Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020.

Background: External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019-2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019-2020 WHO RSV EQA. Methods: Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. Results: An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. Conclusions: The WHO RSV EQA 2019-2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets.

Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications.

Background: The existing World Health Organization (WHO) pneumonia case management guidelines rely on clinical symptoms and signs for identifying, classifying, and treating pneumonia in children up to 5 years old. We aimed to collate an individual patient-level data set from large, high-quality pre-existing studies on pneumonia in children to identify a set of signs and symptoms with greater validity in the diagnosis, prognosis, and possible treatment of childhood pneumonia for the improvement of current pneumonia case management guidelines. Methods: Using data from a published systematic review and expert knowledge, we identified studies meeting our eligibility criteria and invited investigators to share individual-level patient data. We collected data on demographic information, general medical history, and current illness episode, including history, clinical presentation, chest radiograph findings when available, treatment, and outcome. Data were gathered separately from hospital-based and community-based cases. We performed a narrative synthesis to describe the final data set. Results: Forty-one separate data sets were included in the Pneumonia Research Partnership to Assess WHO Recommendations (PREPARE) database, 26 of which were hospital-based and 15 were community-based. The PREPARE database includes 285 839 children with pneumonia (244 323 in the hospital and 41 516 in the community), with detailed descriptions of clinical presentation, clinical progression, and outcome. Of 9185 pneumonia-related deaths, 6836 (74%) occurred in children <1 year of age and 1317 (14%) in children aged 1-2 years. Of the 285 839 episodes, 280 998 occurred in children 0-59 months old, of which 129 584 (46%) were 2-11 months of age and 152 730 (54%) were males. Conclusions: This data set could identify an improved specific, sensitive set of criteria for diagnosing clinical pneumonia and help identify sick children in need of referral to a higher level of care or a change of therapy. Field studies could be designed based on insights from PREPARE analyses to validate a potential revised pneumonia algorithm. The PREPARE methodology can also act as a model for disease database assembly.

Respiratory syncytial virus among children hospitalized with severe acute respiratory infection in Kashmir, a temperate region in northern India.

Background: Severe acute respiratory infections (SARI) are a leading cause of hospitalizations in children, especially due to viral pathogens. We studied the prevalence of respiratory viruses among children aged <5 years hospitalized with severe acute respiratory infections (SARI) in Kashmir, India. Methods: We conducted a prospective observational study in two tertiary care hospitals from October 2013 to September 2014, systematically enrolling two children aged <5 years with SARI per day. We defined SARI as history of fever or measured fever (≥38°C) and cough with onset in the last 7 days requiring hospitalization for children aged 3-59 months and as physician-diagnosed acute lower respiratory infection for children aged <3 months. Trained study staff screened children within 24 hours of hospitalization for SARI and collected clinical data and nasopharyngeal swabs from enrolled participants. We tested for respiratory syncytial virus (RSV) A and B, influenza viruses, rhinoviruses (HRV)/enteroviruses, adenovirus (AdV), bocavirus (BoV), human metapneumovirus (hMPV) A and B, coronaviruses (OC43, NL65, C229E), and parainfluenza viruses (PIV) 1, 2, 3 and 4 using standardized duplex real-time polymerase chain reaction. Results: Among 4548 respiratory illness admissions screened from October 2013 to September 2014, 1026 met the SARI case definition, and 412 were enrolled (ages = 5 days to 58 months; median = 12 months). Among enrolees, 256 (62%) were positive for any virus; RSV was the most commonly detected (n = 118, 29%) followed by HRV/enteroviruses (n = 88, 21%), PIVs (n = 31, 8%), influenza viruses (n = 18, 4%), BoV (n = 15, 4%), coronaviruses (n = 16, 4%), AdV (n = 14, 3%), and hMPV (n = 9, 2%). Fifty-four children had evidence of virus co-detection. Influenza-associated SARI was more common among children aged 1-5 years (14/18, 78%) while most RSV detections occurred in children <12 months (83/118, 70%). Of the RSV viruses typed (n = 116), the majority were type B (94, 80%). Phylogenetic analysis of G gene of RSV showed circulation of the BA9 genotype with 60bp nucleotide duplication. Conclusions: Respiratory viruses, especially RSV, contributed to a substantial proportion of SARI hospitalizations among children <5 years in north India. These data can help guide clinicians on appropriate treatment and prevention strategies.

