[Show abstract][Hide abstract] ABSTRACT: The seasonality of influenza in the tropics complicates vaccination timing. We investigated influenza seasonality in northern India and found influenza positivity peaked in Srinagar (34.09°N) in January–March but peaked in New Delhi (28.66°N) in July–September. Srinagar should consider influenza vaccination in October–November, but New Delhi should vaccinate in May–June.
[Show abstract][Hide abstract] ABSTRACT: Background
The global burden of influenza is increasingly recognized, but data from India remain sparse. We conducted a multi-site population-based surveillance study to estimate and compare rates of influenza-associated hospitalization at two rural Indian health and demographic surveillance system (HDSS) sites at Ballabgarh and Vadu during 2010-2012.
Prospective facility-based surveillance for all hospitalizations (excluding those for trauma, elective surgery and obstetric, ophthalmic or psychiatric reasons) was conducted at 72 health facilities. After collection of clinical details, patients had nasopharyngeal swabs taken and tested by reverse transcription polymerase chain reaction for influenza viruses. Annual healthcare utilization surveys (HUS) were conducted in HDSS households to identify proportion of hospitalizations occurring at non-study facilities to adjust for hospitalizations missed through facility-based surveillance.
HUS showed that 69% and 67% of hospitalizations occurred at study facilities at Ballabgarh and Vadu respectively. Overall, 6,004 patients hospitalized with acute medical illness at participating facilities were enrolled (1,717 from Ballabgarh; 4,287 from Vadu). The proportion of patients with influenza was higher at Vadu than Ballabgarh annually (2010: 21% vs. 5%, p<0.05; 2011: 18% vs. 5%, p<0.05; 2012: 23% vs. 5%, p<0.05). Annual adjusted influenza-associated hospitalization rates were 5-11 fold higher in Vadu (20.3-51.6 per 10,000) versus Ballabgarh (4.4-6.3 per 10,000). At both sites, influenza A/H1N1pdm09 and B predominated during 2010, A/H3N2 and B during 2011, and A/H1N1pdm09 and B during 2012.
The markedly different influenza hospitalization rates by season and across communities in India highlight the need for sustained multi-site surveillance system for estimating national influenza disease burden. That would be the first step for initiating discussions around Influenza prevention and control strategies in the country.
Journal of Infection 09/2014; · 4.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Abstract:
Background and Objective:
Recent antiviral studies from South East Asia, Europe and the United States showed the presence of neuraminidase inhibitor (NAIs) resistance in pandemic influenza 2009 viruses. The study was undertaken to evaluate neuraminidase inhibitor (NAI) resistance of pandemic Influenza virus isolated from India.
Pandemic Influenza viruses, isolated from 2009 to 2013 were analyzed genetically for known resistance markers in NA gene. Pandemic (H1N1) (n= 493) isolates were tested for H274Y mutation by rRT-PCR. Randomly selected resistant and sensitive viruses were confirmed by phenotypic assay.
All Pandemic A/H1N1 isolates remained sensitive except single 2013 isolate. Genetic analysis of single 2013 isolate as well as original clinical material showed H274Y mutation responsible for reduce susceptibility to Oseltamivir and were also confirmed by phenotypic assay.
Emergence of pandemic influenza strain resistant to oseltamivir emphasizes the need for monitoring antiviral resistance as part of National Influenza Program
WHO South East Journal Of Public health. 01/2014; In Press.
[Show abstract][Hide abstract] ABSTRACT: Systematic influenza virus surveillance has been carried out in India since 2004 and has revealed the cocirculation of type B lineages. The genetic diversity of influenza B viruses was observed when full-genome analysis was performed. In 2010, the cocirculation of multiple genotypes was observed.
