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The low pathogenic avian influenza H9N2 virus is a significant zoonotic agent and contributes genes to highly pathogenic avian influenza (HPAI) viruses. H9N2 viruses are prevalent in India with a reported human case. We elucidate the spatio-temporal origins of the H9N2 viruses from India. A total of 30H9N2 viruses were isolated from poultry and environmental specimens (years 2015–2020). Genome sequences of H9N2 viruses (2003-2020) from India were analyzed, revealing several substitutions. We found five reassortant genotypes. The HA, NA and PB2 genes belonged to the Middle-Eastern B sublineage; NP and M to the classical G1 lineage; PB1, PA and NS showed resemblance to genes from either HPAI-H7N3/H5N1 viruses. Molecular clock and phylogeography revealed that the introduction of all the genes to India took place around the year 2000. This is the first report of the genesis and evolution of the H9N2 viruses from India, and highlights the need for surveillance. • Avian influenza H9N2 viruses are of zoonotic concern with pandemic potential. • There is no data on the genesis and detailed gene pool analysis of H9N2 in India. • We report their phylogeography, molecular and evolutionary characterization. • The H9N2 viruses show gradual shift towards mammalian adaptation. • Reassortments of H9N2 have occurred with HPAI H5N1 and H7N3 viruses. [ABSTRACT FROM AUTHOR]

The influenza virus neuraminidase (NA) protein is responsible for actively cleaving the sialic acid (SA) bound to the viral hemagglutinin. In the present study, we identified a combination of five novel amino acid substitutions in the NA, conferring increased substrate binding and altered surface characteristics to a low pathogenic avian influenza (LPAI) H9N2 virus strain. The H9N2 strain reported from India, A/Environmental/India/1726265/2017 (H9N2-1726265) showed the combination of amino acid substitutions T149I, R249W, G346A, W403R and G435R, which were in the vicinity of the enzyme active site cavity. The strain A/chicken/India/99321/2009 (H9N2-99321) did not show these substitutions and was used for comparison. Virus elution was studied using turkey red blood cells (tRBCs). NA enzyme kinetics assays were carried out using the MUNANA substrate, which is an SA analogue. Homology modelling and molecular docking were performed to determine alterations in the surface characteristics and substrate binding. H9N2-1726265 showed enhanced elution from tRBCs. Enzyme kinetics revealed a lower K M of H9N2-1726265 (111.5 μM) as compared to H9N2-99321 (135.2 μM), indicating higher substrate binding affinity of H9N2-1726265, due to which the NA enzyme cleaved the SA more efficiently, leading to faster elution. Molecular docking revealed a greater number of binding interactions of H9N2-1726265 to SA as compared to H9N2-99321 corroborating the greater substrate binding affinity. Changes in the surface charge, hydrophobicity, and contour, were observed in H9N2-1726265 NA due to the five substitutions. Thus, the novel combination of five amino acids near the sialic acid binding site of NA, resulted in altered surface characteristics, higher substrate binding affinity, and virus elution. [Display omitted] • Influenza virus neuraminidase protein (NA) plays a key role in replication. • NA enzyme kinetics are important to determine the activity of the enzyme. • We report combination of novel mutations near the NA active site of an H9N2 strain. • The mutations altered surface properties leading to increased substrate binding. • Enhanced virus elution was observed due to these changes in the virus NA. [ABSTRACT FROM AUTHOR]

Background & objectives: Polio, measles, rubella, influenza and rotavirus surveillance programmes are of great public health importance globally. Virus isolation using cell culture is an integral part of such programmes. Possibility of unintended isolation of SARS-CoV-2 from clinical specimens processed in biosafety level-2 (BSL-2) laboratories during the above-mentioned surveillance programmes, cannot be ruled out. The present study was conducted to assess the susceptibility of different cell lines to SARS-CoV-2 used in these programmes. Methods: Replication of SARS-CoV-2 was studied in RD and L20B, Vero/hSLAM, MA-104 and Madin–Darby Canine Kidney (MDCK) cell lines, used for the isolation of polio, measles, rubella, rotavirus and influenza viruses, respectively. SARS-CoV-2 at 0.01 multiplicity of infection was inoculated and the viral growth was assessed by observation of cytopathic effects followed by real-time reverse transcription–polymerase chain reaction (qRT-PCR). Vero CCL-81 cell line was used as a positive control. Results: SARS-CoV-2 replicated in Vero/hSLAM, and MA-104 cells, whereas it did not replicate in L20B, RD and MDCK cells. Vero/hSLAM, and Vero CCL-81 showed rounding, degeneration and detachment of cells; MA-104 cells also showed syncytia formation. In qRT-PCR, Vero/hSLAM and MA-104 showed 106 and Vero CCL-81 showed 107 viral RNA copies per µl. The 50 per cent tissue culture infectious dose titres of Vero/hSLAM, MA-104 and Vero CCL-81 were 105.54, 105.29 and 106.45/ml, respectively. Interpretation & conclusions: Replication of SARS-CoV-2 in Vero/hSLAM and MA-104 underscores the possibility of its unintended isolation during surveillance procedures aiming to isolate measles, rubella and rotavirus. This could result in accidental exposure to high titres of SARS-CoV-2, which can result in laboratory acquired infections and community risk, highlighting the need for revisiting biosafety measures in public health laboratories. [ABSTRACT FROM AUTHOR]