Multisite surveillance for influenza and other respiratory viruses in India: 2016-2018.

There is limited surveillance and laboratory capacity for non-influenza respiratory viruses in India. We leveraged the influenza sentinel surveillance of India to detect other respiratory viruses among patients with acute respiratory infection. Six centers representing different geographic areas of India weekly enrolled a convenience sample of 5-10 patients with acute respiratory infection (ARI) and severe acute respiratory infection (SARI) between September 2016-December 2018. Staff collected nasal and throat specimens in viral transport medium and tested for influenza virus, respiratory syncytial virus (RSV), parainfluenza virus (PIV), human meta-pneumovirus (HMPV), adenovirus (AdV) and human rhinovirus (HRV) by reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis of influenza and RSV was done. We enrolled 16,338 including 8,947 ARI and 7,391 SARI cases during the study period. Median age was 14.6 years (IQR:4-32) in ARI cases and 13 years (IQR:1.3-55) in SARI cases. We detected respiratory viruses in 33.3% (2,981) of ARI and 33.4% (2,468) of SARI cases. Multiple viruses were co-detected in 2.8% (458/16,338) specimens. Among ARI cases influenza (15.4%) were the most frequently detected viruses followed by HRV (6.2%), RSV (5%), HMPV (3.4%), PIV (3.3%) and AdV (3.1%),. Similarly among SARI cases, influenza (12.7%) were most frequently detected followed by RSV (8.2%), HRV (6.1%), PIV (4%), HMPV (2.6%) and AdV (2.1%). Our study demonstrated the feasibility of expanding influenza surveillance systems for surveillance of other respiratory viruses in India. Influenza was the most detected virus among ARI and SARI cases.

The Burden of Respiratory Syncytial Virus in Children Under 2 Years of Age in a Rural Community in Maharashtra, India.

BACKGROUND: Globally, respiratory syncytial virus (RSV) is a common cause of acute lower tract infection (LRTI) in children younger than 2 years of age, but there are scant population-based studies on the burden of RSV illness in rural communities and no community studies in preterm infants. METHODS: Active surveillance of LRTI was performed in the community and hospital setting for the population of 93 tribal villages in Melghat, Central India, over 4 respiratory seasons. A nasopharyngeal swab was obtained from cases presenting as a severe LRTI for molecular analysis of respiratory pathogens including RSVA and B. RESULTS: High rates of RSV-associated LRTI were found in preterm and term infants beyond 6 months of age, extending into the second year of life. Community severe RSV LRTI rates for 0-11 months of age was 22.4 (18.6-27.0)/1000 child-years (CY) and the hospital-associated rate was 14.1 (11.1-17.8)/1000 CY. For preterm infants, these rates were 26.2 (17.8-38.5)/1000 CY and 12.6 (7.2-22.0)/1000 CY. Comparable rates in the first 6 months were 15.9 (11.8-21.4)/1000 CY and 12.9 (9.3-18.0)/1000 CY in term infants and 26.3 (15.4-45.0)/1000 CY and 10.1 (4.2-24.2)/1000 CY for preterms. The single RSV B season had higher incidences of RSV LRTI in every age group than the 2 RSV A seasons in both preterm and term infants. There were 11 deaths, all term infants. CONCLUSIONS: Studies restricted to the healthcare settings significantly underestimate the burden of RSV LRTI and preterm and term infants have comparable burdens of disease in this rural community.

Mortality From Respiratory Syncytial Virus in Children Under 2 Years of Age: A Prospective Community Cohort Study in Rural Maharashtra, India.

