Diagnostic validation study of rapid urinary tract infection diagnosis kit at peripheral health facilities of West Bengal, India.

Patients reporting to the outpatient departments of peripheral health care settings in India with symptoms of urinary tract infection (UTI) receive one or the other antibiotic before culture confirmation and out of the total culture confirmed UTI cases, in less than one third cases the prescribed antibiotics matches to the antibiotic sensitivity test result. Hence, in this study, an indigenous point-of-care (POCT) rapid diagnostic kit (Rapidogram) for UTI was validated against conventional urine culture and sensitivity to understand its possible applicability at peripheral health care settings. This cross-sectional study was conducted during November 2021 to June 2022 in OPDs of two peripheral hospitals. A sample size of 300 was calculated using prevalence of urinary tract infection (UTI) as 33% for sensitivity and specificity using Buderer's formula. Urine specimens were collected following standard aseptic procedures from the recruited suspected UTI cases and transferred to laboratory maintaining the cold chain. The validation work up was done in two sections: lab validation and field validation. Out of 300 urine samples, 29 were found positive for the growth of UTI pathogen by both methods and 267 were found negative by both methods. Thus, the kit shows very high specificity (99.6%; 97.9-99.9%) and considerably high sensitivity (90.6%; 74.9-98.0%). We also observed higher PPV, NPV, test accuracy (> 96%). Diagnostic Odds Ratio and Youden index were respectively 2581 and 0.89. Clinical data showed that 44% of the suspected UTI cases were prescribed at least one antibiotic before urine test. Mostly they received Norfloxacin whereas the mostly identified organism E.coli was sensitive to Nitrofurantoin. In the context of absence of microbiology facility at peripheral setting and rampant empirical use of antibiotics in UTI, this highly specific and sensitive POCT for UTI may be used as it not only identifies the organism, also shows the antibiotic sensitivity pattern.

Genomic Expedition: Deciphering Human Adenovirus Strains from the 2023 Outbreak in West Bengal, India: Insights into Viral Evolution and Molecular Epidemiology.

Understanding the genetic dynamics of circulating Human Adenovirus (HAdV) types is pivotal for effectively managing outbreaks and devising targeted interventions. During the West Bengal outbreak of 2022-2023, an investigation into the genetic characteristics and outbreak potential of circulating HAdV types was conducted. Twenty-four randomly selected samples underwent whole-genome sequencing. Analysis revealed a prevalent recombinant strain, merging type 3 and type 7 of human mastadenovirus B1 (HAd-B1) species, indicating the emergence of recent strains of species B in India. Furthermore, distinctions in VA-RNAs and the E3 region suggested that current circulating strains of human mastadenovirus B1 (HAd-B1) possess the capacity to evade host immunity, endure longer within hosts, and cause severe respiratory infections. This study underscores the significance of evaluating the complete genome sequence of HAdV isolates to glean insights into their outbreak potential and the severity of associated illnesses.

Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis.

Background: Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods: In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings: Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation: The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

Molecular epidemiology of circulating human adenoviruses among acute respiratory infection patients seeking healthcare facilities in West Bengal, India.

Human adenovirus (HAdV) causes acute respiratory infections leading to mortality in children. This study analyzes the circulating respiratory HAdV genotypes in West Bengal, India during 2018-2022 among symptomatic patients. The overall positivity rate was 6.8%, out of which 26.4% were co-infected with other respiratory viruses. Children aged 2 to 5 years were mostly infected. Phylogenetic analysis revealed that the recombinant HAdV-B type 7/3, which has remarkable outbreak potential, predominantly circulated in this region followed by the non-recombinant HAdV-B type 3/3. Moreover, the amino acid sequences encoded by both the hexon and fiber genes of these two circulating strains possessed a few mutations that mostly diverged from the prototype strain, although the divergence was less pronounced in case of the amino acids encoded by the fiber gene of HAdV-B type 3/3. Overall, the results underscore the need for continuous surveillance of respiratory HAdV types to combat future possible epidemics.

