Severe Acute Respiratory Infection Cases Research Articles

Imputation method to reduce undetected severe acute respiratory infection cases during the coronavirus disease outbreak in Brazil

INTRODUCTION: The coronavirus disease (COVD-19) outbreak has overburdened the surveillance of severe acute respiratory infections (SARIs), including the laboratory network. This study was aimed at correcting the absence of laboratory results of reported SARI deaths. METHODS: The imputation method was applied for SARI deaths without laboratory information using clinico-epidemiological characteristics. RESULTS: Of 84,449 SARI deaths, 51% were confirmed with COVID-19 while 3% with other viral respiratory diseases. After the imputation method, 95% of deaths were reclassified as COVID-19 while 5% as other viral respiratory diseases. CONCLUSIONS: The imputation method was a useful and robust solution (sensitivity and positive predictive value of 98%) for missing values through clinical & epidemiological characteristics.

A Review on Severe Acute Respiratory Infection (SARI) and its Clinical Management in Suspect/Confirmed Novel Coronavirus (nCoV) Cases

SARI is the most of viral infections that cause generalised clinical symptoms that cannot be easily differentiated from other respiratory infections. Monitoring SARI cases of influenza strains such as H1N1 and Sars-Cov-2, which triggers Covid-19, helps create trends of infection nationally and enhances disease monitoring, which informs response and preparedness to containment. In present article information about genome, Clinical management of severe acute respiratory illness (SARI) in suspect/confirmed novel coronavirus (nCoV) cases by immediate implementation of appropriate IPC measures, early supportive therapy and monitoring, management of hypoxemic respiratory failure, management of septic shock and specific anti-Novel-CoV treatments were given.

Influenza vaccine effectiveness against hospitalizations in children and older adults—Data from South America, 2013–2017. A test negative design

BackgroundIn 2013, the Pan American Health Organization established a multi-site, multi-country network to evaluate influenza vaccine effectiveness (VE). We pooled data from five consecutive seasons in five countries to conduct an analysis of southern hemisphere VE against laboratory-confirmed influenza hospitalizations in young children and older adults. MethodsWe used a test-negative design to estimate VE against laboratory-confirmed influenza in hospitalized young children (aged 6─24 months) and older adults (aged ≥60 years) in Argentina, Brazil, Chile, Colombia, and Paraguay. Following country-specific influenza surveillance protocol, hospitalized persons with severe acute respiratory infections (SARI) at 48 sentinel hospitals (March 2013–December 2017) were tested for influenza virus infection by rRT-PCR. VE was estimated for young children and older adults using logistic random effects models accounting for cluster (country), adjusting for sex, age (months for children, and age-in-year categories for adults), calendar year, country, preexisting conditions, month of illness onset and prior vaccination as an effect modifier for the analysis in adults. ResultsWe included 8426 SARI cases (2389 children and 6037 adults) in the VE analyses. Among young children, VE against SARI hospitalization associated with any influenza virus was 43% (95%CI: 33%, 51%) for children who received two doses, but was 20% (95%CI: −16%, 45%) and not statistically significant for those who received one dose in a given season. Among older adults, overall VE against SARI hospitalization associated with any influenza virus was 41% (95%CI: 28%, 52%), 45% (95%CI: 34%, 53%) against A(H3N2), 40% (95%CI: 18%, 56%) against A(H1N1)pdm09, and 20% (95%CI: −40%, 54%) against influenza B viruses. ConclusionsOur results suggest that over the five-year study period, influenza vaccination programs in five South American countries prevented more than one-third of laboratory confirmed influenza-associated hospitalizations in young children receiving the recommended two doses and vaccinated older adults.

The Acute Respiratory Infection Consortium: A Multi-Site, Multi-Disciplinary Clinical Research Network in the Department of Defense.

