CONCLUSION: The TD method is a time series analysis that enables early epidemic alert in real-time without relying on past epidemic information. It can be considered as an alternative approach when it is challenging to set an epidemic threshold based on past period information. This situation may arise when there has been a change in the typical seasonal epidemic pattern of various respiratory viruses, including influenza, following the COVID-19 pandemic.

Identify future epidemic threshold and intensity for influenza-like illness in Iraq by using the moving epidemic method.

Objectives: Influenza-like illness (ILI) entered the Iraq surveillance system in 2021. The alert threshold was determined using the cumulative sum 2 method, which did not provide other characteristics. This study uses the moving epidemic method (MEM) to describe duration and estimate alert thresholds for ILI in Iraq for 2023-2024. Methods: MEM default package was used to estimate influenza 2023-2024 epidemic thresholds. Analysis was repeated using optimum parameter of epidemic timing for fixed criteria method, which is 3.3. Arithmetic means and 95% confidence interval upper limit were used to estimate threshold. Geometric mean and 40%, 90%, and 97.3% confidence interval upper limits were used to estimate intensity levels. Aggregated Centers for Disease Control and Prevention surveillance data were used to detect epidemic thresholds, length, sensitivity, and predictive values. Results: ILI activity starts at week 30 and lasts 7 weeks. Optimized epidemic threshold is 4513 cases, lower than default (4540 cases). Optimized medium-intensity level was higher than default, and high and very high-intensity levels were lower. Conclusions: MEM is essential to determine an influenza epidemic's threshold and intensity levels. Despite requiring 3-5 years of data, using it on data for 2.5 years has resulted in an epidemic threshold slightly higher than the threshold calculated using the cumulative sum 2 method.

Clinical and molecular characterization of children and adults with respiratory bocavirus infection in Mexico: a cross-sectional nested study within the ILI002 prospective observational study.

Background: Human Bocaviruses (HBoV) can cause acute respiratory tract infections. High coinfection rates cloud its pathogenicity. This study sought to describe the clinical features of HBoV1 disease in children and adults with Influenza-like illness (ILI), exploring associations between viral load, clinical features, and seasonality. Methods: Patients who tested positive for HBoV1 by polymerase chain reaction, enrolled from April 2010 to March 2014 in the ILI002 prospective observational cohort study were included in this cross-sectional nested study. Participants were included in ILI002 if they presented with signs and/or symptoms suggestive of influenza-like illness. Samples were tested for viral load, and NP1 and VP1/VP2 phylogenetic analyses, except for the samples lacking suitable and viable clinical material for genotyping. Findings: We identified HBoV1 in 157 (2.8%) of participants. Prevalence was 4.5% in children and 1.8% in adults. Single HBoV1 detection occurred in 41.1% and 46.3% of children and adults, respectively. Children commonly experienced fever (83.3%), cough with sputum (74.4%), and shortness of breath (72.2%). In the multivariate analysis of children, significant positive associations were detected between viral loads and age (0.20 [95% CI: 0.07, 0.33]), and the presence of fever (2.64 [95% CI: 1.35, 3.94]), nasal congestion (1.03 [95% CI: 0.07, 1.99]), dry cough (1.32 [95% CI: 0.42, 2.22]), chest congestion (1.57 [95% CI: 0.33, 2.80]), red eyes (1.25 [95% CI: 0.35, 2.14]), cough with sputum (1.79 [95% CI: 0.80, 2.78]), and other signs and symptoms such as chills, dizziness, and diaphoresis (1.73 [95% CI: 0.19, 3.27]). In contrast, significant negative associations were found between viral loads and percent neutrophils on the blood count (-0.04 [95% CI: -0.06, -0.02]), fatigue (-1.60 [95% CI: -2.46, -0.74]) and the presence of other symptoms or signs, including adenopathy and rash (-1.26 [95% CI: -2.31, -0.21]). Adults commonly experienced sore throat (73.1%), fatigue (77.4%), and headache (73.1%). In the multivariate analysis of adults, significant positive associations were detected between viral load and body mass index (0.13 [95% CI: 0.04, 0.21]), and the presence of confusion (1.54 [95% CI: 0.55, 2.53]), and sore throat (1.03 [95% CI: 0.20, 1.85]), and significant negative associations were detected between viral load and chest congestion (-1.16 [95% CI: -2.07, -0.24]). HBoV1 was detected throughout the year irrespective of season, temperature, and humidity. Interpretation: This study demonstrated the importance of detecting HBoV1 in patients with influenza-like illness either as single infection or co-infection, in both adults and children, and improves the characterization of HBoV1 seasonality, clinical features, and viral load. Phylogenetic analyses show a high conservation. Funding: The Mexican Emerging Infectious Diseases Clinical Research Network (LaRed), CONACYT (Fondo Sectorial SSA/IMSS/ISSSTE, Projects No. 71260 and No. 127088), Fondos federales no. HIM/2015/006, NIAID, NIH through a contract with Westat, Inc. (HHSN2722009000031, HHSN27200002), NCI, NIH (75N91019D00024, 75N91019F00130). Additional information at the end of the manuscript.