Predicting Future Pandemics and Formulating Prevention Strategies: The Role of ChatGPT.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 and its subsequent worldwide spread has emphasized the urgent need for better approaches for predicting and managing infectious disease outbreaks. One potential instrument in this effort is artificial intelligence (AI), and in specific, language models like ChatGPT (Chat Generative Pre-trained Transformer). In the present study, to explore how ChatGPT could predict future pandemics and give suggestions about the prevention strategy, our research team chatted with ChatGPT with several questions on July 12, 2023. Based on our conversation, we can conclude that AI is not a substitute for human expertise, but an adjunct to support early prediction, prevention, and management of future pandemics.

The impact of the COVID-19 pandemic on health-care delivery system for other diseases and antimicrobial resistance threat in India.

India's health-care delivery is challenged with different inequalities and theelivery is challenged with different inequalities and the dual burden of communicable and noncommunicable diseases. Lockdown posed negative effects on the growth and economy of the country; simultaneously, some positive effects, like increased health consciousness and adoption of hygienic practices, were also there. Health-care delivery system faced tremendous challenges in diagnostics, therapeutics, infrastructure for inpatient care, and protection of health-care manpower. During this period, people chose to self medicate which in turn increased the threat of emergence of antimicrobial resistance. Due to shifting priority to COVID from other diseases, resources were shifted to COVID, affecting the management of other acute and chronic diseases. The launching of COVID-19 vaccination campaign showed some hope. However, despite the vaccination drive, strengthening infrastructure, and surveillance system, the devastating second wave could not be avoided due to the conglomeration of the crowd for pilgrimage, election campaign, and tourism in an unrestricted manner. It may be concluded that the fourth wave may be short lasting due to increased herd immunity.

Upsurge in hospitalization of pediatric patients with severe acute respiratory infections in Kolkata and surrounding districts caused by recombinant human respiratory adenovirus type B 7/3.

Globally, different genotypes of human adenoviruses are associated with outbreaks of acute respiratory infection (ARI) though such evidence is lacking from India. In the present study, we report a sudden increase in the positivity of respiratory adenovirus among hospitalized children with ARI from Kolkata and the surrounding districts of West Bengal, India, from December 2022 to date. A sharp rise in the positivity rate of respiratory adenovirus was found which ranged from 22.1% in early December 2022 to 52.6% in mid-March 2023. The overall positivity was 40.4% during the period and children in the 2 to <5 years (51.0%) age group were mostly affected. Single infection with adenovirus was found in 72.4% of cases while co-infection with rhinovirus was the maximum (9.4%). Around 97.5% of positive cases required hospitalization. Cough, breathlessness, and wheeze were the most common clinical features among positive patients. Phylogenetic analysis of the hexon and fiber gene of all the sequenced strains revealed HAdV-B 7/3 recombination with more than 99% homology within themselves. This report of a respiratory adenovirus outbreak in West Bengal, India causing severe illness in the pediatric population underscores the need for regular monitoring of the circulating strains.

Accumulation of Biological and Behavioral Data of Female Sex Workers Using Respondent-Driven Sampling: Protocol for a Systematic Review.

BACKGROUND: Respondent-driven sampling (RDS) is a nonprobability sampling technique that allows the extrapolation of its outcome to the target population. This approach is typically used to overcome the difficulties in studying hidden or difficult-to-reach groups. OBJECTIVE: The purpose of this protocol is to generate a systematic review on the accumulation of biological and behavioral data of female sex workers (FSWs) through different surveys that use the RDS method from around the world in the near future. The future systematic review will discuss the initiation, actualization, and problems of RDS during the accumulation of biological and behavioral data of FSWs through surveys from around the world. METHODS: The behavior and biological data of FSWs will be extracted from peer-reviewed studies published between 2010 and 2022 and that are acquired through RDS. Using PubMed, Google Scholar, the Cochrane database, Scopus, Science Direct, and the Global Health network, all papers that are available will be obtained using the search phrases "respondent-driven" and "Female Sex Workers" OR "FSW" OR "sex workers" OR "SW." According to STROBE-RDS (Strengthening the Reporting of Observational Studies in Epidemiology for Respondent-Driven Sampling) criteria, the data will be retrieved through a data extraction form and will be organized using World Health Organization classifications of areas. The Newcastle-Ottawa Quality Assessment Scale will be used to measure bias risk and overall study quality. RESULTS: The future systematic review that will be generated from this protocol will offer evidence for or against the claim that using the RDS technique to recruit participants from "hidden" or "hard-to-reach" populations is the best strategy. The results will be disseminated through a peer-reviewed publication. Data collection started on April 1, 2023, and the systematic review is expected to be published by December 15, 2023. CONCLUSIONS: A minimum set of parameters for specific methodological, analytical, and testing procedures, including RDS methods to evaluate the overall quality of any RDS survey, will be provided by the future systematic review, in accordance with this protocol, to assist researchers, policy makers, and service providers in improving RDS methods for the surveillance of any key population. TRIAL REGISTRATION: PROSPERO CRD42022346470; https://tinyurl.com/54xe2s3k. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/43722.