BACKGROUND: Although respiratory syncytial virus (RSV) is the most important viral cause of lower respiratory tract infection deaths in infants, there are few data on infant community deaths caused by RSV. METHODS: This was an active surveillance of children younger than 2 years of age in 93 villages, 5 primary health centers, and 3 hospitals serving these villages. Village health workers and counselors at the health facilities monitored all lower respiratory tract infections (LRTIs) in consented subjects. Children with severe, or very severe LRTIs and all who died, had nasopharyngeal swabs collected for detection of RSV by molecular methods. RESULTS: In the 12 134 subjects, there were 2064 episodes of severe LRTIs and 1732 of very severe LRTIs, of which 271 and 195, respectively, had RSV. Fifteen of 16 (94%) children with RSV died of LRTIs, 14 in the community and 1 in the hospital. The case fatality ratios for severe RSV LRTIs in the first 6 months of life were 3/52 (7.1%) and 1/36 (2.8%) in the community and hospital, respectively. Of those with very severe LRTIs in the community, 17.6% died. There were no very severe RSV LRTI hospital deaths. The adjusted RSV LRTI mortality rates ranged from 1.0 to 3.0/1000 child-years (CY) overall, and 2.0 to 6.1/1000 CY, accounting for 20% of the LRTI deaths and 10% of the postneonatal infant mortality. CONCLUSIONS: Community deaths from RSV account for the majority of RSV LRTI deaths, and efforts at prevention should be preferentially directed at populations where access to care is limited.

Efficacy of live attenuated and inactivated influenza vaccines among children in rural India: A 2-year, randomized, triple-blind, placebo-controlled trial.

BACKGROUND: Influenza is a cause of febrile acute respiratory infection (FARI) in India; however, few influenza vaccine trials have been conducted in India. We assessed absolute and relative efficacy of live attenuated influenza vaccine (LAIV) and inactivated influenza vaccine (IIV) among children aged 2 to 10 years in rural India through a randomized, triple-blind, placebo-controlled trial conducted over 2 years. METHODS AND FINDINGS: In June 2015, children were randomly allocated to LAIV, IIV, intranasal placebo, or inactivated polio vaccine (IPV) in a 2:2:1:1 ratio. In June 2016, vaccination was repeated per original allocation. Overall, 3,041 children received LAIV (n = 1,015), IIV (n = 1,010), nasal placebo (n = 507), or IPV (n = 509). Mean age of children was 6.5 years with 20% aged 9 to 10 years. Through weekly home visits, nasal and throat swabs were collected from children with FARI and tested for influenza virus by polymerase chain reaction. The primary outcome was laboratory-confirmed influenza-associated FARI; vaccine efficacy (VE) was calculated using modified intention-to-treat (mITT) analysis by Cox proportional hazards model (PH) for each year. In Year 1, VE was 40.0% (95% confidence interval (CI) 25.2 to 51.9) for LAIV and 59.0% (95% CI 47.8 to 67.9) for IIV compared with controls; relative efficacy of LAIV compared with IIV was -46.2% (95% CI -88.9 to -13.1). In Year 2, VE was 51.9% (95% CI 42.0 to 60.1) for LAIV and 49.9% (95% CI 39.2 to 58.7) for IIV; relative efficacy of LAIV compared with IIV was 4.2% (95% CI -19.9 to 23.5). No serious adverse vaccine-attributable events were reported. Study limitations include differing dosage requirements for children between nasal and injectable vaccines (single dose of LAIV versus 2 doses of IIV) in Year 1 and the fact that immunogenicity studies were not conducted. CONCLUSIONS: In this study, we found that LAIV and IIV vaccines were safe and moderately efficacious against influenza virus infection among Indian children. TRIAL REGISTRATION: Clinical Trials Registry of India CTRI/2015/06/005902.

Global burden of influenza-associated lower respiratory tract infections and hospitalizations among adults: A systematic review and meta-analysis.