Clinical Profile, Intensive Care Needs and Predictors of Outcome Among Children Admitted with Non-COVID Severe Acute Respiratory Illness (SARI) During the Pandemic.

OBJECTIVES: To study the epidemiology of non-coronavirus disease-2019 (non-COVID-19) respiratory viral infections with respect to their clinical profile, intensive care needs and predictors of outcome once the non-pharmacological interventions (NPI) during the coronavirus disease-2019 (COVID-19) pandemic were relaxed. METHODS: Retrospective analysis of children with Severe Acute Respiratory Illness (SARI) who were SARS-CoV-2 negative, admitted to the Pediatric Emergency/Intensive Care Unit (PICU) from July 2021 through October 2021 was conducted. RESULTS: One hundred and thirty nine children with median age of 11 (4-28.5) mo were included. Besides respiratory symptoms in all, diarrhea was reported in 90 (64.7%) children. Nearly half (n = 66; 47%) presented in hypoxemic respiratory failure (SpO2 <88%). Fifty-two (37.4%) children had co-morbidities, commonest being congenital heart disease in 12 (23.1%). Baseline parameters revealed leukopenia (specifically lymphopenia) 39 (28%), elevated aspartate transaminase [Serum glutamic-oxaloacetic transaminase (SGOT)] in 108 (77.6%), elevated N-acetyl-cysteine-activated creatinine kinase (CK-NAC) 23 (79%) and lactate dehydrogenase (LDH) 15 (88%). Intensive care needs included mechanical ventilation 51 (36.6%), vasoactive support 34 (24.5%), and renal replacement therapy 10 (7.1%). Forty-two (30.2%) children developed multi-organ dysfunction syndrome (MODS). One hundred and three (74.1%) children were discharged, 31 (22.3%) died, and 5 (3.6%) left against medical advice. On multivariate regression analysis, elevated liver enzymes (>5 times normal), hypoxemic respiratory failure at admission, hypotensive shock and MODS predicted mortality. CONCLUSIONS: A surge in non-COVID SARI was observed once lockdown measures were relaxed. Nearly 1/3rd progressed to multi-organ failure and died. Elevated liver enzymes, hypoxemic respiratory failure at admission, hypotensive shock and MODS predicted death.

Detection and genotyping of enteroviruses in 3 960 influenza-negativeinfluenza-like illness cases in Chongqing / 公共卫生与预防医学

Objective To understand the epidemiological characteristics and genotype distribution of enterovirus (EV) in influenza-negative influenza-like illness (ILI) cases in Chongqing, and to provide a scientific basis for EV prevention and control. Methods Throat swab samples of influenza-negative ILI cases were collected from surveillance sites. The samples were detected for EV using real-time RT-PCR. The VP4 regions of positive samples were amplified and sequenced for genotyping. Results A total of 3 960 influenza-negative ILI samples were collected from January to December 2021, and 316 (7.98%) of them were EV-positive. EV could be detected in influenza-negative ILI cases in Chongqing all year round. The months with high EV-positive rates were January (11.60%), April (10.56%), May (11.79%), June (12.62%), and July (10.33%). There was a statistically significant difference in the detection rate of EV in ILI cases in different regions, gender, and age groups (χ2=29.647，χ2=4.192，χ2=69.176，P<0.05). A total of 213 EV-positive cases were successfully genotyped, including 17 genotypes of EV-A, EV-B, and EV-C and 5 genotypes of HRV-B. The dominant genotypes were CV-A4 (32.86%), CV-A2 (23.00%), CA-6 (12.21%), and CA-10 (11.74%). EV-D and novel EV were not identified in this study. Conclusion EV is an important pathogen in ILI cases in Chongqing. The prevalence of EV in ILI cases in Chongqing has typical regional, seasonal and population characteristics. Prevention and control should be carried out in Chongqing according to the epidemic characteristics of EV.