The ongoing coronavirus disease (COVID-19) pandemic is a global public health emergency. Adherence to biosafety practices is mandatory to protect the user as well as the environment, while handling infectious agents. A biological safety cabinet (BSC) is the most important equipment used in diagnostic and research laboratories in order to safeguard the product, the person, and the environment. The World Health Organization has emphasized the use of validated BSCs in order to ensure quality of the results. There are different classes of BSCs that are used in various work environments based on the need. It is imperative to use appropriate levels of biosafety and types of BSCs in laboratories based on the risk assessment of the pathogen used. During the development of COVID-19 laboratories and training of laboratory staff, we came across several queries about the functions and selection of BSCs and realized that the knowledge about the detailed information on selections and applications of BSCs is scanty. There are several guidelines regarding the biosafety aspects for diagnostic and research laboratories handling infectious pathogens from national and international agencies. However, there is no detailed information on the use of appropriate types of BSCs and their functions in the context of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2). In view of this, the present paper describes in detail the selection and applications of BSCs, which could be useful for laboratories handling or planning to handle SARS-CoV-2 and suspected samples. [ABSTRACT FROM AUTHOR]

Turkey red blood cells (tRBCs) are an essential reagent used in the laboratory diagnosis of influenza viruses. Fresh tRBCs when stored at 4 °C have a shelf life of less than a week. Previous studies have shown the utility of glutaraldehyde-fixed tRBCs, with an increased shelf life, for use in hemagglutination (HA) assays. In the present study, we report their functionality after storage for 18 months, at -80 °C. Three influenza A subtypes, namely, H3N2, H1N1 and H5N1, were used in the study. Hemagglutination assay was performed using freshly prepared 0.5 % tRBCs suspension and stored 1 % glutaraldehyde-fixed tRBCs. There was no significant difference in the HA titers obtained using fresh and stored tRBCs. The validation of the HA assay was carried out, to determine the specificity, linearity, precision, accuracy, and robustness of the assay. All of the titers were within the acceptable range, indicating the validity of the HA assay using stored tRBCs. Hemagglutination inhibition assay was also performed to compare the antibody titers obtained using stored and fresh tRBCs. The stored RBCs also gave equivalent antibody titers, as compared to the fresh tRBCs. Thus, the present study demonstrates the utility of glutaraldehyde-fixed tRBCs after one and a half years of storage. • Turkey red blood cells (tRBC) are used for HA and HAI assays of influenza viruses. • Use of Glutaraldehyde-fixed tRBCs in these assays has been demonstrated previously. • We demonstrate their applicability after 18 months' storage at −80 °C. • There was no significant difference in HA and HAI titers using fresh and stored tRBCs. • This is the first report of the use of stored tRBCs after prolonged storage. [ABSTRACT FROM AUTHOR]

• NA gene sequencing of 67 HPAI H5N1 viruses revealed NA mutations in nine viruses. • A novel NA I117T mutation of HPAI H5N1 virus conferred resistance to NA inhibitors. • NAI susceptibility studied using fluorometric MUNANA assays and in ovo assays. • The I117T and I117V variants showed different levels of NAI susceptibility. • Natural occurrence of NAI-resistant I117T-mutant H5N1 virus is a cause of concern. Occurrence of avian influenza (AI) with Neuraminidase (NA) mutations which confer reduced neuraminidase inhibitor (NAI) susceptibility has remained a cause of concern. The susceptibility to NAIs of 67 highly pathogenic avian influenza H5N1 viruses isolated during 2006–2012 in India was tested in phenotypic fluorescence-based NA inhibition assay, sequence analysis and in ovo. One isolate showed a novel NA I117T amino acid substitution (N2 numbering) and eight isolates showed previously known NAI-resistance marker mutations (I117V, E119D, N294S, total 9/67). The overall incidence of resistant variants was 13.4%. The novel I117T substitution reduced oseltamivir susceptibility by 18.6-fold and zanamivir susceptibility by 11.8-fold, compared to the wild type AI H5N1virus, thus showed cross-resistance to both oseltamivir and zanamivir in NA inhibition assays. However, the other two isolates with I117V substitution were sensitive to both the NAIs. In addition, the comparison of growth of the I117T and I117V variants in presence of NAI's in the in ovo assays exhibited difference in growth levels. The present study reports the natural occurrence of a novel I117T mutation in AI H5N1 virus conferring cross-resistance to oseltamivir and zanamivir highlighting the urgent need of antiviral surveillance of AI viruses. [ABSTRACT FROM AUTHOR]

Highlights • Avian influenza H9N2 susceptibility to oseltamivir & zanamivir was studied in eggs. • NA substitution R292 K was selected in Passage 1 with oseltamivir. • NA substitution E119D was selected in Passage 2 with zanamivir. • NAI assays showed highly reduced susceptibility of mutant viruses to respective drugs. • Mutant viruses reverted to wild type without drug pressure in P2 and P3. Abstract Identification of amino-acid substitutions in the neuraminidase (NA) of low-pathogenic avian influenza (AI) H9N2 viruses is important to study the susceptibility to NA inhibitors (NAI). To identify mutations under NAI selective pressure, the virus was serially passaged with increasing levels of either oseltamivir or zanamivir in ovo , and the growth of the viruses in the presence and absence of NAI's compared. Mutations R292 K in the presence of oseltamivir and E119D in presence of zanamivir were observed within passage one and two respectively. The R292 K mutation reduced oseltamivir susceptibility significantly (2,523-fold) and moderately reduced susceptibility to zanamivir. The E119D mutation significantly reduced susceptibility to zanamivir (415-fold) and remained susceptible to oseltamivir. Genetic stability of the mutations assessed by serial passages of the mutant viruses in eggs without drug pressure resulted in the loss of these mutations, making the virus susceptible to both the drugs. Molecular modeling and dynamics simulations revealed that the R292 K mutation disrupted oseltamivir binding similar to other group 2 NAs, while a different mechanism was noted for zanamivir binding for both R292 K and E119D mutations. The study highlights the need for regular susceptibility screening of circulating AI viruses. [ABSTRACT FROM AUTHOR]