BACKGROUND: Influenza illness burden is substantial, particularly among young children, older adults, and those with underlying conditions. Initiatives are underway to develop better global estimates for influenza-associated hospitalizations and deaths. Knowledge gaps remain regarding the role of influenza viruses in severe respiratory disease and hospitalizations among adults, particularly in lower-income settings. METHODS AND FINDINGS: We aggregated published data from a systematic review and unpublished data from surveillance platforms to generate global meta-analytic estimates for the proportion of acute respiratory hospitalizations associated with influenza viruses among adults. We searched 9 online databases (Medline, Embase, CINAHL, Cochrane Library, Scopus, Global Health, LILACS, WHOLIS, and CNKI; 1 January 1996-31 December 2016) to identify observational studies of influenza-associated hospitalizations in adults, and assessed eligible papers for bias using a simplified Newcastle-Ottawa scale for observational data. We applied meta-analytic proportions to global estimates of lower respiratory infections (LRIs) and hospitalizations from the Global Burden of Disease study in adults ≥20 years and by age groups (20-64 years and ≥65 years) to obtain the number of influenza-associated LRI episodes and hospitalizations for 2016. Data from 63 sources showed that influenza was associated with 14.1% (95% CI 12.1%-16.5%) of acute respiratory hospitalizations among all adults, with no significant differences by age group. The 63 data sources represent published observational studies (n = 28) and unpublished surveillance data (n = 35), from all World Health Organization regions (Africa, n = 8; Americas, n = 11; Eastern Mediterranean, n = 7; Europe, n = 8; Southeast Asia, n = 11; Western Pacific, n = 18). Data quality for published data sources was predominantly moderate or high (75%, n = 56/75). We estimate 32,126,000 (95% CI 20,484,000-46,129,000) influenza-associated LRI episodes and 5,678,000 (95% CI 3,205,000-9,432,000) LRI hospitalizations occur each year among adults. While adults <65 years contribute most influenza-associated LRI hospitalizations and episodes (3,464,000 [95% CI 1,885,000-5,978,000] LRI hospitalizations and 31,087,000 [95% CI 19,987,000-44,444,000] LRI episodes), hospitalization rates were highest in those ≥65 years (437/100,000 person-years [95% CI 265-612/100,000 person-years]). For this analysis, published articles were limited in their inclusion of stratified testing data by year and age group. Lack of information regarding influenza vaccination of the study population was also a limitation across both types of data sources. CONCLUSIONS: In this meta-analysis, we estimated that influenza viruses are associated with over 5 million hospitalizations worldwide per year. Inclusion of both published and unpublished findings allowed for increased power to generate stratified estimates, and improved representation from lower-income countries. Together, the available data demonstrate the importance of influenza viruses as a cause of severe disease and hospitalizations in younger and older adults worldwide.

Results from the WHO external quality assessment for the respiratory syncytial virus pilot, 2016-17.

BACKGROUND: External quality assessments (EQAs) for the molecular detection of respiratory syncytial virus (RSV) are necessary to ensure the provision of reliable and accurate results. One of the objectives of the pilot of the World Health Organization (WHO) Global RSV Surveillance, 2016-2017, was to evaluate and standardize RSV molecular tests used by participating countries. This paper describes the first WHO RSV EQA for the molecular detection of RSV. METHODS: The WHO implemented the pilot of Global RSV Surveillance based on the WHO Global Influenza Surveillance and Response System (GISRS) from 2016 to 2018 in 14 countries. To ensure standardization of tests, 13 participating laboratories were required to complete a 12 panel RSV EQA prepared and distributed by the Centers for Disease Control and Prevention (CDC), USA. The 14th laboratory joined the pilot late and participated in a separate EQA. Laboratories evaluated a RSV rRT-PCR assay developed by CDC and compared where applicable, other Laboratory Developed Tests (LDTs) or commercial assays already in use at their laboratories. RESULTS: Laboratories performed well using the CDC RSV rRT-PCR in comparison with LDTs and commercial assays. Using the CDC assay, 11 of 13 laboratories reported correct results. Two laboratories each reported one false-positive finding. Of the laboratories using LDTs or commercial assays, results as assessed by Ct values were 100% correct for 1/5 (20%). With corrective actions, all laboratories achieved satisfactory outputs. CONCLUSIONS: These findings indicate that reliable results can be expected from this pilot. Continued participation in EQAs for the molecular detection of RSV is recommended.

