Severe Acute Respiratory Illness Cases Research Articles

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.

Incidence of influenza virus-associated Severe Acute Respiratory Infections in three districts in 2018 at Gharbia governorate, Egypt.

Influenza remains a contributor to substantial global morbidity and mortality. There is very limited data on disease burden in Egypt. The purpose of this study was to estimate the incidence of influenza-associated Severe Acute Respiratory Illness (SARI) in three districts in Gharbia governorate in 2018. This study Followed the World Health Organization (WHO) manual for estimating disease burden associated with seasonal influenza. The hospital admission database was screened for SARI patients in three districts at Gharbia governorate in 2018. A hospital admission survey (HAS) was used to define the catchment population. The incidence rate estimation was computed as the number of influenza-positive SARI cases per 100,000 population. A total of 180 SARI cases were identified in the catchment area. The median age was 23 years [IQR: 2-53], and 45% were males. Out of the total SARI cases, 33.3% influenza was confirmed by the laboratory test of RP-PCR. Influenza A(H3N2) virus predominated representing 55.0% of patients, thanA(H1N1) 26.7% and Flu-B virus 18.3%. Influenza prevailed in winter and spring; no deaths from influenza were reported. The annual incidence of influenza-associated SARIs found higher in <2 years (282 /100,000) and ≥65 years patients (215/100,000) at significant level p<0.001. The WHO Manual for estimating disease burden associated with seasonal influenza was successfully operationalized in the three districts of Gharbia governorate. It can be used in other districts. A considerable burden was associated with influenza viruses requiring hospitalization, especially among the older adult group.

Effect of COVID-19 pandemic on influenza; observation of a tertiary level virology laboratory.

The lockdown enforced amid the COVID-19 pandemic has affected the occurrence and trends of various respiratory virus infections, with a particular focus on influenza. Our study seeks to analyze the repercussions of the COVID-19 pandemic on the positivity of the influenza virus throughout a 4-year span, encompassing both the pre-COVID-19 era (2018 and 2019) and the COVID-19 period (2020 and 2021). Data collected from patients clinically diagnosed with Influenza-like Illness and Severe Acute Respiratory Illness (SARI) from January 2018 to December 2021 for influenza virus detection were acquired and analyzed through multiplex RT-qPCR. The statistical analysis was conducted using SPSS (Statistical Package for Social Sciences) Version 21.0 Software. A total of 4464 samples were tested over 4years (2018-2021), with 3201 samples from the pre-COVID era and 1263 samples from the COVID era. Influenza A positivity dropped from 17.7 to 9.57% and Influenza B positivity decreased from 3.74 to 2.61%. Subtyping revealed changes in prevalence for both viruses. Seasonal variations showed more pronounced peaks in the pre-COVID-19 era with reduced activity during lockdown. Influenza A saw a resurgence in August 2021. Throughout the COVID-19 pandemic (2020-2021) SARI cases did not decrease. The positivity rate for Influenza A slightly rose to 7.79% from 4.23% in the COVID period (2020-2021). This increase correlates with heightened hospitalization rates during the pandemic, sparking concerns of potential coinfection with coronavirus and Influenza A. The notable drop in influenza cases in 2020-2021 is likely due to stringent precautions, lockdowns, drug repurposing, and prioritized testing, indicating no reduction in influenza transmission. Increased influenza positivity in SARI patients during COVID-19 highlights a heightened risk of coinfection. Emphasizing solely on COVID-19 may lead to underreporting of other respiratory pathogens, including influenza viruses.

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

AbstractIntroductionSevere 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.MethodsSamples 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.ResultsBetween 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.DiscussionThe 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.