[Show abstract][Hide abstract] ABSTRACT: Human respiratory syncytial virus (RSV) is one of the most important respiratory viruses causing acute respiratory tract infections amongst children. Based on genotyping of the attachment glycoprotein (G) gene, it is divided into two groups, RSV-A and RSV-B. Infection with one group does not confer immunity against the other and children infected with one antigenic group are more likely to be reinfected with the heterologous group. We tested 854 samples of patients with influenza like illness (ILI)/ severe respiratory illness (SARI) during the period 2009-2012 for RSV using a conventional multiplex RT-PCR and found 159 (18.61%) samples to be positive for RSV of which 130 (15.22%) were positive for RSV-B and 29 (3.39%) for RSV-A suggesting that RSV-B was the predominant group circulating in western India during the study period. Seasonal RSV outbreaks were observed in the monsoon and winter months. RSV was more prevalent amongst children in the 0-24 month age group (21.53%) in comparison to children in the 24-60 month age group (13.01%). Phylogenetic analysis using the G gene of 27 representative RSV-A positive samples revealed that all sequences belonged to the NA1 genotype. Of these, 5 sequences exhibited the novel 72 nucleotide duplication in the C-terminal of the G gene first reported from Ontario, Canada and clustered in the newly designated ON1 genotype. Also, 32 of the 33 RSV-B sequences exhibited the 60 nucleotide duplication associated with genotype BA and phylogenetic analysis showed that these sequences belonged to the genotype BA9 and BA12. We also found one RSV-B sequence belonging to genotype GB2, which has not been previously reported in India.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 10/2013; · 3.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Human metapneumovirus (HMPV) is an important respiratory virus implicated in respiratory infections. The purpose of this study was to develop a one-step real-time RT-PCR assay that can detect all four lineages of HMPV and to identify the HMPV lineages circulating in Pune, India. Conserved regions of the nucleoprotein gene were used to design real-time primers and a probe. A total of 224 clinical samples that were positive for different respiratory viruses (including 51 samples that were positive for HMPV) were tested using the real time RT-PCR assay, and the specificity of the assay was observed to be 100 %. Using in vitro-synthesized RNA, the sensitivity of the assay was ascertained to be 100 copies of the target gene per reaction. Phylogenetic analysis of the nucleoprotein (N) and attachment glycoprotein (G) genes confirmed that this assay detected all lineages of HMPV. A2, B1 and B2 strains were observed during the study period. Our assay is highly sensitive and specific for all known lineages of HMPV, making it a valuable tool for rapid detection of the virus. A2 and B2 were the predominant subtypes circulating in Pune, Western India.
Archives of Virology 08/2013; · 2.28 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Two complete genomes of human respiratory syncytial virus subtype A (HRSV-A), with and without a 72-nucleotide duplication in the C-terminal glycoprotein G gene, were sequenced and analyzed. Characterization of these genomes will improve understanding of the diversity, emergence, virulence, pathogenicity, and transmissibility of a novel RSV-A genotype with a 72-nucleotide G gene duplication.
[Show abstract][Hide abstract] ABSTRACT: Rapid and accurate diagnosis of viral respiratory infections is crucial for patient management. Multiplex Reverse Transcriptase Polymerase Chain Reaction (mRT-PCR) is used increasingly to diagnose respiratory infections and has shown to be more sensitive than viral culture and antigen detection. Objective of the present study was to develop a one-step mRT-PCR that could detect 18 respiratory viruses in three sets. The method was compared with real time RT-PCR (rRT-PCR) for its sensitivity and specificity. Clinical specimens from 843 pediatric patients with respiratory symptoms were used in the study. 503 (59.7%) samples were detected positive by mRT-PCR. Of these 462 (54.8%) exhibited presence of a single pathogen and 41 (4.9%) had multiple pathogens. rRT-PCR detected 439 (52.1%) positive samples, where 419 (49.7%) exhibited one virus and 20 (2.4%) showed co-infections. Concordance between mRT-PCR and rRT-PCR was 91.9% and kappa correlation 0.837. Sensitivity and specificity of mRT-PCR was 99.5% and 83.7% while that of rRT-PCR was 86.9% and 99.4% respectively. Rhinovirus (17.2%) was the most frequently detected virus followed by respiratory syncytial virus B (15.4%), H1N1pdm09 (8.54%), parainfluenza virus -3 (5.8%) and metapneumovirus (5.2%). In conclusion, mRT-PCR is a rapid, cost effective, specific and highly sensitive method for detection of respiratory viruses.