IntroductionAcute respiratory infections (ARI) result in substantial annual morbidity among military personnel and decrease operational readiness. Herein, we summarize the research efforts of the Infectious Disease Clinical Research Program (IDCRP) related to ARIs.MethodsThe ARI Research Area of the IDCRP was established in response to the 2009 emergence of pandemic influenza A/H1N1. That year, IDCRP investigators deployed the ARI Consortium Natural History Study (ARIC NHS), a multi-centered, longitudinal observational study to assess etiology, epidemiology, and clinical characteristics of influenza-like illness (ILI) and severe acute respiratory infections (SARI) in the U.S. military. The success of this initial effort spurred implementation of several new initiatives. These include the FluPlasma trial, designed to evaluate the efficacy of hyperimmune anti-influenza plasma for the treatment of severe influenza; the self-administered live-attenuated influenza vaccine (SNIF) trial, which assessed the immunogenicity and acceptance of a self-administered live-attenuated influenza vaccine in military personnel; the Study to Address Threats of ARI in Congregate Military Populations (ATARI), a prospective study of ILI transmission, etiology and epidemiology in recruits; and the Flu Breath Test (FBT) study, a preliminary study of exhaled volatile organic compounds (VOC) in influenza patients. In addition, the InFLUenza Patient-Reported Outcome (FLU-PRO) survey, a daily diary to measure influenza symptoms during clinical trials, was developed. Lastly, the Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD (PAIVED) study, a two-year randomized trial designed to compare the effectiveness of the three types of licensed vaccines, launched in Fall 2018.ResultsThe on-going ARIC NHS has enrolled over 2000 ILI and SARI cases since its inception, providing data on burden and clinical manifestations of ARI in military personnel and their families. The FluPlasma 2 trial concluded subject enrollment in 2018. Preliminary results from ATARI study show a high frequency of respiratory viruses circulating during the first two weeks of recruit training. Based on assessment of FLU-PRO responses, which were found to be reliable and reproducible, the survey may be a useful tool in clinical trials and epidemiological studies. The Flu Breath Study will complete enrollment in 2019. Findings from PAIVED are intended to provide evidence needed for assessing influenza vaccination policy in the military.ConclusionsThe ARI burden in the armed services remains significant every year and the threat is dynamic given emergent and evolving threats, such as influenzas. With strong successes to date, future initiatives of the ARI Research Area will focus on interventional studies, ARI transmission dynamics in congregate military settings, and determinants of risk of pandemic influenza and other emergent respiratory viruses.

Influenza-associated morbidity and mortality in Tunisia

Abstract Background Influenza is a highly contagious viral infection representing a public health problem worldwide with more than 10% of the population affected each year. In addition, severe complications and deaths may occur especially among high-risk groups. Our objectives was to assess the severity of influenza in Tunisia from 2015 to 2017 and to identify the isolated circulating viruses. Methods Basedon the network of ILI (Influenza-like illness) and SARI (Severe acute respiratory infection) Sentinel Sites and the National Influenza Center, we conducted a descriptive analysis of all data collected from 2015 to 2017. The case definitions of ILI and SARI were those recommended by WHO. Data entry was using Epi-Data and data analysis using SPSS-20. Results The total number of SARI cases during 2016-17 season was 614. The hospitalization rate was 0.7% which was higher than the 2015-16 season (0.19%). The majority of these severe cases were males (60,3%) and the group aged more than 65 years was the most affected. Comorbidities were reported in 58,7% of the cases, especially cardiovascular diseases, obesity and asthma. In 2016-17, the viruses identified in SARI cases were type A(H3N2) (47,7%), type B (40,9%) and type A (H1N1) pmd09 (4%). The lethality rate was lower than in the previous season (0.32% vs 20%) with two deaths reported in February. These deaths were due to virus B and virus AH3N2, comparing to 77% of deaths due to virus A (H1N1) pmd09 the season before. Conclusions Influenza severity vary from a season to another. The 2016-17 season was marked by higher rates of hospitalization but a lower lethality rate. This may be due to a lower circulation of the type A (H1N1) pmd09 virus, which virulence is much discussed. Influenza surveillance remains essential to detect any emerging novel pathogen and to guide decision-makers for future strategies. Key messages Seasonal influenza epidemics continue to have significant morbidity and mortality. Epidemiological and virological surveillance are highly essential for an early detection of epidemics and novel strains.