The pandemic influenza A(H1N1) 2009 virus caused significant morbidity and mortality worldwide thus necessitating the need to understand the host factors that influence its control. Previously, the complement system has been shown to provide protection during the seasonal influenza virus infection, however, the role of individual complement pathways is not yet clear. Here, we have dissected the role of intact complement as well as of its individual activation pathways during the pandemic influenza virus infection using mouse strains deficient in various complement components. We show that the virus infection in C3-/- mice results in increased viral load and 100% mortality, which can be reversed by adoptive transfer of naïve wild-type (WT) splenocytes, purified splenic B cells, or passive transfer of immune sera from WT, but not C3-/- mice. Blocking of C3a and/or C5a receptor signaling in WT mice using receptor antagonists and use of C3aR-/- and C5aR-/- mice showed significant mortality after blocking/ablation of C3aR, with little or no effect after blocking/ablation of C5aR. Intriguingly, deficiency of C4 and FB in mice resulted in only partial mortality (24%-32%) suggesting a necessary cross-talk between the classical/lectin and alternative pathways for providing effective protection. In vitro virus neutralization experiments performed to probe the cross-talk between the various pathways indicated that activation of the classical and alternative pathways in concert, owing to coating of viral surface by antibodies, is needed for its efficient neutralization. Examination of the virus-specific complement-binding antibodies in virus positive subjects showed that their levels vary among individuals. Together these results indicate that cooperation between the classical and alternative pathways not only result in efficient direct neutralization of the pandemic influenza virus, but also lead to the optimum generation of C3a, which when sensed by the immune cells along with the antigen culminates in generation of effective protective immune responses. [ABSTRACT FROM AUTHOR]

A letter is presented regarding avian surveys conducted in India from 1954 to 1981 to determine the role of wild and migratory birds in transmission of arboviruses.

Avian influenza (AI) H9N2 viruses are endemic in many bird species, and human infections of H9N2 viruses have been reported. Oseltamivir phosphate (Tamiflu ® ) is the available antiviral drug for the treatment and prophylaxis of influenza. There are no reports of use of embryonated chicken egg as a model to study susceptibility of AI viruses to oseltamivir carboxylate (OC), the active metabolite. The present study was undertaken to explore the use of embryonated chicken eggs as a model for testing OC against the AI H9N2 viruses. A total of three AI H9N2 viruses, isolated in poultry in India, were used. Various virus dilutions were tested against 14 μg/ml of OC. Three methods, namely (1) the in vitro virus–drug treatment, (2) drug delivery and virus challenge by allantoic route, and (3) drug delivery by albumen route and virus challenge by allantoic route were explored. The viruses were also tested using the fluorescence-based neuraminidase inhibitor (NAI) assay. There was significant inhibition (p < 0.05) of the H9N2 viruses in presence of OC. The infectious virus titers as well as hemagglutination titers were significantly lower in presence of OC as compared to controls. The in vitro treatment of virus and drug; and drug and virus delivery at the same time by allantoic route showed significantly higher inhibition (p < 0.05) of virus growth than that by the albumen route. In the NAI assay, the half maximal inhibitory concentration (IC 50 ) values of the H9N2 viruses were within the standard range for known susceptible reference virus. In conclusion, the H9N2 viruses used in the study were susceptible to OC. Embryonated chicken egg could be used as a model to study susceptibility of AI viruses to antiviral drugs. [ABSTRACT FROM AUTHOR]

In view of the emerging avian influenza (AI) viruses, it is important to study the susceptibility of AI viruses to inactivating agents for preparation of antigens and inactivated vaccines. The available information on susceptibility of both the high and low pathogenic AI viruses to different inactivating agents is inadequate and ambiguous. It has been shown that different subtypes of influenza viruses require different physical and chemical conditions for inactivation of infectivity. The present study was undertaken to evaluate the use of beta-propiolactone (BPL), formalin and ether for inactivation and its impact on antigenicity of AI viruses. A total of nine high and low pathogenic AI viruses belonging to four influenza A subtypes were included in the study. The H5N1 viruses were from the clades 2.2, 2.3.2.1 and 2.3.4. The H9N2 virus included in the study was of the G1 genotype, while the H11N1 and H4N6 viruses were from the Eurasian lineage. The viruses were treated with BPL, formalin and with ether. The confirmation of virus inactivation was performed by two serial passages of inactivated viruses in embryonated chicken eggs. The infectivity of all tested AI viruses was eliminated using 0.1% BPL and 0.1% formalin. Ether eliminated infectivity of all tested low pathogenic AI viruses; however, ether with 0.2% or 0.5% Tween-20 was required for inactivation of the highly pathogenic AI H5N1 viruses. Treatment with BPL, ether and formalin retained virus hemagglutination (HA) titers. Interestingly ether treatment resulted in significant rise in HA titers ( P < 0.05) of all tested AI viruses. This data demonstrated the utility of BPL, formalin and ether for the inactivation of infectivity of AI viruses used in the study for the preparation of inactivated virus antigens for research and diagnosis of AI. [ABSTRACT FROM AUTHOR]

The authors discuss a study regarding the pathogenicity of the avian influenza (AI) H11N1 virus that was isolated from the wild aquatic bird Eurasian spoonbill in Maharashtra, India. Topics addressed include the virus' inoculation in ten-day old embryonated chicken eggs, the intranasal inoculation of mice with the H11N1 virus, and pathological changes showed by the AI H11N1 virus in the airways and lungs. Also mentioned are histopathological findings in the infected mice's lung tissues.