Journal of virological methods 01/2013; · 2.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: BACKGROUND and OBJECTIVE:
Recent influenza antiviral resistance studies in South East Asia, Europe and the United States reveal adamantane and neuraminidase inhibitor (NAIs) resistance. The study was undertaken to evaluate antiviral resistance of Influenza viruses isolated from various parts of India.
METHODS: Influenza viruses, isolated from 2004 to 2011 were analyzed genetically for known resistance markers byM2 and NA gene sequencing. Influenza A/H1N1 (n=206), A/H3N2 (n=371) viruses for amantadine resistance and A/H1N1 (n=206), A/H3N2 (n=272) and Type B (n=326) for oseltamivir resistance were sequenced. Pandemic (H1N1) (n= 493) isolates were tested for H274Y mutation by rRT-PCR. Randomly selected resistant and sensitive influenza A/ H1N1 and A/H3N2 viruses were confirmed by phenotypic assay.
Serine to asparagine (S3IN) mutation was detected in six isolates of 2007-2008.One dual-resistant A/H1N1 was detected for the first time in India with leucine to phenylalanine (L26F) mutation in M2 gene and H274Y mutation in NA gene. A/H3N2 viruses showed an incremental trend in resistance to amantadine from 22.5% in 2005 to 100% in 2008 onwards with S3IN mutation. Fifty of the sixty one (82%) A/H1N1 viruses tested in 2008-2009 were oseltamivir resistant with H274Y mutation, while all A/H3N2, pandemic A/H1N1 and Type B isolates remained sensitive. Genetic results were also confirmed by phenotypic analysis of randomly selected 50 resistant A/ H1N1 and 40 sensitive A/H3N2 isolates.
Emergence of influenza strains resistant to amantadine and oseltamivir in spite of negligible usage of antivirals emphasizes the need for monitoring antiviral resistance as part of National Influenza Program
The Indian Journal of Medical Research 01/2013; · 1.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Some parts of world, including India observed a recrudescent wave of influenza A/H1N1pdm09 in 2012. We undertook a study to examine the circulating influenza strains, their clinical association and antigenic characteristics to understand the recrudescent wave of A/H1N1pdm09 from November 26, 2012 to Feb 28, 2013 in Kashmir, India. Of the 751 patients (545 outpatient and 206 hospitalized) presenting with acute respiratory infection at a tertiary care hospital in Srinagar; 184 (24.5%) tested positive for influenza. Further type and subtype analysis revealed that 106 (58%) were influenza A (H1N1pdm09 =105, H3N2=1) and 78 (42%) were influenza B. The influenza positive cases had a higher frequency of chills, nasal discharge, sore throat, body aches and headache, compared to influenza negative cases. Of the 206 patients hospitalized for pneumonia/acute respiratory distress syndrome or an exacerbation of an underlying lung disease, 34 (16.5%) tested positive for influenza (22 for H1N1pdm09, 11 for influenza B). All influenza-positive patients received oseltamivir and while most patients responded well to antiviral therapy and supportive care, 6 patients (4 with H1N1pdm09 and 2 with influenza B) patients died of progressive respiratory failure and multi-organ dysfunction. Following a period of minimal circulation, H1N1pdm09 re-emerged in Kashmir in 2012-2013, causing serious illness and fatalities. As such the healthcare administrators and policy planners need to be wary and monitor the situation closely.
[Show abstract][Hide abstract] ABSTRACT: Influenza is vaccine-preventable; however, the burden of severe influenza in India remains unknown. We conducted a population-based study to estimate the incidence of laboratory confirmed influenza-associated hospitalizations in a rural community in western India.
We conducted active surveillance for hospitalized patients with acute medical illnesses or acute chronic disease exacerbations in Pune during pandemic and post pandemic periods (May 2009-April 2011). Nasal and throat swabs were tested for influenza viruses. A community health utilization survey estimated the proportion of residents hospitalized with respiratory illness at non-study facilities and was used to adjust incidence estimates from facility-based surveillance.