Economic Cost of Severe Acute Respiratory Infection Associated to Influenza in Colombian Children: A Single Setting Analysis

Influenza is considered a leading public health problem because its large economic burden of disease worldwide, especially in low-and middle-income countries, such as Colombia. We aimed to estimate the economic costs of influenza-confirmed patients in a pediatric hospital in Cartagena, Colombia. We conducted a retrospective costing analysis. We estimated the direct (direct medical and out-of-pocket expenditures) and indirect costs for influenza-confirmed severe acute respiratory infection cases from a societal perspective. Total economic costs were calculated adding direct medical costs, out-of-pocket expenditures, and indirect costs owing to loss of productivity of caregivers. Mean, median, 95% confidence interval (95% CI) and interquartile range (IQR) of costs were measured. All costs are reported in USD ($1.00 = COP$2000.7) RESULTS: Forty-four cases were included in the analysis: 30 had influenza B, 10 influenza A and B, and 4 influenza AH1N1. Thirty patients were hospitalized in the general ward, 14 went to the intensive care unit. The average duration of stay was ∼9 days (95% CI, 6.3-11.5). The median direct medical cost for hospitalized case in general ward was $743.50 (IQR $590.20-$1404.60) and in intensive care unit $4669.80 (IQR $1614.60-$7801.50). The economic cost per hospitalized case was $1826.10 (IQR $1343.30-$2376.50); direct medical costs represented 93.8% of this cost. The median indirect cost was $82.10 (IQR $41.10-$133.40) and the median out-of-pocket expenditure per case was $45.70 (IQR $29.50-$64.90). Severe acute respiratory infection is an important source of economic burden for the health system, families, and society in Colombia. Seasonal influenza vaccination should be strengthened to prevent more cases and save economic resources.

Identification of Adenovirus Species in Iranian Pediatric Population With Severe Acute Respiratory Infections

Aim: In this study we aimed to find the rate of human adenovirus (HAdV) infections and identify HAdVs molecular epidemiology in children younger than 5 years old with clinical diagnosis of severe acute respiratory infections in Iran. Patients & methods: A semi-nested PCR with in-house designed primers for HAdV was performed on 200 oropharyngeal swabs collected within 5 days from the onset of symptoms. The positive samples were subjected to sequencing and a phylogenetic tree was drawn. Results: Out of 200 specimens, 71 (35.5%) cases were positive for HAdVs. Detected strains matched with HAdV species B (80.3%), C (15.5%), D (2.8%) and E (1.8%). HAdV- B14/55 and HAdV-B3 were the most prevalent types, respectively. Conclusion: This study showed that infections with HAdV species B, were common in children, who were clinically diagnosed as severe acute respiratory infection cases in Iran. The results could be useful for future epidemiological researches.

Pathogenic characteristics of hospitalized severe acute respiratory infections in Shanghai, China, 2015-2017

Objective: To understand the epidemiological and pathogenic characteristics of hospitalized severe acute respiratory infections (SARI) in Shanghai, China. Methods: From 2015 to 2017, one Tertiary hospital and one Secondary hospital were chosen as the surveillance sites. Two respiratory tract specimens per case were collected from SARI cases aged 15 years and older. One specimen was tested for 22 respiratory pathogens by RT-PCR, and the other specimen was cultured for 6 respiratory bacteria. Results: A total of 287 SARI cases were enrolled for sampling and lab testing. 70.73% of the cases were aged 60 years and older, with 41.46% (119/287) were positive for at least one pathogen. Influenza virus was the predominant pathogen, accounting for 17.77% (51/287) of all SARI cases. Human rhinovirus/Enterovirus and Coronavirus were both accounting for 7.32% (21/287), followed by Mycoplasma pneumoniae (5.57%, 16/287). The positive rates of parainfluenza virus, bocavirus, adenovirus, respiratory syncytial virus and human metapneumo virus were all less than 5%. Bacterial strains were identified in seven SARI cases, including Klebsiella pneumoniae (3 strains), Staphylococcus aureus (2 strains), Streptococcus pneumoniae (1 strain) and Pseudomonas aeruginosa (1 strain). Two or Three pathogens were co-detected from 40 cases, accounting for 33.61% of 119 positive cases. The most common co-detected pathogens were influenza virus and Mycoplasma pneumoniae (10 cases). Influenza cases peaked in winter-spring and summer. Mycoplasma pneumoniae peaked in winter-spring season and overlapped with influenza. The positive rates of pathogens were not significantly different between different age groups. Conclusions: Various respiratory pathogens can be detected from SARI cases aged 15 years and older. Influenza virus was the predominant pathogen and the co-detection of influenza virus with Mycoplasma pneumoniae the most common one.