Burden of influenza-associated respiratory and circulatory mortality in India, 2010-2013.

BACKGROUND: Influenza causes substantial morbidity and mortality worldwide, however, reliable burden estimates from developing countries are limited, including India. We aimed to quantify influenza-associated mortality for India utilizing 2010-2013 nationally representative data sources for influenza virus circulation and deaths. METHODS: Virological data were obtained from the influenza surveillance network of 10 laboratories led by National Institute of Virology, Pune covering eight states from 2010-2013. Death data were obtained from the nationally representative Sample Registration System for the same time period. Generalized linear regression with negative binomial distribution was used to model weekly respiratory and circulatory deaths by age group and proportion of specimens positive for influenza by subtype; excess deaths above the seasonal baseline were taken as an estimate of influenza-associated mortality counts and rates. Annual excess death rates and the 2011 India Census data were used to estimate national influenza-associated deaths. RESULTS: Estimated annual influenza-associated respiratory mortality rates were highest for those ≥65 years (51.1, 95% confidence interval (CI) = 9.2-93.0 deaths/100 000 population) followed by those <5 years (9.8, 95% CI = 0-21.8/100 000). Influenza-associated circulatory death rates were also higher among those ≥65 years (71.8, 95% CI = 7.9-135.8/100 000) as compared to those aged <65 years (1.9, 95% CI = 0-4.6/100 000). Across all age groups, a mean of 127 092 (95% CI = 64 046-190,139) annual influenza-associated respiratory and circulatory deaths may occur in India. CONCLUSIONS: Estimated influenza-associated mortality in India was high among children <5 years and adults ≥65 years. These estimates may inform strategies for influenza prevention and control in India, such as possible vaccine introduction.

Human respiratory syncytial virus and influenza seasonality patterns-Early findings from the WHO global respiratory syncytial virus surveillance.

BACKGROUND: Human respiratory syncytial virus (RSV) causes illnesses among all age groups and presents a burden to healthcare services. To better understand the epidemiology and seasonality of RSV in different geographical areas, the World Health Organization (WHO) coordinated a pilot initiative to access the feasibility of establishing RSV surveillance using the existing Global Influenza Surveillance and Response System (GISRS) platform. OBJECTIVES: To describe and compare RSV and influenza seasonality in countries in the northern andsouthern temperate, and tropics during the period January 2017 to April 2019. METHODS: Fourteen countries in six WHO regions participating in the GISRS were invited for the pilot. Hospitalized patients presenting with severe acute respiratory illness (SARI), SARI without fever and outpatients presenting with acute respiratory illness (ARI) were enrolled from January 2017 to April 2019. The expected minimum sample size was 20 samples per week, year-round, per country. Real-time RT-PCR was used to detect RSV and influenza viruses. Results were uploaded to the WHO FluMart platform. RESULTS: Annual seasonality of RSV was observed in all countries, which overlapped to a large extent with the influenza activity. In countries, in temperate regions RSV peaked in the autumn/winter months. In Egypt, a subtropical country, RSV activity peaked in the cooler season. In the tropical regions, RSV peaked during the rainy seasons. CONCLUSION: Early findings from the WHO RSV surveillance pilot based on the GISRS suggest annual seasonal patterns for of RSV circulation that overlap with influenza. RSV surveillance needs to be continued for several more seasons to establish seasonality patterns to inform prevention and control strategies.

Laboratory-Confirmed Avian Influenza A(H9N2) Virus Infection, India, 2019.

A 17-month-old boy in India with severe acute respiratory infection was laboratory confirmed to have avian influenza A(H9N2) virus infection. Complete genome analysis of the strain indicated a mixed lineage of G1 and H7N3. The strain also was found to be susceptible to adamantanes and neuraminidase inhibitors.

Molecular characterization of influenza A(H1N1)pdm09 viruses circulating at various geographical locations in India, 2017.