Viral aetiology of severe acute respiratory illness among patients admitted during the 2022 peri-Hajj period

Severe acute respiratory illness (SARI) among pilgrims continues to be an important healthcare issue. The aim of this study was to describe the viral aetiology of patients admitted to hospitals in the holy cities of Makkah and Madinah during the 2022 peri-Hajj period. This is a retrospective analysis of patients admitted to hospitals with SARI. Patients were tested with multiplex polymerase chain reaction for the most common viral aetiologies. In total, 179 cases of SARI were identified during the study period. Of these, 101 (56.4%) were males, 78 (43.6%) were females, and 78 (43.6%) were Saudi. The mean age was 58.60 years (standard deviation 20.5) years. The most common age group was ≥65 years (n=68, 36%), followed by 55-59 years (n=37, 19%). The most common comorbidities were diabetes mellitus (n=67, 36%), hypertension (n=65, 35%) and chronic lung disease (n=34, 18%). Eighty-five (47.5%) patients tested negative and 94 (42.5%) tested positive for various viral aetiologies. The most frequently detected viruses were severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (n=28, 15%) and influenza (n=22, 12%); of the influenza cases, 16 were influenza A (6 (43%) were H3N2), and six were influenza B. The only case of Middle East respiratory syndrome coronavirus (MERS-CoV) was in a citizen, and none of the visitors or residents had MERS-CoV. Of the total cases, 27 (14%) died during the follow-up period. In a binary regression analysis, only age was associated with mortality (P=0.002). The most commonly detected viruses among patients admitted to hospital with SARI were SARS-CoV-2 and influenza. It is important to continue surveillance of admitted and non-admitted patients in different Hajj periods to identify any shift in the aetiologic agents.

The attributable fraction of respiratory syncytial virus among patients of different ages with influenza-like illness and severe acute respiratory illness in a high HIV prevalence setting, South Africa, 2012-2016

ObjectivesThe detection of respiratory syncytial virus (RSV) in upper airway samples does not necessarily infer causality of illness. We aimed to calculate the attributable fraction (AF) of RSV in clinical syndromes across age groups. MethodsUsing unconditional logistic regression models, we estimated the AF of RSV-associated influenza-like illness (ILI) and severe acute respiratory illness (SARI) cases by comparing RSV detection prevalence among ILI and SARI cases to those of healthy controls in South Africa, 2012-2016. The analysis, stratified by HIV serostatus, was conducted in the age categories <1, 1-4, 5-24, 25-44, 45-64, and ≥65 years. ResultsWe included 12,048 individuals: 2687 controls, 5449 ILI cases, and 5449 SARI cases. RSV-AFs for ILI were significant in <1, 1-4, 5-and 24, 25-44-year age groups: 84.9% (95% confidence interval [CI] 69.3-92.6%), 74.6% (95% CI 53.6-86.0%), 60.8% (95% CI 21.4-80.5%) and 64.1% (95% CI 14.9-84.9%), respectively. Similarly, significant RSV-AFs for SARI were 95.3% (95% CI 91.1-97.5) and 83.4% (95% CI 70.9-90.5) in the <1 and 1-4-year age groups respectively. In HIV-infected persons, RSV was significantly associated with ILI cases vs controls in individuals aged 5-44 years. ConclusionHigh RSV-AFs in young children confirm RSV detection is associated with severe respiratory illness in South African children, specifically infants. These estimates will assist with refining burden estimates and cost-effectiveness models.

End-of-season influenza vaccine effectiveness during the Southern Hemisphere 2022 influenza season – Chile, Paraguay, and Uruguay

ObjectivesThis study estimated the 2022 end-of-season influenza vaccine effectiveness (VE) against severe acute respiratory illness (SARI) hospitalization in Chile, Paraguay, and Uruguay. MethodsWe pooled surveillance data from SARI cases in 18 sentinel surveillance hospitals in Chile (n = 9), Paraguay (n = 2), and Uruguay (n = 7) from March 16-November 30, 2022. VE was estimated using a test-negative design and logistic regression models adjusted for country, age, sex, presence of ≥1 comorbidity, and week of illness onset. VE estimates were stratified by influenza virus type and subtype (when available) and influenza vaccine target population, categorized as children, individuals with comorbidities, and older adults, defined per countries’ national immunization policies. ResultsAmong the 3147 SARI cases, there were 382 (12.1%) influenza test-positive case patients; 328 (85.9%) influenza case patients were in Chile, 33 (8.6%) were in Paraguay, and 21 (5.5%) were in Uruguay. In all countries, the predominant subtype was influenza A(H3N2) (92.6% of influenza cases). Adjusted VE against any influenza-associated SARI hospitalization was 33.8% (95% confidence interval: 15.3%, 48.2%); VE against influenza A(H3N2)-associated SARI hospitalization was 30.4% (95% confidence interval: 10.1%, 46.0%). VE estimates were similar across target populations. ConclusionDuring the 2022 influenza season, influenza vaccination reduced the odds of hospitalization among those vaccinated by one-third. Health officials should encourage influenza vaccination in accordance with national recommendations.