Congenital rubella syndrome surveillance in India, 2016-21: Analysis of five years surveillance data.

Background: In India, facility-based surveillance for congenital rubella syndrome (CRS) was initiated in 2016 to estimate the burden and monitor the progress made in rubella control. We analyzed the surveillance data for 2016-2021 from 14 sentinel sites to describe the epidemiology of CRS. Method: We analyzed the surveillance data to describe the distribution of suspected and laboratory confirmed CRS patients by time, place and person characteristics. We compared clinical signs of laboratory confirmed CRS and discarded case-patients to find independent predictors of CRS using logistic regression analysis and developed a risk prediction model. Results: During 2016-21, surveillance sites enrolled 3940 suspected CRS case-patients (Age 3.5 months, SD: 3.5). About one-fifth (n = 813, 20.6%) were enrolled during newborn examination. Of the suspected CRS patients, 493 (12.5%) had laboratory evidence of rubella infection. The proportion of laboratory confirmed CRS cases declined from 26% in 2017 to 8.7% in 2021. Laboratory confirmed patients had higher odds of having hearing impairment (Odds ratio [OR] = 9.5, 95% confidence interval [CI]: 5.6-16.2), cataract (OR = 7.8, 95% CI: 5.4-11.2), pigmentary retinopathy (OR = 6.7, 95 CI: 3.3-13.6), structural heart defect with hearing impairment (OR = 3.8, 95% CI: 1.2-12.2) and glaucoma (OR = 3.1, 95% CI: 1.2-8.1). Nomogram, along with a web version, was developed. Conclusions: Rubella continues to be a significant public health issue in India. The declining trend of test positivity among suspected CRS case-patients needs to be monitored through continued surveillance in these sentinel sites.

Sexually transmitted infections among key populations in India: A protocol for systematic review.

BACKGROUND: Sexually transmitted infections (STIs) are one of the leading causes of health, and economic burdens in the developing world, leading to considerable morbidity, mortality, and stigma. The incidence and prevalence of the four curable STIs viz. syphilis, gonorrhoea, chlamydia, and trichomoniasis vary remarkably across different geographical locations. In India, the prevalence of four curable STI among general populations is in between 0 to 3.9 percent. However, it is assumed that STI prevalence is much higher among subpopulations practicing high-risk behaviour. Like men who have sex with men (MSM), transgender (TG), injecting drug users (IDU), and female sex workers (FSW). OBJECTIVES: In the present circumstances, a systematic review is necessary to integrate the available data from previously published peer-reviewed articles and published reports from several competent authorities to provide the prevalence and geographical distribution of the four curable STIs among the key population of India. METHODS: All available articles will be retrieved from PubMed, Google Scholar, Cochrane database, Scopus, Science Direct, and the Global Health network using the appropriate search terms. The data will be extracted through data extraction form as per PICOS (population, intervention, comparison, outcome, study design) framework. Risk of bias and quality assessment will be performed according to the situation with the help of available conventional protocol. DISCUSSION: The future systematic review, generated from the present protocol, may provide evidence of the prevalence and geographical distribution of the four curable STIs among the key population of India. We hope that the findings of the future systematic review will strengthen the existing surveillance system in India, to determine the above-mention STIs prevalence among key populations in India. Protocol registration number: International Prospective Register for Systematic Reviews (PROSPERO) number CRD42022346470.

Emergence of a unique SARS-CoV-2 Delta sub-cluster harboring a constellation of co-appearing non-Spike mutations.