Avian influenza (AI) H9N2 has been reported from poultry in India. A seroepidemiological study was undertaken among poultry workers to understand the prevalence of antibodies against AI H9N2 in Pune, Maharashtra, India. A total of 338 poultry workers were sampled. Serum samples were tested for presence of antibodies against AI H9N2 virus by hemagglutination inhibition (HI) and microneutralization (MN) assays. A total of 249 baseline sera from general population from Pune were tested for antibodies against AI H9N2 and were negative by HI assay using ≥40 cut-off antibody titre. Overall 21 subjects (21/338 = 6.2%) were positive for antibodies against AI H9N2 by either HI or MN assays using ≥40 cut-off antibody titre. A total of 4.7% and 3.8% poultry workers were positive for antibodies against AI H9N2 by HI and MN assay respectively using 40 as cut-off antibody titre. This is the first report of seroprevalence of antibodies against AI H9N2 among poultry workers in India. [ABSTRACT FROM AUTHOR]

Introduction: Hemagglutination (HA) and hemagglutination inhibition (HI) assays are conventionally used for detection and identification of influenza viruses. HI assay is also used for detection of antibodies against influenza viruses. Primarily turkey or chicken erythrocytes [red blood cells (RBCs)] are used in these assays, as they are large, nucleated, and sediment fast, which makes it easy to determine the titer. Human influenza viruses agglutinate RBCs from chicken, human, and guinea pig, but not from horse. Human influenza viruses bind preferentially to sialic acid (SA) linked to galactose (Gal) by α 2, 6 linkage (SA α 2, 6-Gal), whereas avian influenza (AI) viruses bind preferentially to SA α 2, 3-Gal linkages. With this background, the present study was undertaken to study erythrocyte binding preferences and receptor specificities of AI viruses isolated from India. Materials and methods: A total of nine AI virus isolates (four subtypes) from India and three reference AI strains (three subtypes) were tested in HA and HI assays against mammalian and avian erythrocytes. The erythrocytes from turkey, chicken, goose, guinea pig and horse were used in the study. The receptor specificity determination assays were performed using goose and turkey RBCs. The amino acids present at 190 helix, 130 and 220 loops of the receptor-binding domain of the hemagglutinin protein were analyzed to correlate amino acid changes with the receptor specificity. Results: All tested highly pathogenic avian influenza (HPAI) H5N1 viruses reacted with all five types of RBCs in the HA assay; AI H9N2 and H5N2 viruses did not react with horse RBCs. For H5N1 viruses guinea pig and goose RBCs were best for both HA and HI assays. For H9N2 viruses, guinea pig, fowl and turkey RBCs were suitable. For other tested AI subtypes, avian and guinea pig RBCs were better. Eight isolates of H5N1, one H4N6 and one H7N1 virus showed preference to avian sialic acid receptors. Importantly, two isolates of HPAI H5N1, H9N2 and H11N1 viruses showed receptor specificity preference to both avian and mammalian sialic acid (α-2, 3 and α-2, 6) receptors. Conclusions: Use of different types of RBCs resulted in titer variations in HA and HI assays. This showed that RBCs giving optimum HA and HI titers would increase sensitivity of detection and would be more appropriate for identification and antigenic analysis of AI viruses. Analysis of 16 amino acids in the receptor-binding domain of the hemagglutinin of HPAI H5N1 viruses revealed that the only variation observed was in S221P amino acid position. Two H5N1 viruses showed S221P amino acid change, out of which only one H5N1 virus showed preference to α 2, 6 sialic acid receptor. One H5N1 virus isolate with amino acid S at 221 position, showed preference to α 2,3 as well as α 2,6 sialic acid receptors. This indicated that factor(s) other than S221P mutation in the hemagglutinin are probably involved in determining receptor specificity of H5N1 viruses. This is the first report of receptor specificity and erythrocyte binding preferences of AI viruses from India. [ABSTRACT FROM AUTHOR]

Introduction: More than 70 outbreaks of the highly pathogenic avian influenza (HPAI) H5N1 have been reported in poultry in the western and north-eastern parts of India. Therefore, in view of the recent HPAI H5N1 outbreaks in poultry, active AI surveillance encompassing wild, resident, migratory birds and poultry was undertaken during 2009-2011 in the State of West Bengal. Methods: A total of 5722 samples were collected from West Bengal; 3522 samples (2906 fecal droppings + 616 other environmental samples) were from migratory birds and 2200 samples [1604 tracheal, cloacal swabs, environmental samples, tissue samples + 596 blood (serum)] were from domestic ducks and poultry. All tracheal, cloacal and environmental samples were processed for virus isolation. Virus isolates were detected using hemagglutination assay and identified using hemagglutination inhibition (HI) and reverse transcriptase polymerase chain reaction (RT-PCR) assays. Sequencing and phylogenetic analysis of partial region of the hemagglutinin and neuraminidase genes was done. Intravenous pathogenicity index assays were performed in chickens to assess pathogenicity of AI virus isolates. Serum samples were tested for detection of antibodies against AI viruses using HI assay. Results: A total of 57 AI H9N2, 15 AI H4N6 and 15 Newcastle Disease (NDV) viruses were isolated from chickens, from both backyard and wet poultry markets; AI H4N6 viruses were isolated from backyard chickens and domestic ducks. Characterization of AI H9N2 and H4N6 viruses revealed that they were of low pathogenicity. Domestic ducks were positive for antibodies against H5 and H7 viruses while chickens were positive for presence of antibodies against AI H9N2 and NDV. Conclusions: In the current scenario of HPAI H5N1 outbreaks in West Bengal, this report shows presence of low pathogenic AI H9N2 and H4N6 viruses in chickens and domestic ducks during the period 2009-2011. This is the first report of isolation of H4N6 from India. Antibodies against AI H5 and H7 in ducks highlight the probable role of domestic ducks in the transmission of AI viruses. Human infections of H9N2 have been reported from China and Hong Kong. This necessitates implementation of prevention and control measures to limit the spread of AI viruses. [ABSTRACT FROM AUTHOR]