The burden of RSV-associated illness in children aged < 5 years, South Africa, 2011 to 2016

BackgroundVaccines and monoclonal antibodies to protect the very young infant against the respiratory syncytial virus (RSV)-associated illness are effective for limited time periods. We aimed to estimate age-specific burden to guide implementation strategies and cost-effectiveness analyses.MethodsWe combined case-based surveillance and ecological data to generate a national estimate of the burden of RSV-associated acute respiratory illness (ARI) and severe acute respiratory illness (SARI) in South African children aged < 5 years (2011–2016), including adjustment for attributable fraction. We estimated the RSV burden by month of life in the < 1-year age group, by 3-month intervals until 2 years, and then 12 monthly intervals to < 5 years for medically and non-medically attended illness.ResultsWe estimated a mean annual total (medically and non-medically attended) of 264,112 (95% confidence interval (CI) 134,357–437,187) cases of RSV-associated ARI and 96,220 (95% CI 66,470–132,844) cases of RSV-associated SARI (4.7% and 1.7% of the population aged < 5 years, respectively). RSV-associated ARI incidence was highest in 2-month-old infants (18,361/100,000 population, 95% CI 9336–28,466). The highest incidence of RSV-associated SARI was in the < 1-month age group 14,674/100,000 (95% CI 11,175–19,645). RSV-associated deaths were highest in the first and second month of life (110.8 (95% CI 74.8–144.5) and 111.3 (86.0–135.8), respectively).ConclusionsDue to the high burden of RSV-associated illness, specifically SARI cases in young infants, maternal vaccination and monoclonal antibody products delivered at birth could prevent significant RSV-associated disease burden.

Clinicoepidemiological Profile and Diagnosis of Severe Acute Respiratory Syndrome Coronavirus-2 and Influenza Viruses in Patients with Severe Acute Respiratory Illness by Real-time Reverse Transcription Polymerase Chain Reaction: A Cross-sectional Study

Introduction: Severe Acute Respiratory Illness (SARI) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARSCoV-2) and influenza viruses represent a significant global public health concern. The disease spectrum ranges from mild to life-threatening conditions. Surveillance of hospitalised SARI patients is an essential public health tool used to identify cause of the disease, track changes in circulating viruses and serve as an alert mechanism for potential pandemic viruses. Aim: To determine the rate of SARS-CoV-2 and influenza virus positivity among SARI cases and to investigate the epidemiological and clinical characteristics of the patients. Materials and Methods: A cross-sectional study was conducted on 400 SARI patients admitted to Guru Nanak Dev Hospital, Amritsar, Punjab, India between February 2021 and June 2022. The clinical, demographic, and epidemiological data, as well as co-morbidities of all patients were recorded. Oropharyngeal and nasopharyngeal samples were collected and tested for SARSCoV-2, Influenza A, Influenza A (H3N2), Influenza A (H1N1) pdm09-pandemic 2009, and Influenza B using real-time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) test. Statistical analysis was performed using Statistical Package for the Social Sciences (SPSS) version 23.0 for Windows. Results: Out of the 400 SARI patients, 117 (29.25%) tested positive for SARS-CoV-2, 14 (3.5%) for Influenza A, 7 (1.75%) for Influenza A (H1N1) pdm09, and 4 (1%) for Influenza A (H3N2). The majority of cases in both SARS-CoV-2 and influenza were in the 41-60 years age group (47.86% and 57.14%, respectively). Males were predominantly infected in SARS-CoV-2 positive patients (62/117, 52.99%), while females were more infected in influenza positive cases (9/14, 64.28%). The most common presenting symptoms were fever, cough, dyspnoea, and sore throat in both cases. Hypertension, diabetes mellitus, Chronic Obstructive Pulmonary Disease (COPD), and coronary artery disease were the most common co-morbidities observed. Conclusion: Evaluation of clinical and epidemiological profiles of SARI patients can aid in better understanding and management of outbreaks. Close monitoring and quarantine measures will be necessary to prevent extensive transmission within the community

Dichotomous outcomes vs. survival regression models for identification of predictors of mortality among patients with severe acute respiratory illness during COVID-19 pandemics.