Background & objectives: Influenza virological surveillance is an essential tool for the early detection of novel genetic variants of epidemiologic and clinical significance. This study was aimed to genetically characterize A(H1N1)pdm09 virus circulating in 2017 and to compare it with the global data. Methods: The regional/State Viral Research and Diagnostic Laboratories (VRDLs) provided influenza diagnosis for referred clinical samples and shared influenza A(H1N1)pdm09 positives with the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, India, for hemagglutinin (HA) gene phylogenetic analysis. Sites at Manipal, Jaipur and Dibrugarh performed the sequencing and shared the sequence data for analysis. The antiviral susceptibility of influenza viruses was assessed for known molecular marker H275Y at the ICMR-NIV, Pune. Results: All the eight VRDLs had well-established influenza diagnostic facilities and showed increased activity of influenza A(H1N1)pdm09 during 2017. Phylogenetic analysis showed that the viruses from the different regions of the country were similar to A/Michigan/45/2015 strain which was the 2017-2018 recommended vaccine strain and were clustered with the globally circulating clade 6B.1 with signature mutations S84N, S162N and I216T. The clade 6B.1 showed further subgrouping with additional mutations S74R, S164T and I295V; however, there was no significant association between the presence of these mutations and severity of disease due to influenza. All the study viruses were sensitive to oseltamivir. Interpretation & conclusions: During the study period, all the study sites reported globally circulating A/Michigan/45/2015 vaccine strain of influenza A(H1N1)pdm09 viruses and remained sensitive to oseltamivir. Further genetic and antigenic characterization of influenza viruses is recommended to address public health concerns.

Seroprevalence of influenza A H1N1 (swine) infection in the human population in a cantonment.

BACKGROUND: Various serosurveys and studies were conducted globally on pandemic influenza. H1N1 virus reported so far provides ample evidence of differing perspectives, regarding its epidemiology especially with regard to prevalence, populations groups, and behaviour related to vaccine acceptance. A multigroup, cross-sectional survey among 658 healthy subjects was carried out, in Pune among students, health-care workers (HCWs), and soldiers to assess the seroprevalence of pandemic influenza H1N1 virus and its associated factors. METHODS: The total sample size, based on forecasted prevalence of 33%, worked out to be 640. We studied 658 subjects including 103 students, 201 HCWs, and 354 serving soldiers. The sample for each group was selected from the respective study population by simple random sampling using a random number table. Haemagglutination inhibition test was carried out at the National Institute of Virology. RESULTS: The overall seroprevalence of pandemic influenza H1N1 (2009) virus was found to be 46.5% (95% confidence interval 42.6-50.4) which was adjusted to 39.4% after excluding those vaccinated. The availability of vaccine for high-risk group such as HCWs did not find much favour with the HCWs who did not accept vaccine for various reasons. Whereas only one student was vaccinated, 21.4% of HCWs and 32.5% of soldiers were vaccinated. CONCLUSION: Based on high seroprevalence of antibodies against H1N1 virus during pandemic, vaccination of general population is not recommended. However, high-risk groups and HCWs need to be protected with flu vaccine. There is a need to encourage HCWs for accepting vaccination.

Emerging/re-emerging viral diseases & new viruses on the Indian horizon.

Infectious diseases remain as the major causes of human and animal morbidity and mortality leading to significant healthcare expenditure in India. The country has experienced the outbreaks and epidemics of many infectious diseases. However, enormous successes have been obtained against the control of major epidemic diseases, such as malaria, plague, leprosy and cholera, in the past. The country's vast terrains of extreme geo-climatic differences and uneven population distribution present unique patterns of distribution of viral diseases. Dynamic interplays of biological, socio-cultural and ecological factors, together with novel aspects of human-animal interphase, pose additional challenges with respect to the emergence of infectious diseases. The important challenges faced in the control and prevention of emerging and re-emerging infectious diseases range from understanding the impact of factors that are necessary for the emergence, to development of strengthened surveillance systems that can mitigate human suffering and death. In this article, the major emerging and re-emerging viral infections of public health importance have been reviewed that have already been included in the Integrated Disease Surveillance Programme.

A case report of the enterovirus-D68 associated severe acute respiratory illness in a pediatric case from India.