Molecular detection of enterovirus D68 among children with acute respiratory tract infection in Ghana.

BackgroundAcute respiratory tract infections of viral origin remain a leading cause of morbidity, mortality and economic loss regardless of age or gender. A small number of acute respiratory tract infection cases caused by enterovirus D68 (EV-D68) have been reported regularly to Centers for Disease Control and Prevention since 1987 by countries in North America, Europe and Asia. However, in 2014 and 2015, the number of reported confirmed EV-D68 infections was much greater than in previous years. The National Influenza Centre (NIC), Ghana carries out surveillance of respiratory infections, focusing on those caused by influenza virus; however, there is inadequate information on other viruses causing respiratory infections in Ghana, including EV-D68.ObjectivesTo investigate the association of EV-D68 with Severe Acute Respiratory Infections (SARI) and Influenza-Like Illness (ILI) in Ghana.MethodsThis was a retrospective cross-sectional study which involved archived human respiratory specimens stored at –80 °C at the NIC from 2014 to 2015. Using a random sampling method, oropharyngeal and nasopharyngeal swabs from patients with SARI and ILI that were negative by real-time PCR for human influenza viruses were screened for EV-D68 using real-time reverse transcription-polymerase chain reaction (rRT-PCR).ResultsEnterovirus D68 was detected in 4 (2.2%) out of 182 SARI samples tested. EV-D68 was detected in children younger than 5 years (4 – 100% of positives) and was not detected in children older than 5 years. Enterovirus D68 was detected more frequently in SARI cases (3%) than in ILI cases (1.2%).ConclusionThis study has shown for the first time the presence of EV-D68 in acute respiratory infections in Ghana. The results confirmed minimal EV-D68 circulation in the Ghanaian population.

Estimation of influenza and respiratory syncytial virus hospitalizations using sentinel surveillance data-La Paz, Bolivia. 2012-2017.

ObjectiveThe objective was to estimate the number of hospitalizations associated with influenza and RSV using data from severe acute respiratory infection (SARI) sentinel surveillance from El Alto‐La Paz. Bolivia.MethodsAll persons who met the case definition for SARI at one sentinel hospital had a clinical sample collected and analyzed by rRT‐PCR for influenza and by indirect immunofluorescence for RSV. The SARI‐influenza and SARI‐RSV case counts were stratified by six age groups. The proportion of cases captured in the sentinel hospital in relation to the non‐sentinel hospitals of area was multiplied by the age‐specific census population, to build the denominators. The annual incidence and a 95% confidence interval (CI) were estimated.ResultsDuring 2012‐2017, n = 2606 SARI cases were reported (average incidence 120/100 000 inhabitants [95% CI: 116‐124]); the average incidence of influenza‐associated SARI hospitalization was 15.3/100 000 (95% CI: 14.1‐16.7), and the average incidence of RSV‐associated SARI hospitalization was 9/100 000 inhabitants (95% CI: 8.1‐10.1). The highest incidence of influenza was among those less than one year of age (average 174.7/100 000 [range: 89.1‐299.5]), followed by those one to four years of age (average 51.8/100 000 [range: 19.8‐115.4]) and then those 65 years of age and older (average 47.7/100 000 [range: 18.8‐117]). For RSV, the highest incidence was highest among those less than one year of age (231/100 000 [range: 119.9‐322.9]).ConclusionInfluenza and RSV represent major causes of hospitalization in La Paz, Bolivia—with the highest burden among children under one year of age. Our estimates support current prevention strategies in this age group.