As the studies predicting mortality in severe acute respiratory illness (SARI) have inferred associations either from dichotomous outcomes or from time-event models, we identified some clinical-epidemiological characteristics and predictors of mortality by comparing and discussing two multivariate models. To identify factors associated with death among all SARI hospitalizations occurred in Botucatu (Brazil)/regardless of the infectious agent, and among the COVID-19 subgroup, from March 2020 to 2022, we used a multivariate Poisson regression model with binomial outcomes and Cox proportional hazards (time-event). The performance metrics of both models were also analyzed. A total of 3,995 hospitalized subjects were included, of whom 1338 (33%) tested positive for SARS-CoV-2. We identified 866 deaths, of which 371 (43%) were due to the COVID-19. In the total number of SARI cases, using both Poisson and Cox models, the predictors of mortality were the presence of neurological diseases, immunosuppression, obesity, older age, and need for invasive ventilation support. However, the Poisson test also revealed that admission to an intensive care unit and the COVID-19 diagnosis were predictors of mortality, with the female gender having a protective effect against death. Likewise, Poisson proved to be more sensitive and specific, and indeed the most suitable model for analyzing risk factors for death in patients with SARI/COVID-19. Given these results and the acute course of SARI and COVID-19, to compare the associations and their different meanings is essential and, therefore, models with dichotomous outcomes are more appropriate than time-to-event/survival approaches.

Clinical profile, etiology, outcome and new-onset diabetes: A SARI case series

Introduction: The world is currently facing the SARS-CoV-2 pandemic with evolving 2nd wave. The COVID-19 patients present most commonly with Severe Acute Respiratory Illness (SARI) in an emergency room with acute onset fever, cough, and breathlessness. However, not all SARI cases as per definition are due to COVID-19 infection, which is well proven in this case series of 113 cases of SARI. This is just the opposite of the other SARI series done in the pre-COVID-19 era. Also, no previous SARI case series data has shown significant association with Diabetes Mellitus, including new-onset diabetes thus figuring out the major Pathophysiological association of COVID-19 with glucose metabolism and has a bearing on the pathogenesis, treatment, and outcome of COVID-19 infection and perpetuity of pandemic of this magnitude. Here we raise concern for the first time about the growing association of an infectious pandemic with the lifestyle disorders which are non-communicable diseases but carry with them the potential of fertile soil for rapidly spreading epidemics. Aim and objective: To find out the etiology, clinical profile, treatment outcome, and mortality rate in different sub-groups of SARI cases in a tertiary care hospital and the incidence of new-onset Diabetes Mellitus in them and to investigate theoretically the hypothesis that maintaining normal glucose metabolism could prevent progression of a mild Flu-like illness (FLI) to a severe form of Severe Acute Respiratory Illness (SARI) and consequent complications such as Cytokine Storm Syndrome and Multi-Organ failure. Design: Retrospective, single-center case series of 113 SARI patients at a tertiary care hospital in Agra India between 1 March- 30 October 2020. Main outcome: The demographics, clinical, pathological, imaging, and treatment outcome data were collected. The SARI cases analyzed were defined as “Severe acute respiratory infections (SARIs) an acute respiratory illness of recent onset (within seven days) manifested by fever (≥ 38 °C), cough and shortness of breath or difficulty in breathing requiring hospitalization and were sub-classified according to the primary etiology producing SARI in them. The findings were compiled and compared. Conclusion: Of the 113 patients of SARI – 32.7% were associated with Diabetes, with 9.74% new-onset Diabetes and 26% previously known Diabetes. This was mainly due to SARS-CoV-2 (24 Diabetics out of 52 COVID-19 cases- 46.1%). The Average hospitalization stay of SARI cases was 10 days with a maximum in SARS-CoV-2 and a minimum stay of 5.22 days in Bacterial Pneumonia and 5.66 days in Koch’s Lungs. The death rate was maximum (4 out of 26) 15.3%. Hospitalized TB/Koch’s Lung patients who presented as SARI and 3.8% in Bacterial Pneumonia, 2.43% in SARS-CoV-2, and &lt; 1% in Sepsis. Those SARI cases who were euglycemic at the time of initial presentation recovered early and carried a good prognosis with less mortality as compared to those who were hyperglycemic on presentation. Also, those FLI cases who maintained euglycemia or did not have any other risk factor which predisposes them to stress (Diabetes, Prolonged fasting, Obesity, major organ disorder, Psychological disorder, and Cancer) did not progress to SARI as the endogenous steroid secretion and sympathetic activation did not occur, the intracellular pH levels remained in the alkaline range. 10.18% of cases developed new-onset diabetes (a total of 11 cases) out of which 10 were in COVID-19. Thus 19.2% incidence of new-onset diabetes in SARS-CoV-2 and a prevalence of 26.9% in SARS-CoV-2, making total diabetes 46.1% in SARS-CoV-2, and out of all SARI cases, 26% of patients developed pulmonary fibrosis with consequent long-term complications. In COVID-19 patients, it was seen only in diabetics SARS CoV-2 male patients, thus no death in non-diabetic females in COVID-19 in this case series.