Since, early 2000s, there have been several clusters of enterovirus-D68 (EV D68) associated respiratory illness reported from various countries. Recent largest and most wide-spread outbreak of EV-D68 associated severe acute respiratory illness (SARI) occurred in North America. Present report describes a case of EV-D68 associated severe acute respiratory illness from India with a whole genome sequence. The case was identified through retrospective analysis of Influenza SARI surveillance sample collected during September 2017 using Next Generation sequencing. EV D68 positive child aged two years and presented with asthma like symptoms for which he was admitted to ICU. The child tested negative for Influenza, RSV, Rhinovirus, PIV, hMPV and adenovirus, on real time RT-PCR. And on NGS full EV D68 genome was retrieved belonging to sub-clade B3. In ICU, child received anti-bacterial and anti-viral therapy. The child recovered with-out any sequelae and was discharged one week later. Present report highlights the importance of studying this emergent virus EV-D68 through prospective studies to understand the burden and epidemiological pattern in the country and its implications.

Association of Single Nucleotide Polymorphisms in TNFA and IL10 Genes with Disease Severity in Influenza A/H1N1pdm09 Virus Infections: A Study from Western India.

Susceptibility to severe influenza A/H1N1pdm09 virus is multifactorial. The present study was carried out in 246 patients infected with A/H1N1pdm09 virus to find out whether single nucleotide polymorphisms (SNPs) in the genes coding for proinflammatory and anti-inflammatory cytokines are associated with disease severity. Among the cases, 129 had mild disease, whereas 117 had severe disease. There were 27 fatal cases. TNFA rs1800629, IFNG rs2430561, IL10 rs1800872, IL10 rs1800896, and CCL2 rs1024611 SNPs were genotyped by polymerase chain reaction-based methods. A significantly higher frequency of TNFA rs1800629 "G/A" genotype was observed in severe and fatal cases compared with mild and survived cases, respectively. In a dominant mode, IL10 rs1800896 "G" allele was significantly negatively associated with disease severity. IL10 rs1800896 "C/A" genotype was significantly associated with fatality in influenza A/H1N1pdm09 infections. The results suggest that SNPs in the IL10 and TNFA genes might be associated with disease severity in influenza A/H1N1pdm09-infected patients.

Respiratory viruses in returning Hajj & Umrah pilgrims with acute respiratory illness in 2014-2015.

BACKGROUND & OBJECTIVES: Respiratory tract infections are common among Hajj and Umrah pilgrims which pose a public health risk of spread of respiratory infections. Influenza has been reported from Indian Hajj and Umrah returning pilgrims, but data on other respiratory pathogens are sparse in India. Here we report the presence of common respiratory viral pathogens in returning Hajj and Umrah pilgrims suffering from acute respiratory illness (ARI) in 2014-2015. METHODS: Respiratory specimens (nasopharyngeal and throat swabs) were collected from 300 consenting pilgrims with ARI in the past one week and tested for influenza and Middle East Respiratory Syndrome coronavirus (MERS-CoV) and other respiratory viruses using in-house standardized quantitative real-time reverse-transcription polymerase chain reaction. Clinical features among the pathogen positive and negative patients were compared. The patients received symptomatic treatment and antivirals where appropriate and were followed telephonically to collect data on illness outcome. RESULTS: Ninety seven (32.3%) of the 300 participants were tested positive for any virus, most common being influenza viruses (n=33, 11%). Other respiratory viruses that were detected included human coronaviruses [n=26, 8.7%; OC43 (n=19, 6.3%) and C229E (n=7, 2.3%)], rhinovirus (n=20, 6%), adenoviruses (n=8, 2.6%), parainfluenza viruses (n=7, 2.3%), respiratory syncytial virus (n=3, 1%) and bocaviruses (n=2, 0.6%). Clinical features observed in pathogen positive and pathogen negative patients did not differ significantly. Eighteen influenza positive patients were treated with oseltamivir. INTERPRETATION & CONCLUSIONS: Pilgrims returning from mass gatherings are often afflicted with respiratory pathogens with a potential to facilitate transmission of respiratory pathogens across international borders. The study reinforces the need for better infection prevention and control measures such as vaccination, health education on cough etiquette and hand hygiene.