Evaluating tools to define influenza baseline and threshold values using surveillance data, Egypt, season 2016/17

BackgroundEstablishing influenza thresholds and transmission intensity can help evaluate seasonal changes in influenza severity and potential pandemics. We aimed to evaluate the moving epidemic method (MEM) for calculating influenza thresholds for season 2016/17 in Egypt using four parameters, to identify the most useful parameter. Also to measure the agreement between both the country-specific statistical empirical method and World Health Organization method to MEM for determining the length and intensity level of activity of the influenza season. MethodsRoutinely epidemiological and laboratory data from sentinel surveillance sites for Severe Acute Respiratory Infection (SARI) and influenza-like illness (ILI) were used for calculating thresholds for seasons between 2010/11 and 2015/16 to test 2016/17 season. The parameters calculated were: screened ILI consultation rate × 1000, screened ILI composite parameter, influenza positivity percentage among sampled SARI cases, and influenza positivity percentage among sampled ILI and SARI cases. These parameters assess seasonality and intensity of influenza activity using the three proposed methods (mentioned above). Agreement between the three methods was done using several approaches. ResultsThe intensity of influenza activity by MEM was lower than the other two methods. Agreement between MEM and each of the other two techniques varied appreciably from good to very good for seasonal duration, and poor to fair for intensity level. In addition, parameters including laboratory data showed a pattern of bi-wave activity; the first wave occurred in winter mostly between epidemiological weeks 39 and 52 and the second occurred in spring mostly between weeks 12 and 17. ConclusionParameters including laboratory data were more useful in defining seasonality of influenza. Further exploration of the MEM model in future seasons may help to provide a more comprehensive understanding of its use and application.

Influenza-associated Hospitalization in Children Younger Than 5 Years of Age in Suzhou, China, 2011-2016.

Studying the burden and risk factors associated with severe illness from influenza infection in young children in eastern China will contribute to future cost-effectiveness analyses of local influenza vaccine programs. We conducted prospective, severe acute respiratory infection (SARI) surveillance at Suzhou University-Affiliated Children's Hospital to estimate influenza-associated hospitalizations in Suzhou University-Affiliated Children's Hospital by month in children younger than 5 years of age from October 2011 to September 2016. SARI was defined as fever (measured axillary temperature ≥ 38°C) and cough or sore throat or inflamed/red pharynx in the 7 days preceding hospitalization. We combined SARI surveillance data with healthcare utilization survey data to estimate and characterize the burden of influenza-associated SARI hospitalizations in Suzhou within this age group in the 5-year period. Of the 36,313 SARI cases identified, 2,297 from respiratory wards were systematically sampled; of these, 259 (11%) were influenza positive. Estimated annual influenza-associated SARI hospitalization rates per 1,000 children younger than 5 years of age ranged from 4 (95% confidence interval [CI], 2-5) in the 2012-2013 season to 16 (95% CI, 14-19) in the 2011-2012 season. The predominant viruses were A/H3N2 (59%) in 2011-12, both A/H1N1pdm09 (42%) and B (46%) in 2012-13, A/H3N2 (71%) in 2013-14, A/H3N2 (55%) in 2014-15 and both A/H1N1pdm09 (50%) and B (50%) in 2015-16. The age-specific influenza-associated SARI hospitalization rates for the 5-year period were 11 (95% CI, 8-15) per 1,000 children 0-5 months of age; 8 (95% CI, 7-10) per 1,000 children 6-23 months of age and 5 (95% CI, 4-5) per 1,000 children 24-59 months of age, respectively. From 2011 to 2016, influenza-associated SARI hospitalization rates in children aged younger than 5 years of age in Suzhou, China, were high, particularly among children 0-5 months of age. Higher hospitalization rates were observed in years where the predominant circulating virus was influenza A/H3N2. Immunization for children > 6 months, and maternal and caregiver immunization for those < 6 months, could reduce influenza-associated hospitalizations in young children in Suzhou.