Syndromic surveillance of respiratory infections during protracted conflict: experiences from northern Syria 2016-2021

ObjectiveNorthern Syria faces a large burden of influenza-like illness (ILI) and severe acute respiratory illness (SARI). This study aimed to investigate the trends of Early Warning and Response Network (EWARN) reported ILI and SARI in northern Syria between 2016 and 2021 and the potential impact of SARS-CoV-2. MethodsWe extracted weekly EWARN data on ILI/ SARI and aggregated cases and consultations into 4-week intervals to calculate case positivity. We conducted a seasonal-trend decomposition to assess case trends in the presence of seasonal fluctuations. ResultsIt was observed that 4-week aggregates of ILI cases (n = 5,942,012), SARI cases (n = 114,939), ILI case positivity, and SARI case positivity exhibited seasonal fluctuations with peaks in the winter months. ILI and SARI cases in individuals aged ≥5 years surpassed those in individuals aged <5 years in late 2019. ILI cases clustered primarily in Aleppo and Idlib, whereas SARI cases clustered in Aleppo, Idlib, Deir Ezzor, and Hassakeh. SARI cases increased sharply in 2021, corresponding with a severe SARS-CoV-2 wave, compared with the steady increase in ILI cases over time. ConclusionRespiratory infections cause widespread morbidity and mortality throughout northern Syria, particularly with the emergence of SARS-CoV-2. Strengthened surveillance and access to testing and treatment are critical to manage outbreaks among conflict-affected populations.

Severe acute respiratory illness surveillance for influenza in Kenya: Patient characteristics and lessons learnt.

BackgroundWe describe the epidemiology and clinical features of Kenyan patients hospitalized with laboratory‐confirmed influenza compared with those testing negative and discuss the potential contribution of severe acute respiratory illness (SARI) surveillance in monitoring a broader range of respiratory pathogens.MethodsWe described demographic and clinical characteristics of SARI cases among children (<18 years) and adults, separately. We compared disease severity (clinical features and treatment) of hospitalized influenza positive versus negative cases and explored independent predictors of death among SARI cases using a multivariable logistic regression model.ResultsFrom January 2014 to December 2018, 11,166 persons were hospitalized with SARI and overall positivity for influenza was ~10%. There were 10,742 (96%) children (<18 years)—median age of 1 year, interquartile range (IQR = 6 months, 2 years). Only 424 (4%) of the SARI cases were adults (≥18 years), with median age of 38 years (IQR 28 years, 52 years). There was no difference in disease severity comparing influenza positive and negative cases among children. Children hospitalized with SARI who had an underlying illness had greater odds of in‐hospital death compared with those without (adjusted odds ratio 2.11 95% CI 1.09–4.07). No further analysis was done among adults due to the small sample size.ConclusionKenya's sentinel surveillance for SARI mainly captures data on younger children. Hospital‐based platforms designed to monitor influenza viruses and associated disease burden may be adapted and expanded to other respiratory viruses to inform public health interventions. Efforts should be made to capture adults as part of routine respiratory surveillance.