Identifying and warning against spatial conflicts of land use from an ecological environment perspective: A case study of the Ili River Valley, China.

Spatial conflicts of land use (SCLU) arise during land-use change, which causes an imbalance of land-use spatial patterns and negatively affects society, the economy, and ecology. Previous research has focused on identifying and measuring SCLU, with less attention on the negative effects. The incorporation of risk assessment methods to evaluate potential conflict risks has been limited. The current study presents methods for measuring SCLU and assessing potential conflict risks from the ecological environment perspective. The spatial comprehensive conflicts index and potential conflict risk index were used to identify and measure the SCLU and to assess and warn against potential conflict risks, respectively, based on a case study in the Ili River Valley in China. The impacts of terrain restriction and land-use change on the SCLU were explored. Results indicate that (1) the SCLU area in the Ili River Valley decreased by 2,608 km2 from 2010 to 2020, compared to the previous decade, the degree of conflict weakened, and the main body of the SCLU gradually shifted northwest. (2) The potential risk areas cover 20,268 km2 in 2020-2030 and are mainly distributed in the "Khorgas City-Huocheng County-Yining City-Yining County" group of towns, as well as along the Ili-Kunes rivers and in the ecological protection zone in the south of the Ili River Valley, which shows the clustering along the city and distribution along the river in the spatial pattern. (3) Topography had a significant impact on the SCLU, and the main types of land-use change in the severe-conflict zone were the reduction of grassland and the expansion of arable and built-up land. For future conflict mitigation in the Ili River Valley, cautioning against urban sprawl and safeguarding land ecological security is critical. This study systematically investigates and analyzes SCLU across three dimensions: theory, methodology, and application to produce a theoretical and practical framework to identify SCLU and assess potential conflict risks.

Time trend of respiratory viruses before and during the COVID-19 pandemic in severe acute respiratory virus infection in the Sultanate of Oman between 2017 and 2022.

Introduction: Severe acute respiratory illness (SARI) is a potentially lethal condition, necessitating thorough medical care. COVID-19 underscored the SARI threat, but other high-risk pathogens require monitoring alongside SARS-CoV-2. Oman instituted a comprehensive testing system to gauge the prevalence of these pathogens between 2017 and 2021, aiding resource allocation and public health responses to potential respiratory pathogen outbreaks. Methods: Samples from SARI cases admitted to ICU were tested for pathogens using the Fast-Track Diagnostic (FTD) molecular assay, a respiratory virus panel (RVP) that tests for 21 pathogens, including 20 viruses, by qPCR. Results: Between 2017 and 2022, ~30 000 samples were analysed using the RVP panel. Among SARI patients, 8%-42% tested positive for respiratory pathogens, with 4% showing multiple infectious agents, especially in children under 10. A drop in positivity during 2020-2021 can be attributed to SARS-CoV-2 control measures, followed by a rebound in infections in early 2022. Discussion: The COVID-19 pandemic heightened awareness of respiratory pathogens' spread without adequate control measures. Influenza A/B, human rhinoviruses and respiratory syncytial virus constituted over 50% of severe acute respiratory illness cases in Oman over the past 5 years. During the pandemic, the incidence of these infections significantly declined, demonstrating the efficacy of COVID-19 prevention measures in reducing spread of other pathogens.

Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis.

Background: Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods: In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings: Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation: The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

Epidemiology of Influenza-like Illness and Respiratory Viral Etiology in Adult Patients in Taiyuan City, Shanxi Province, China between 2018 and 2019.