CHARACTERISTICS OF INFLUENZA INFECTION IN 2017 AND CURRENT PRACTICE: A RETROSPECTIVE STUDY AT A COLLEGE HOSPITAL IN JEDDAH

Saudi Arabia has recentlystarted a surveillance process for seasonal influenza outbreaks. Special interest should be given to the influenza-associated severe acute respiratory infection (SARI) to describe the epidemiological and clinical characteristics and current practice of influenza-associated SARI in 2017. A retrospective observational study was conducted at IbnSina National College Hospital in Jeddah in 2018. Review of medical records was done using checklists for in-patients who did rapid influenza diagnostic tests during 2017 using nasopharyngeal swabs and for whom coronavirus RT-PCR test was also performed by the “Saudi National Health Laboratory”. Data collection included time of admission, demographic, clinical, and laboratory data, treatment, and outcome. Among 300 in-patients with fever, 31.3% had SARI due to influenza A rather than B but not H1N1 or MERS-CoV infection. SARI cases clustered during July and September (‘Ramadan’ and ‘Hajj’ periods). The risk of flu-related complications was high (45.7%) and included mostly children &lt; 5 and presented mainly with pneumonia (21.3%). The main presentations were fever (83%), flu-like symptoms (41.9%), nonproductive cough (33%), dyspnea (25%), vomiting (14.9%), and abdominal pain (8.5%). Patients had lymphocytosis (27.7%) and neutropenia (20.2%).All received antiviral oseltamivir (16% received it late, 3.4% did not continue after discharge) and 90.4% received empirical antibiotics. All recovered completely with no ICU admission. Seasonal influenza A-associated SARI in 2017 in our hospital coincided with ‘Ramadan’ and ‘Hajj’ periods, presented with typical symptoms, and had a high risk of complications, especially pneumonia. It was amenable to antiviral therapy with a favorable outcome. Most patients received empirical antibiotics and a few did not receive proper antiviral therapy. Physicians should consider early antiviral treatment in patients with suspected SARI during influenza seasons. There is a need for national recommendations to guide antibiotic strategies and regimens in influenza-associated SARI.

Influenza related pneumonia in children under five years old in Indonesia : An analysis of the risk factors

Abstract&#x0D; Background: Pneumonia is more commonly among children under five years old and caused by several risk factors. Pneumonia causes 1.9 – 2.2 million children death worldwide every year, in which 1.3 million (81%) generally occurs in first 2 years of life. Seventy two percent of pneumonia occurs in children under five years old in 15 countries. Indonesia was the 7th highest in the world. The prevalence of pneumonia in Indonesia was 18.5/1000 population and only 1.6/1000 received treatment. This study aim to elaborate the risk factors of the influenza related pneumonia in children under five years old.&#x0D; Method: The pneumonia control program in Ministry of Health focuses on early detection and treatment for bacterial pneumonia in community. Severe acute respiratory infection (SARI) can develop fatal pneumonia. We collected data from the pneumonia surveillance database in the Acute Respiratory Infection subdirectorate. Results: Influenza related pneumonia was 13% of acute lower respiratory infection in pediatric. The number of children under five years old death estimation was 28,000-115,000 and 99% happened in developing countries. The aim of this review is to understand influenza related pneumonia in Indonesia and global. Summary: In Indonesia, proportion of influenza from SARI surveillance was 12% and mainly in children under five years old (36%). Pneumonia was 18% of SARI cases with positive influenza. The effect of Influenza become pneumonia remain unclear.

Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016.

In 2010, Yemen started the surveillance for severe acute respiratory infections (SARIs) by establishing 2 sentinel sites in Sana’a and Aden city. This study aims to determine the proportions of influenza and noninfluenza viruses among SARI patients and to determine the severity of SARI and its associated factors. The data of SARI patients who were admitted to SARI surveillance sites at Al Johory hospital in Sana’a and Al Wahdah hospital in Aden city during the period 2011-2016 were analyzed. The proportions of positive influenza viruses (type A, B) and noninfluenza viruses (respiratory syncytial, adenovirus, human parainfluenza, and human metapneumovirus), intensive care unit (ICU) admission rate, and fatality rate among SARI patients were calculated. A total of 1811 of SARI patients were admitted during 2011-2016. Of those, 78% were <15 years old. A total of 89 (5%) patients had influenza viruses and 655 (36%) had noninfluenza viruses. The overall ICU admission rate was 40% and the case-fatality rate was 8%. Infection by influenza type (A, B) and mixed (adenovirus, human parainfluenza) was significantly associated with lower ICU admission. Age <15 years old, infection with influenza B, pre-existence of chronic diseases, and admission to Aden site were significantly associated with higher fatality rate among patients. In conclusion; SARI patients in Yemen had a high ICU admission and case-fatality rates. Influenza type B, chronic diseases, and admission to Aden site are associated with higher fatality rate. Expanding surveillance sites and panel of laboratory tests to involve other pathogens will help to provide accurate diagnosis for SARI etiology and give more comprehensive picture. Training staff for SARI case management will help to reduce severe outcomes.