Among 9,426 hospitalizations, 3,391 (36%) patients were enrolled; 665 of 3,179 (20.9%) tested positive for influenza. Of 665 influenza positives, 340 (51%) were pandemic A(H1N1)pdm09 and 327 (49%) were seasonal, including A/H3 (16%), A/H1 (3%) and influenza B (30%). The proportion of patients with influenza peaked during August 2009 (39%) and 2010 (42%). The adjusted annual incidence of influenza hospitalizations was 46.8/10,000 during pandemic and 40.5/10,000 during post-pandemic period with comparable incidence of A(H1N1)pdm09 during both periods (18.8 and 20.3, respectively). The incidence of both pH1N1 and seasonal hospitalized influenza disease was highest in the 5-29 year olds.
We document the previously unrecognized burden of influenza hospitalization in a rural community following the emergence of influenza A(H1N1)pdm09 viruses in India. During peak periods of influenza activity circulation i.e during the monsoon period, 20% of all hospital admissions in the community had influenza positivity. These findings can inform development of influenza prevention and control strategies in India.
PLoS ONE 01/2013; 8(5):e55918. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To assess case definitions for influenza in a rural community in India.
Residents of the study area who were hospitalized for any acute medical condition for at least one night between May 2009 and April 2011 were enrolled. Respiratory specimens were collected and tested for influenza viruses in a reverse-transcription polymerase chain reaction (PCR). The PCR results were taken as the "gold standard" in evaluating the performance of several case definitions.
Of the 3179 patients included in the final analysis, 21% (665) were PCR-positive for influenza virus, 96% reported fever and 4% reported shortness of breath. The World Health Organization (WHO) case definition for severe acute respiratory illness had a sensitivity of 11% among patients aged < 5 years and of 3% among older patients. When shortness of breath was excluded from the definition, sensitivities increased (to 69% and 70%, respectively) and corresponding specificities of 43% and 53% were recorded. Among patients aged ≥ 5 years, WHO's definition of a case of influenza-like illness had a sensitivity of 70% and a specificity of 53%. The addition of "cough and reported or measured fever" increased sensitivity to 80% but decreased specificity to 42%.
The inclusion of shortness of breath in WHO's case definition for severe acute respiratory illness may grossly underestimate the burden posed by influenza in hospitals. The exclusion of shortness of breath from this definition or, alternatively, the inclusion of "cough and measured or reported fever" may improve estimates of the burden.
Bulletin of the World Health Organisation 11/2012; 90(11):804-12. · 5.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Influenza A virus encodes for eleven proteins, of which HA, NA, NS1 and PB1-F2 have been implicated in viral pathogenicity and virulence. Thus, in addition to the HA and NA gene segments, monitoring diversity of NS1 and PB1-F2 is also important.
55 out of 166 circulating influenza A strains (31 H1N1 and 24 H3N2) were randomly picked during 2007-2009 and NS and PB1-F2 genes were sequenced. Phylogenetic analysis was carried out with reference to the prototype strains, concurrent vaccine strains and other reference strains isolated world wide.
Comparative analysis of both nucleotide and deduced amino acid sequences, revealed presence of NS gene with A/PR/8/34(H1N1)-like mutations (H4N, Q21R, A22V, K44R, N53D, C59R, V60A, F103S and M106I) in both RNA-binding and effector domain of NS1 protein, and G63E, the HPAI-H5N1-like mutation in NEP/NS2 of five A/H1N1 strains of 2007 and 2009. NS1 of other A/H1N1 strains clustered with concurrent A/H1N1 vaccine strains. Of 31 A/H1N1 strains, five had PB1-F2 similar to the H3N2 strains; six had non-functional PB1-F2 protein (11 amino acids) similar to the 2009 pandemic H1N1 strains and rest 20 strains had 57 amino acids PB1-F2 protein, similar to concurrent A/H1N1 vaccine strain. Interestingly, three A/H1N1 strains with H3N2-like PB1-F2 protein carried primitive PR8-like NS gene. Full gene sequencing of PB1 gene confirmed presence of H3N2-like PB1 gene in these A/H1N1 strains.
Overall the study highlights reassortment event involving gene segments other than HA and NA in the co-circulating A/H1N1 and A/H3N2 strains and their importance in complexity of influenza virus genetics. In contrast, NS and PB1-F2 genes of all A/H3N2 eastern India strains were highly conserved and homologous to the concurrent A/H3N2 vaccine strains suggesting that these gene segments of H3N2 viruses are evolutionarily more stable compared to H1N1 viruses.