The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus.

INTRODUCTION: Following the initial outbreak of A/H1N1pdm09, periodic resurgences of the virus, with variable morbidity and mortality, have been reported from various parts of India including the temperate Kashmir region of northern India. An outbreak of A/H1N1 was reported in early 2015 across India with a high morbidity and mortality. We studied patients during the outbreak in Kashmir. METHODS: Patients (n=1780, age 1 month to 90 years, median 35 years) presenting with acute respiratory illness to a tertiary care hospital in Srinagar, Kashmir from October 2014 to April 2015 were recruited. After clinical data recording, combined throat and nasal swabs were collected in viral transport medium and tested by real-time RT-PCR for influenza viruses. All influenza A positive samples were further subtyped using primers and probes for A/H1N1pdm09 and A/H3 whereas influenza B samples were further subtyped into B/Yamagata and B/Victoria lineages. Virus isolation, hemagglutination inhibition testing, sequencing and phylogenetic analysis was carried out using standard procedures. Testing for H275Y mutation was done to determine sensitivity to oseltamivir. All patients received symptomatic therapy and influenza positive patients were administered oseltamivir. RESULTS: Of the 1780 patients, 540 (30%) required hospitalization and 533 tested positive for influenza [influenza A=517(A/H1N1pdm09=437, A/H3N2=78 with co-infection of both in 2 cases); influenza B=16 (B/Yamgata=15)]. About 14% (n=254) had been vaccinated against influenza, having received the NH 2014-15 vaccine, 27 (11.3%) of these testing positive for influenza.  Sixteen patients, including 4 pregnant females, died due to multi-organ failure. HA sequencing depicted that 2015 isolates belonged to Clade 6B.1. No H275Y mutation was reported from A/H1N1 positives. CONCLUSION: Resurgent outbreak of A/H1N1pdm09, with emergence of clade 6B.1, in 2014-15 resulted in high rate of hospitalizations, morbidity and mortality. Periodic resurgences and appearance of mutants emphasize continued surveillance so as to identify newer mutations with potential for outbreaks and severe outcomes.

Estimation of community-level influenza-associated illness in a low resource rural setting in India.

OBJECTIVE: To estimate rates of community-level influenza-like-illness (ILI) and influenza-associated ILI in rural north India. METHODS: During 2011, we conducted household-based healthcare utilization surveys (HUS) for any acute medical illness (AMI) in preceding 14days among residents of 28villages of Ballabgarh, in north India. Concurrently, we conducted clinic-based surveillance (CBS) in the area for AMI episodes with illness onset ≤3days and collected nasal and throat swabs for influenza virus testing using real-time polymerase chain reaction. Retrospectively, we applied ILI case definition (measured/reported fever and cough) to HUS and CBS data. We attributed 14days of risk-time per person surveyed in HUS and estimated community ILI rate by dividing the number of ILI cases in HUS by total risk-time. We used CBS data on influenza positivity and applied it to HUS-based community ILI rates by age, month, and clinic type, to estimate the community influenza-associated ILI rates. FINDINGS: The HUS of 69,369 residents during the year generated risk-time of 3945 person-years (p-y) and identified 150 (5%, 95%CI: 4-6) ILI episodes (38 ILI episodes/1,000 p-y; 95% CI 32-44). Among 1,372 ILI cases enrolled from clinics, 126 (9%; 95% CI 8-11) had laboratory-confirmed influenza (A (H3N2) = 72; B = 54). After adjusting for age, month, and clinic type, overall influenza-associated ILI rate was 4.8/1,000 p-y; rates were highest among children <5 years (13; 95% CI: 4-29) and persons≥60 years (11; 95%CI: 2-30). CONCLUSION: We present a novel way to use HUS and CBS data to generate estimates of community burden of influenza. Although the confidence intervals overlapped considerably, higher point estimates for burden among young children and older adults shows the utility for exploring the value of influenza vaccination among target groups.