National burden of influenza-associated hospitalizations in Cambodia, 2015 and 2016.

IntroductionThe burden of influenza in Cambodia is not well known, but it would be useful for understanding the impact of seasonal epidemics and pandemics and to design appropriate policies for influenza prevention and control. The severe acute respiratory infection (SARI) surveillance system in Cambodia was used to estimate the national burden of SARI hospitalizations in Cambodia.MethodsWe estimated age-specific influenza-associated SARI hospitalization rates in three sentinel sites in Svay Rieng, Siem Reap and Kampong Cham provinces. We used influenza-associated SARI surveillance data for one year to estimate the numerator and hospital admission surveys to estimate the population denominator for each site. A national influenza-associated SARI hospitalization rate was calculated using the pooled influenza-associated SARI hospitalizations for all sites as a numerator and the pooled catchment population of all sites as denominator. National influenza-associated SARI case counts were estimated by applying hospitalization rates to the national population.ResultsThe national annual rates of influenza-associated hospitalizations per 100 000 population was highest for the two youngest age groups at 323 for < 1 year and 196 for 1–4 years. We estimated 7547 influenza-associated hospitalizations for Cambodia with almost half of these represented by children younger than 5 years.DiscussionWe present national estimates of influenza-associated SARI hospitalization rates for Cambodia based on sentinel surveillance data from three sites. The results of this study indicate that the highest burden of severe influenza infection is borne by the younger age groups. These findings can be used to guide future strategies to reduce influenza morbidity.

Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda.

BackgroundPrecision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential.MethodsUsing a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens.ResultsAmong 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses.ConclusionsUsing a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.

Severe Acute Respiratory Infection (SARI) sentinel surveillance in the country of Georgia, 2015-2017.

BackgroundSevere Acute Respiratory Infection (SARI) causes substantial mortality and morbidity worldwide. The country of Georgia conducts sentinel surveillance to monitor SARI activity and changes in its infectious etiology. This study characterizes the epidemiology of SARI in Georgia over the 2015/16 and 2016/17 influenza seasons, compares clinical presentations by etiology, and estimates influenza vaccine effectiveness using a test-negative design.MethodsSARI cases were selected through alternate day systematic sampling between September 2015 and March 2017 at five sentinel surveillance inpatient sites. Nasopharyngeal swabs were tested for respiratory viruses and Mycoplasma pneumoniae using a multiplex diagnostic system. We present SARI case frequencies by demographic characteristics, co-morbidities, and clinical presentation, and used logistic regression to estimate influenza A vaccine effectiveness.Results1,624 patients with SARI were identified. More cases occurred in February (28.7%; 466/1624) than other months. Influenza was the dominant pathogen in December-February, respiratory syncytial virus in March-May, and rhinovirus in June-November. Serious clinical symptoms including breathing difficulties, ICU hospitalization, and artificial ventilation were common among influenza A and human metapneumovirus cases. For influenza A/H3, a protective association between vaccination and disease status was observed when cases with unknown vaccination status were combined with those who were unvaccinated (OR: 0.53, 95% CI: 0.30, 0.97).ConclusionsMulti-pathogen diagnostic testing through Georgia’s sentinel surveillance provides useful information on etiology, seasonality, and demographic associations. Influenza A and B were associated with more severe outcomes, although the majority of the population studied was unvaccinated. Findings from sentinel surveillance can assist in prevention planning.