Background & objectives: An outbreak of influenza was investigated between June 24 and July 30, 2009 in a residential school at Panchgani, Maharashtra, India. The objectives were to determine the aetiology, study the clinical features in the affected individuals and, important epidemiological and environmental factors. The nature of public health response and effectiveness of the control measures were also evaluated. Methods: Real time reverse transcriptase polymerase chain reaction was performed on throat swabs collected from 82 suspected cases to determine the influenza types (A or B) and sub-types [pandemic (H1N1) 2009, as well as seasonal influenza H1N1, H3N2]. Haemagglutination inhibition assay was performed on serum samples collected from entire school population (N = 415) to detect antibodies for pandemic (H1N1) 2009, seasonal H1N1, H3N2 and influenza B/Yamagata and B/Victoria lineages. Antibody titres ≥ 10 for pandemic (H1N1) 2009 and ≥ 20 for seasonal influenza A and B were considered as positive for these viruses. Results: Clinical attack rate for influenza-like illness was 71.1 per cent (295/415). The attack rate for pandemic (H1N1) 2009 cases was 42.4 per cent (176/415). Throat swabs were collected from 82 cases, of which pandemic (H1N1) 2009 virus was detected in 15 (18.3%), influenza type A in (6) 7.4 per cent and influenza type B only in one case. A serosurvey carried out showed haemagglutination inhibition antibodies to pandemic (H1N1) 2009 in 52 per cent (216) subjects in the school and 9 per cent (22) in the community. Interpretation & conclusion: Our findings confirmed an outbreak of pandemic (H1N1) 2009 due to local transmission among students in a residential school at Panchgani, Maharashtra, India. [ABSTRACT FROM AUTHOR]

Background: In India, Pune was one of the badly affected cities during the influenza A (H1N1) 2009 pandemic. We undertook serosurveys among the risk groups and general population to determine the extent of pandemic influenza A (H1N1) 2009 virus infections. Methods: Pre-pandemic sera from the archives, collected during January 2005 to March 2009, were assayed for the determination of baseline seropositivity. Serosurveys were undertaken among the risk groups such as hospital staff, general practitioners, school children and staff and general population between 15th August and 11th December 2009. In addition, the PCR-confirmed pandemic influenza A (H1N1) 2009 cases and their household contacts were also investigated. Haemagglutination-inhibition (HI) assays were performed using turkey red blood cells employing standard protocols. A titre of ≥1:40 was considered seropositive. Results: Only 2 (0.9%) of the 222 pre-pandemic sera were positive. The test-retest reliability of HI assay in 101 sera was 98% for pandemic H1N1, 93.1% for seasonal H1N1 and 94% for seasonal H3N2. The sera from 48 (73.8%) of 65 PCR-confirmed pandemic H1N1 cases in 2009 were positive. Seropositivity among general practitioners increased from 4.9% in August to 9.4% in November and 15.1% in December. Among hospital staff, seropositivity increased from 2.8% in August to 12% in November. Seropositivity among the schools increased from 2% in August to 10.7% in September. The seropositivity among students (25%) was higher than the school staff in September. In a general population survey in October 2009, seropositivity was higher in children (9.1%) than adults (4.3%). The 15-19 years age group showed the highest seropositivity of 20.3%. Seropositivity of seasonal H3N2 (55.3%) and H1N1 (26.4%) was higher than pandemic H1N1 (5.7%) (n = 2328). In households of 74 PCR-confirmed pandemic H1N1 cases, 25.6% contacts were seropositive. Almost 90% pandemic H1N1 infections were asymptomatic or mild. Considering a titre cut off of 1:10, seropositivity was 1.5-3 times as compared to 1:40. Conclusions: Pandemic influenza A (H1N1) 2009 virus infection was widespread in all sections of community. However, infection was significantly higher in school children and general practitioners. Hospital staff had the lowest infections suggesting the efficacy of infection-control measures. [ABSTRACT FROM AUTHOR]