Sentinel surveillance for influenza A viruses in Lahore District Pakistan in flu season 2015\u20132016

BackgroundInfluenza A virus (IAV) remains an important global public health threat with limited epidemiological information available from low-and-middle-income countries. The major objective of this study was to describe the proportions, temporal and spatial distribution, and demographic and clinical characteristics of IAV positive patients with influenza like illness (ILI) and severe acute respiratory illness (SARI) in Lahore, Pakistan.MethodsProspective surveillance was established in a sentinel hospital from October 2015 to May 2016. All eligible outpatients and inpatients with ILI or SARI were enrolled in the study. Nasal and/or throat swabs were collected along with clinico-epidemiological data. Samples were tested by real-time RT-PCR (rRT-PCR) to identify IAV and subtype. The descriptive analysis of data was done in R software.ResultsOut of 311 enrolled patients, 284 (91.3%) were ILI and 27 (8.7%) were SARI cases. A distinct peak of ILI and SARI activity was observed in February. Fifty individuals (16%) were positive for IAV with peak positivity observed in December. Of 50 IAV, 15 were seasonal H3N2, 14 were H1N1pdm09 and 21 were unable to be typed. The majority of IAV positive cases (98%) presented with current or history of fever, 88% reported cough and 82% reported sore throat. The most common comorbidities in IAV positive cases were hepatitis C (4%), obesity (4%) and tuberculosis (6%). The highest incidence of patients reporting to the hospital was seen three days post symptoms onset (66/311) with 14 of these (14/66) positive for IAV.ConclusionDistinct trends of ILI, SARI and IAV positive cases were observed which can be used to inform public health interventions (vaccinations, hand and respiratory hygiene) at appropriate times among high-risk groups. We suggest sampling from both ILI and SARI patients in routine surveillance as recommended by WHO.

Risk Factors of Influenza-Associated Respiratory Illnesses Reported to a Sentinel Hospital of Lahore, Pakistan: 2015-2016.

Epidemiological data about determinants of influenza A virus (IAV) in the Pakistani population is scarce. We aimed to conduct a prospective hospital-based active surveillance study from October 2015 to May 2016 to identify potential risk factors associated with IAV infection among patients with influenza-like illness (ILI) and severe acute respiratory illness (SARI). Surveillance was conducted in Lahore General Hospital, selected as a sentinel site in Lahore District, Pakistan. Nasal/throat samples were collected along with epidemiological and clinical data from enrolled patients. Real-time reverse-transcription polymerase chain reaction (rRT-PCR) was performed to identify IAV and its subtypes (H1N1pdm09, H3N2). Data were analyzed to determine risk factors and risk markers associated with IAV infections. A total of 311 suspected ILI and SARI cases were enrolled in the study, and among these 50 were IAV-positive. Of these 50 confirmed cases of IAV, 14 were subtyped as H1N1pdm09 and 15 were H3N2; the remaining 21 were untyped. A final multivariable model identified four independent risk factors/markers for IAV infection: exposure history to ILI patients within last 7 days and gender being male were identified as risk factors of IAV infection, while use of antibiotics prior to hospital consultation and presence of fever were identified as risk markers. We concluded that adopting nonpharmaceutical interventions like hand hygiene, masks, social distancing, and where possible, avoiding identified risk factors could decrease the risk of IAV infection and may prevent imminent outbreaks of IAV in the community.

Strategies to provide care to Non-COVID Patients in the COVID Era: An Experience from a Tertiary Care Institute in Northern India

With the COVID-19 pandemic the health system is facing dual burden of cases, one being the COVID-19 or Severe Acute Respiratory Illness (SARI) cases and the second being the other Non-COVID cases. The Non-COVID cases due to the burden of the SARI cases became almost neglected by the Health System increasing the sufferings of the Non-COVID cases. In the current COVID times All India Institute of Medical Sciences, Gorakhpur continued to provide the health care to the Non-COVID cases. The current manuscript provides the detailed strategy and results of the various strategies used to provide care to such Non-COVID patients with minimum risk to the healthcare staff.