Overview of three influenza seasons in Georgia, 2014-2017.

BackgroundInfluenza epidemiological and virologic data from Georgia are limited. We aimed to present Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) surveillance data and characterize influenza viruses circulating in the country over three influenza seasons.MethodsWe analyzed sentinel site ILI and SARI data for the 2014–2017 seasons in Georgia. Patients’ samples were screened by real-time RT-PCR and influenza viruses isolated were characterized antigenically by haemagglutination inhibition assay and genetically by sequencing of HA and NA genes.Results32% (397/1248) of ILI and 29% (581/1997) of SARI patients tested were positive for influenza viruses. In 2014–2015 the median week of influenza detection was week 7/2015 with B/Yamagata lineage viruses dominating (79%); in 2015–2016—week 5/2016 was the median with A/H1N1pdm09 viruses prevailing (83%); and in 2016–2017 a bimodal distribution of influenza activity was observed—the first wave was caused by A/H3N2 (55%) with median week 51/2016 and the second by B/Victoria lineage viruses (45%) with median week 9/2017. For ILI, influenza virus detection was highest in children aged 5–14 years while for SARI patients most were aged >15 years and 27 (4.6%) of 581 SARI cases died during the three seasons. Persons aged 30–64 years had the highest risk of fatal outcome, notably those infected with A/H1N1pdm09 (OR 11.41, CI 3.94–33.04, p<0.001). A/H1N1pdm09 viruses analyzed by gene sequencing fell into genetic groups 6B and 6B.1; A/H3N2 viruses belonged to genetic subclades 3C.3b, 3C.3a, 3C.2a and 3C.2a1; B/Yamagata lineage viruses were of clade 3 and B/Victoria lineage viruses fell in clade1A.ConclusionIn Georgia influenza virus activity occurred mainly from December through March in all seasons, with varying peak weeks and predominating viruses. Around one third of ILI/ SARI cases were associated with influenza caused by antigenically and genetically distinct influenza viruses over the course of the three seasons.

Epidemiology and molecular characterization of Respiratory Syncytial Virus in Argentina 2017

Background: Human respiratory syncytial virus (RSV) is one of the most frequent cause of respiratory infections, and the main cause of severe cases of bronchiolitis and pneumonia in infants and young children. Viral strains have been separated into two major subtypes (RSV-A and RSV-B), and nucleotide sequence analysis has led to the identification of 11 RSV-A and 23 RSV-B genotypes. Multiple genotypes can co-circulate during successive epidemic seasons, but a new genotype (or one spreading from another country) may replace previously dominant strains. Methods & Materials: The main aim of this study was to investigate the genetic diversity and patterns of the co-circulating genotypes of RSV-A and RSV-B strains in Argentina, and the possible associations between individual RSV genotypes and case definitions. Results: The National Reference Laboratory of Influenza and Other Respiratory Viruses (NRLIRV) received clinical samples of hospitalized children less than 5 years old and elderly, according to different case definitions during the acute phase of the illness: severe acute respiratory infection (SARI) with or without fever, influenza like illness with or without fever and acute respiratory infection. Between epidemiological weeks (EW) 1 and 43, 520 clinical samples were received from different provinces of the country: Chaco, Tucuman, La Rioja and Buenos Aires city collected from January to October 2017, in order to perform subtyping by real time RT-PCR and genotyping by G gene sequencing (969 nt). RSV was detected in 238 samples (55.5%) of the total diagnosed. Initially, RSV circulated in Chaco (EW 1) followed by Tucuman (EW 5-8). Ninety percentage (124/138) and 10% (14/138) of the subtyped samples belonged to A and B, respectively. All group A strains sequenced (10) were closely related to the genetic group ON1 with the 72-nt duplication (originated in Canada). Conclusion: A co-circulation of RSV A and B groups was detected, being group A the predominant and most of these viruses were collected from pediatric and adult patients with SARI case definition with and without fever. Continued genotyping and molecular epidemiological surveillance of RSV are essential to further understanding RSV evolution and transmission in communities and healthcare settings.