• First report of use of fixed & stored tRBCs for HA & HI assays of influenza viruses. • No significant difference between mean HA & HI titers using fresh & fixed tRBCs. • HA & HI titers using fixed tRBCs before and after storing at -80 ºC were equivalent. • Application as a ready-to-use reagent for laboratory diagnosis of influenza viruses. Hemagglutination (HA) and hemagglutination inhibition (HI) assays are conventionally used for the detection and identification of influenza viruses, using red blood cells (RBCs) from mammalian and avian sources. However, there could be limitations for availability of fresh RBCs due to situations such as pandemics, public health emergencies, outbreaks in avian species, lack of animal facilities, animal ethics concerns; or resource-constrained laboratories, and laboratories which do not carry out HA and HI assays routinely. Turkey RBCs (tRBCs) are widely used for HA and HI assays of influenza viruses. The present study explored the possibility of the use of glutaraldehyde-fixed tRBCs, which could be stored at -80 ºC and readily used for HA and HI assays. A total of nine subtypes of human and avian influenza viruses, A H1N1, H3N2, H4N6, H5N1, H6N1, H7N9, H9N2, H11N1 and type B, were used in the study. Turkey RBCs were fixed with glutaraldehyde. The HA and HI assays were performed three times by two different operators using fresh and glutaraldehyde fixed tRBCs. The significance of difference in HA and HI titers between fixed and fresh RBCs was compared using 't-test'. The performance of fixed RBCs was evaluated before and after storing at -80 ºC for three weeks. There was no significant difference (p > 0.05) between mean HA and HI titers using fresh and glutaraldehyde-fixed turkey RBCs. In addition, the HA and HI titers using fixed tRBCs before and after storing at -80 ºC were equivalent, indicating suitability of the fixed and stored RBCs. This is the first report of the use of fixed and stored tRBCs for HA and HI assays of influenza viruses, highlighting their applicability as a ready-to-use reagent for laboratory diagnosis of influenza. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented which discusses the seroprevalence of H1N1 pandemic influenza in 2011 and seasonal influenza viruses among pigs in Maharashtra and Gujarat State in India.

Antiviral susceptibility screening of avian influenza (AI) H9N2 viruses is crucial considering their role at the animal-human interface and potential to cause human infections. The Matrix 2 (M2) inhibitors (amantadine and rimantadine) have been used for prophylaxis and treatment of influenza A virus infections, however, resistance to these drugs has been widely reported. Information about amantadine susceptibility of H9N2 viruses from India is scanty. Matrix genes of 48H9N2 viruses isolated from India during 2009–2017 were sequenced and M2 trans-membrane region sequences were screened for mutations which are known to confer resistance to amantadine namely, L26F, V27A, A30 T/V, S31N and G34E. All the viruses isolated during the year 2009 were sensitive to amantadine. However, resistance started to appear since the year 2010 and all the viruses isolated from the year 2015 onwards showed presence of molecular markers conferring resistance to amantadine. Majority of the resistant viruses exhibited S31 N mutation. Four isolates showed presence of V27A + S31 N dual mutations. Comparison of the M2 sequences from other Asian countries showed different patterns of amantadine resistance wherein phylogenetic analysis of the M genes of the strains from Pakistan formed a separate cluster. In conclusion, the present study reports prevalence and gradual increase of amantadine resistance among AI H9N2 viruses in India, emphasizing the importance of the antiviral surveillance. • Amantadine resistance mutations in avian influenza H9N2 reported worldwide. • Reports on H9N2 amantadine susceptibility from India are scanty. • H9N2 isolates from India from 2009 to 2017 were screened for resistance markers. • All viruses from the year 2015 onwards showed amantadine resistance markers. • Highlights importance of antiviral surveillance of avian influenza. [ABSTRACT FROM AUTHOR]

India has reported highly pathogenic avian influenza (HPAI) H5N1 virus outbreaks since 2006, with the first human case reported in 2021. These included viruses belonging to the clades 2.2, 2.2.2, 2.2.2.1, 2.3.2.1a, and 2.3.2.1c. There are currently no data on the gene pool of HPAI H5N1 viruses in India. Molecular clock and phylogeography analysis of the HA and NA genes; and phylogenetic analysis of the internal genes of H5N1 viruses from India were carried out. Sequences reported from 2006 to 2015; and sequences from 2021 that were available in online databases were used in the analysis. Five separate introductions of H5N1 viruses into India were observed, via Indonesia or Korea (2002), Bangladesh (2009), Bhutan (2010), and China (2013, 2018) (clades 2.2, 2.2.2, 2.2.2.1, 2.3.2.1a, 2.3.2.1c, and 2.3.4.4b). Phylogenetic analysis revealed eight reassortant genotypes. The H5N1 virus isolated from the human case showed a unique reassortant genotype. Amino acid markers associated with adaptation to mammals were also present. This is the first report of the spatio-temporal origins and gene pool analysis of H5N1 viruses from India, highlighting the need for increased molecular surveillance. [ABSTRACT FROM AUTHOR]

Introduction Following the withdrawal of Sabin type 2 from trivalent oral poliovirus vaccine (tOPV) in 2016, the introduction of ≥1 dose of inactivated poliovirus vaccine (IPV) in routine immunization was recommended, either as 1 full dose (0.5mL, intramuscular) or 2 fractional doses of IPV (fIPV—0.1mL, intradermal). India opted for fIPV. We conducted a comparative assessment of IPV and fIPV. Methods This was a 4-arm, open-label, multicenter, randomized controlled trial. Infants were enrolled and vaccines administered according to the study design, and the blood was drawn at age 6, 14, and 18 weeks for neutralization testing against all 3 poliovirus types. Results Study enrolled 799 infants. The seroconversion against type 2 poliovirus with 2 fIPV doses was 85.8% (95% confidence interval [CI]: 80.1%-90.0%) when administered at age 6 and 14 weeks, 77.0% (95% CI: 70.5-82.5) when given at age 10 and 14 weeks, compared to 67.9% (95% CI: 60.4-74.6) following 1 full-dose IPV at age 14 weeks. Conclusion The study demonstrated the superiority of 2 fIPV doses over 1 full-dose IPV in India. Doses of fIPV given at 6 and 14 weeks were more immunogenic than those given at 10 and 14 weeks. Clinical Trial Registry of India (CTRI). Clinical trial registration number was CTRI/2017/02/007793. [ABSTRACT FROM AUTHOR]