To determine the epidemiological status of influenza and understand the distribution of common respiratory viruses in adult patients with influenza-like illness (ILI) cases in Taiyuan City, Shanxi Province, China, epidemiological data between 2018 and 2019 were retrieved from the China Influenza Surveillance Information System, and two sentinel ILI surveillance hospitals were selected for sample collection. All specimens were screened for influenza virus (IFV) and the other 14 common respiratory viruses using real-time polymerase chain reaction. The results of the 2-year ILI surveillance showed that 26,205 (1.37%) of the 1,907,869 outpatients and emergency patients presented with ILI, with an average annual incidence of 297.75 per 100,000 individuals, and ILI cases were predominant in children <15 years (21,348 patients, 81.47%). Of the 2713 specimens collected from adult patients with ILI, the overall detection rate of respiratory viruses was 20.13%, with IFV being the most frequently detected (11.79%) and at a relatively lower rate than other respiratory viruses. Further subtype analysis indicated an alternating or mixed prevalence of H1N1 (2009), H3N2, Victoria, and Yamagata subtypes. This study provides a baseline epidemiological characterization of ILI and highlights the need for a nationwide detection and surveillance system for multiple respiratory pathogens.

External quality assessment for laboratories in pan-India ILI/SARI surveillance for simultaneous detection of influenza virus and SARS-CoV-2.

Introduction: The Indian Council of Medical Research has set up a nationwide network of 28 laboratories for simultaneous surveillance of influenza virus and SARS-CoV-2 in ILI/SARI patients, using an in-house developed and validated multiplex real-time RTPCR assay. The aim of this study was to ensure the quality of testing by these laboratories by implementing an external quality assessment program (EQAP). Methods: For this EQAP, a proficiency test (PT) panel comprising tissue-culture or egg-grown influenza virus and SARS-CoV-2 was developed. The PT panel was distributed to all the participant laboratories, which tested the panel and submitted the qualitative results online to the EQAP provider. The performance of the laboratories was evaluated on qualitative criteria but cycle threshold (Ct) values were also gathered for each sample. Results: On a qualitative basis, all the laboratories achieved the criteria of 90% concordance with the results of the PT panel provider. Ct values of different samples across the laboratories were within ≤ ±3 cycles of the corresponding mean values of the respective sample. The results of this EQAP affirmed the quality and reliability of testing being done for simultaneous surveillance of influenza virus and SARS-CoV-2 in India.

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Ili Valley is an important ecological barrier in western China and an important economic zone of the Belt and Road Initiative. Exploring the driving factors of ecosystem service value (ESV) based on land use change is of great significance for optimizing regional ecological environment and coordinating human-land relationship. Based on three periods of land use data from 2000 to 2020 in Yili Valley, we used ArcGIS 10.8 and Origin to analyze the characteristics of land use change, temporal and spatial variations of ESV, and the synergy and trade-offs of ecosystem services, and explored the driving factors affecting the spatial differentiation of ESV and the interaction among factors by using Geo-Detector. The results showed that land use change in the study area was obvious from 2000 to 2020, with the area of grassland and water area being greatly reduced and the largest increase for the area of construction land. The ESV of grassland and water area and the service function of water resource supply decreased significantly. ESV high value areas were transformed to low value areas. Synergy was the dominant relationship among ecosystem services in the study area, which showed an increasing trend. Elevation was the main driving factor of ESV spatial differentiation in Yili Valley, and the low elevation plain area suitable for human activities on both sides of the basin was the low ESV value area. The interaction between all factors was manifested as enhanced relationship, while the explanatory power of natural factors was higher than that of social and economic factors.

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.

IMPORTANCE: Respiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza surveillance program. We describe the results of influenza and SARS-CoV-2 testing of samples collected from 16 sentinel surveillance sites located throughout Uganda as well as SARS-CoV-2 testing and sequencing in other health centers. The surveillance system showed that both SARS-CoV-2 and influenza can be monitored in communities at the national level. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will help facilitate the timely release of SARS-CoV-2 information for COVID-19 pandemic mitigation and provide important information regarding the persistent threat of influenza.