Study on clinical symptoms and influencing factors of influenza-associated severe acute respiratory illness in children younger than 5 years old in Suzhou of China, 2011-2017

Objective: To study the influencing factors of influenza-associated severe acute respiratory illness (SARI) in children younger than 5 years of old in Suzhou, and to provide evidence to support the improvement of prevention and control strategies for influenza in children. Methods: We conducted a prospective influenza surveillance for hospitalized SARI and outpatient influenza-like illness (ILI) at Children's Hospital of Soochow University from April 2011 to March 2017. We compared the clinical and other characteristics of influenza-positive patients with SARI to those with ILI to find the differences and to identify influencing factors of influenza-associated SARI, using χ2 test and unconditional logistic regression. Results: We found 786 cases of influenza-associated ILI and 413 cases of influenza-associated SARI during the study period. Cough, runny nose, shortness of breath, asthma or wheezing were more common in influenza-associated SARI than in influenza-associated ILI (P<0.01). Univariate and multivariate logistic regression showed that the influencing factors which significantly associated with increased risk of influenza-associated SARI were as follows: younger age (<6 months OR=3.6, 6-23 months aOR=2.5), respiratory infection history within 3 months (aOR=4.5), chronic lung disease history (OR=3.4), fever above 39.0 ℃ (39.0-39.9 ℃ aOR=2.4, ≥40.0 ℃ aOR=6.0), and the presence of A/H1N1 (aOR=2.3), A/H3N2 (aOR=1.9). Conclusion: Children younger than 2 years old, with a history of chronic lung disease, a history of respiratory infection within 3 months, or with a fever peak above 39.0 ℃ should seek medical advice as soon as possible or receive annual influenza vaccination to reduce the incidence of influenza-associated serious outcomes.

Genetic analysis of Enterovirus D68 associated with pneumonia in children from South India.

EV-D68 is an emerging enterovirus infection associated with severe acute respiratory illness (SARI), acute flaccid myelitis (AFM) and acute flaccid paralysis (AFP). While EV-D68 outbreaks and sporadic cases are reported globally, a single case has been reported from India. The present study aims to investigate the molecular epidemiology and clinical characteristics of EV-D68-associated SARI cases from South India. We screened influenza-negative archived throat swab specimens from Influenza-Like Illness (ILI) and SARI cases (n=959; 2016 to 2018 period) for enteroviruses by pan-enterovirus real-time RT-PCR. Thirteen samples positive for enteroviruses were typed by PCR and sequencing based on VPI, VP2 and/or 5'NCR regions. One EV-D68 RNA sample was subjected to next-generation sequencing for whole genome characterisation. Among 13 enterovirus cases, four were ECHO-11, three EV-D68, two CV-A16 and one each EV-71, CV-B1, CV-B2 and CV-A9. All three cases of EV-D68 infection were reported in children below 2 years of age from Kerala state of South India during June and July 2017. The patients developed pneumonia without any neurological complications. Sequencing based on VPI and 5'NCR regions showed that EV-D68 strains belong to the novel subclade B3. The EV-D68 complete genome identified with two unique amino acid substitutions in VP1 (T-246-I) and 3D (K-344-R) regions. This study reiterates the EV-D68 novel subclade B3 circulation in India and indicates the urgent need for structured EV-D68 surveillance in the country to describe the epidemiology.

Virus detections among patients with severe acute respiratory illness, Northern Vietnam.

Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2–3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7–22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.

Epidemiology and Genetic Variability of Circulating Influenza B Viruses in Uruguay, 2012-2019.

Influenza B viruses (IBV) are an important cause of morbidity and mortality during interpandemic periods in the human population. Two phylogenetically distinct IBV lineages, B/Yamagata and B/Victoria, co-circulate worldwide and they present challenges for vaccine strain selection. Until the present study, there was little information regarding the pattern of the circulating strains of IBV in Uruguay. A subset of positive influenza B samples from influenza-like illness (ILI) outpatients and severe acute respiratory illness (SARI) inpatients detected in sentinel hospitals in Uruguay during 2012–2019 were selected. The sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes showed substitutions at the amino acid level. Phylogenetic analysis reveals the co-circulation of both lineages in almost all seasonal epidemics in Uruguay, and allows recognizing a lineage-level vaccine mismatch in approximately one-third of the seasons studied. The epidemiological results show that the proportion of IBV found in ILI was significantly higher than the observed in SARI cases across different groups of age (9.7% ILI, 3.2% SARI) and patients between 5–14 years constituted the majority (33%) of all influenza B infection (p < 0.05). Interestingly, we found that individuals >25 years were particularly vulnerable to Yamagata lineage infections.