Surveillance and detection of polioviruses (PV) remain crucial to monitoring eradication progress. Intratypic differentiation (ITD) using the real-time RT-PCR kit is key to the surveillance workflow, where viruses are screened after cell culture isolation before a subset are verified by sequencing. The ITD kit is a series of real-time RT-PCR assays that screens cytopathic effect (CPE)-positive cell cultures using the standard WHO method for virus isolation. Because ITD screening is a critical procedure in the poliovirus identification workflow, validation of performance of real-time PCR platforms is a core requirement for the detection of poliovirus using the ITD kit. In addition, the continual update and improvement of the ITD assays to simplify interpretation in all platforms is necessary to ensure that all real-time machines are capable of detecting positive real-time signals. Four platforms (ABI7500 real-time systems, Bio-Rad CFX96, Stratagene MX3000P, and the Qiagen Rotor-Gene Q) were validated with the ITD kit and a redesigned poliovirus probe. The poliovirus probe in the real-time RT-PCR pan-poliovirus (PanPV) assay was re-designed with a double-quencher (Zen™) to reduce background fluorescence and potential false negatives. The updated PanPV probe was evaluated with a panel consisting of 184 polioviruses and non-polio enteroviruses. To further validate the updated PanPV probe, the new assay was pilot tested in five Global Polio Laboratory Network (GPLN) laboratories (Madagascar, India, Philippines, Pakistan, and Democratic Republic of Congo). The updated PanPV probe performance was shown to reduce background fluorescence and decrease the number of false positives compared to the standard PanPV probe. [ABSTRACT FROM AUTHOR]

Background: In January 2011, human cases with hemorrhagic manifestations in the hospital staff were reported from a tertiary care hospital in Ahmadabad, India. This paper reports a detailed epidemiological investigation of nosocomial outbreak from the affected area of Ahmadabad, Gujarat, India. Principal Findings: Samples from 3 suspected cases, 83 contacts, Hyalomma ticks and livestock were screened for Crimean-Congo hemorrhagic fever (CCHF) virus by qRT-PCR of which samples of two medical professionals (case C and E) and the husband of the index case (case D) were positive for CCHFV. The sensitivity and specificity of indigenous developed IgM ELISA to screen CCHFV specific antibodies in human serum was 75.0% and 97.5% respectively as compared to commercial kit. About 17.0% domestic animals from Kolat, Ahmadabad were positive for IgG antibodies while only two cattle and a goat showed positivity by qRT-PCR. Surprisingly, 43.0% domestic animals (Buffalo, cattle, sheep and goat) showed IgG antibodies in the adjoining village Jivanpara but only one of the buffalo was positive for CCHFV. The Hyalomma anatolicum anatolicum ticks were positive in PCR and virus isolation. CCHFV was isolated from the blood sample of case C, E in Vero E-6 cells and Swiss albino mice. In partial nucleocapsid gene phylogeny from CCHFV positive human samples of the years 2010 and 2011, livestock and ticks showed this virus was similar to Tajikistan (strain TAJ/H08966), which belongs in the Asian/middle east genetic lineage IV. Conclusions: The likely source of CCHFV was identified as virus infected Hyalomma ticks and livestock at the rural village residence of the primary case (case A). In addition, retrospective sample analysis revealed the existence of CCHFV in Gujarat and Rajasthan states before this outbreak. An indigenous developed IgM ELISA kit will be of great use for screening this virus in India. Author Summary: A nosocomial outbreak of CCHFV occurred in January 2011, in a tertiary care hospital in Ahmadabad, Gujarat State in western India. Out of a total five cases reported, contact transmission occurred to three treating medical professionals, all of whom succumbed to the disease. The only survivor was the husband of the index case. These results highlight the importance of considering CCHFV as a potential aetiology for Hemorrhagic fever (HF) cases in India. This also underlines the need for strict barrier nursing and patient isolation while managing these patients. During the investigation presence of CCHFV RNA in Hyalomma anatolicum ticks and livestock were detected in the village from where the primary case (case A) was reported. Further retrospective investigation confirmed two CCHF human cases in Rajkot village 20 kilometres to the west of Ahmadabad in 2010, and CCHFV presence in the livestock 200 kilometres to the north in the neighbouring State Rajasthan. This report shows the presence of CCHFV in human, ticks and animals in Gujarat, India. The fact of concern is the spread of this disease from one state to another due to trading of livestock. [ABSTRACT FROM AUTHOR]

Background: In January 2011, human cases with hemorrhagic manifestations in the hospital staff were reported from a tertiary care hospital in Ahmadabad, India. This paper reports a detailed epidemiological investigation of nosocomial outbreak from the affected area of Ahmadabad, Gujarat, India. Principal Findings: Samples from 3 suspected cases, 83 contacts, Hyalomma ticks and livestock were screened for Crimean- Congo hemorrhagic fever (CCHF) virus by qRT-PCR of which samples of two medical professionals (case C and E) and the husband of the index case (case D) were positive for CCHFV. The sensitivity and specificity of indigenous developed IgM ELISA to screen CCHFV specific antibodies in human serum was 75.0% and 97.5% respectively as compared to commercial kit. About 17.0% domestic animals from Kolat, Ahmadabad were positive for IgG antibodies while only two cattle and a goat showed positivity by qRT-PCR. Surprisingly, 43.0% domestic animals (Buffalo, cattle, sheep and goat) showed IgG antibodies in the adjoining village Jivanpara but only one of the buffalo was positive for CCHFV. The Hyalomma anatolicum anatolicum ticks were positive in PCR and virus isolation. CCHFV was isolated from the blood sample of case C, E in Vero E-6 cells and Swiss albino mice. In partial nucleocapsid gene phylogeny from CCHFV positive human samples of the years 2010 and 2011, livestock and ticks showed this virus was similar to Tajikistan (strain TAJ/H08966), which belongs in the Asian/middle east genetic lineage IV. Conclusions: The likely source of CCHFV was identified as virus infected Hyalomma ticks and livestock at the rural village residence of the primary case (case A). In addition, retrospective sample analysis revealed the existence of CCHFV in Gujarat and Rajasthan states before this outbreak. An indigenous developed IgM ELISA kit will be of great use for screening this virus in India. [ABSTRACT FROM AUTHOR]

Background: The world has recently overcome the first influenza pandemic of the 21st century caused by a novel H1N1 virus (pH1N1) which is a triple reassortant comprising genes derived from avian, human, and swine influenza viruses and antigenically quite different from seasonal H1N1 strains. Although the case fatality rates have decreased in many developed countries, the situation is still alarming in many developing countries including India where considerable numbers of new cases are appearing everyday. There is still a high morbidity and mortality of susceptible adult as well as young population without having underlying health issues due to the influenza infection. Results: To achieve a better understanding of the risk posed by the pH1N1 and to understand its pathogenicity, we studied the host gene expression response to Indian isolate of pH1N1 infection and compared it with seasonal H1N1 infection. The response was studied at four different time points (4, 8, 16 and 24 h) post infection (hpi) in A549 cells using microarray platform. We found that pH1N1 induces immune response earlier than seasonal H1N1 viruses, but at the later stages of infection there is a suppression of host immune responses. The infection with pH1N1 resulted in considerable decrease in the expression of cytokine and other immune genes namely IL8, STAT1, B2 M and IL4 compared to seasonal H1N1. Conclusion: We propose that the inability to induce strong innate immune response could be a reason for the high transmissibility, pathogenicity and mortality caused by pH1N1 virus. [ABSTRACT FROM AUTHOR]

Background: To understand the molecular mechanism of host responses to highly pathogenic avian influenza virus infection and to get an insight into the means through which virus overcomes host defense mechanism, we studied global gene expression response of human lung carcinoma cells (A549) at early and late stages of infection with highly pathogenic avian Influenza A (H5N1) virus and compared it with a reverse genetics modified recombinant A (H5N1) vaccine virus using microarray platform. Results: The response was studied at time points 4, 8, 16 and 24 hours post infection (hpi). Gene ontology analysis revealed that the genes affected by both the viruses were qualitatively similar but quantitatively different. Significant differences were observed in the expression of genes involved in apoptosis and immune responses, specifically at 16 hpi. Conclusion: We conclude that subtle differences in the ability to induce specific host responses like apoptotic mechanism and immune responses make the highly pathogenic viruses more virulent. [ABSTRACT FROM AUTHOR]

Background: A focal H5N1 outbreak in poultry was reported from Manipur, a north-eastern state, of India, in 2007. The aim of this study was to genetically characterize the Manipur isolate to understand the relationship with other H5N1 isolates and to trace the possible source of introduction of the virus into the country. Results: Characterization of the complete genome revealed that the virus belonged to clade 2.2. It was distinctly different from viruses of the three EMA sublineages of clade 2.2 but related to isolates from wild migratory waterfowl from Russia, China and Mongolia. The HA gene, had the cleavage site GERRRRKR, earlier reported in whooper swan isolates from Mongolia in 2005. A stop codon at position 29 in the PB1-F2 protein could have implications on the replication efficiency. The acquisition of polymorphisms as seen in recent isolates of 2005-07 from distinct geographical regions suggests the possibility of transportation of H5N1 viruses through migratory birds. Conclusion: Considering that all eight genes of the earlier Indian isolates belonged to the EMA3 sublineage and similar strains have not been reported from neighbouring countries of the subcontinent, it appears that the virus may have been introduced independently. [ABSTRACT FROM AUTHOR]

• IAV blocks autophagy and induces apoptosis. • Vitamin D restores autophagic flux. • Vitamin D reduces IAV induced apoptosis. Vitamin D3/Calcitriol supplementation in humans is associated with reduced incidence and severity during influenza A virus (IAV) infection. Apoptosis in response to IAV infection is a major contributor to host cell death and tissue damage; however, its modulation by Vitamin D3 remains unclear. In this study, we demonstrate the efficacy of Vitamin D3 in preventing apoptosis induction by pandemic influenza A (H1N1)pdm09 virus in human alveolar cells (A549). Human alveolar epithelial cell line A549 was used to assess the cytotoxic effects of IAV infection. Immunoblotting and fluorescence microscopy were used to study apoptosis and autophagy. The results of the present study demonstrate that IAV induces apoptosis by subversion of host autophagy via down-regulating components of autophagic machinery involved in autophagosome-lysosome fusion and lysosomal activity. Vitamin D3 restores the autophagic flux inhibited by IAV by upregulating the expression of Syntaxin-17 (STX17) and V-type proton ATPase subunit (ATP6V0A2) thereby causing a concomitant decrease in cellular apoptosis via a Vitamin D3 receptor (VDR) dependent mechanism. The present study suggests that Vitamin D3 is a potentially useful agent for limiting IAV-induced cellular injury via its pro-autophagic action. [ABSTRACT FROM AUTHOR]