Accumulation of diverse mutations across the structural and nonstructural genes is leading to rapid evolution of SARS-CoV-2, altering its pathogenicity. We performed whole genome sequencing of 239 SARS-CoV-2 RNA samples collected from both adult and pediatric patients across eastern India (West Bengal), during the second pandemic wave in India (April-May 2021). In addition to several common spike mutations within the Delta variant, a unique constellation of eight co-appearing non-Spike mutations was identified, which revealed a high degree of positive mutual correlation. Our results also demonstrated the dynamics of SARS-CoV-2 variants among unvaccinated pediatric patients. 41.4% of our studied Delta strains harbored this signature set of eight co-appearing non-Spike mutations and phylogenetically out-clustered other Delta sub-lineages like 21J, 21A, or 21I. This is the first report from eastern India that portrayed a landscape of co-appearing mutations in the non-Spike proteins, which might have led to the evolution of a distinct Delta subcluster. Accumulation of such mutations in SARS-CoV-2 may lead to the emergence of "vaccine-evading variants." Hence, monitoring of such non-Spike mutations will be significant in the formulation of any future vaccines against those SARS-CoV-2 variants that might evade the current vaccine-induced immunity, among both the pediatric and adult populations.

Vertical Transmission Rate of Human Immunodeficiency Virus Exposed Twin Pregnancies and Associated Factors in West Bengal, India: a Retrospective Cohort Study.

Twin pregnancies are often associated with adverse obstetric outcomes. The mother-to-child transmission of the human immunodeficiency virus (HIV) in twin pregnancies has been less explored. Therefore, the present study aimed to determine the risk of vertical transmission of HIV in HIV-exposed twin pregnancies compared with that of singleton pregnancies and to explore the associated factors. We conducted a retrospective cohort study involving 348 HIV-exposed babies (58 twins and 290 singletons) through a systematic sampling from the program database of West Bengal, India, from April 2016 to March 2021. HIV vertical transmission rates were compared between single and twin live births. The effects of factors such as maternal age, timing of maternal HIV diagnosis, duration of antiretroviral treatment, mode of delivery, birth weight, and the sex of the baby were determined. The HIV transmission rate for twin pregnancies (15.5%) was significantly higher than that for single live births (5.5%) (adjusted odds ratio [OR] = 3.38 [1.17-9.69]). Among twin deliveries, maternal HIV diagnosis during the intrapartum and postpartum period was associated with HIV transmission (crude OR = 11.0, [2.2-54.9]). Perinatal HIV transmission is more common in twin pregnancies and is associated with the time of detection of maternal HIV. Therefore, early HIV detection and additional antiretroviral regimens should be considered for twin pregnancies.

Syndemic effect of COVID-19 outbreak on HIV care delivery around the globe: A systematic review using narrative synthesis.

Background: The burden of the COVID-19 pandemic on healthcare systems worldwide has been compromising the progress made in the fight against HIV. This paper aims to determine how the COVID-19 pandemic has impacted HIV comprehensive care service delivery globally as well as to consolidate the evidence and recommendations that may be useful in averting future crisis. Methods: This review adheres to PRISMA guidelines. PubMed, DOAJ, Science Direct and other sources like Google Scholar and citations from included studies were searched methodically to locate studies evaluating the effects of COVID on services for HIV care. The NIH and JBI quality assessment tools were used for the quality assessment of individual studies. Results: In the present review 31 eligible studies were included and the impact on HIV care cascade were summarised under six themes: Lab services, Treatment and allied services, Counselling services, Outreach services, Psycho-social impact and Implementation of sustainable strategies. The studies also presented many innovative alternatives which were lucidly highlighted in the present article. Conclusion: Current evidence depicts multiple factors are responsible for the interruption of HIV care service delivery during the pandemic, especially in low resources settings. The prospective, alternative solutions that have been used to circumvent the threat have also been addressed in this review, in addition to the negative aspects that have been observed. Transition with new innovative, sustainable care paradigms may prove to be the building blocks in removing HIV-AIDS as a public health threat. Registration: Open Science Framework (DOI: 10.17605/OSF.IO/74GHM).

Existing Policies/Guidelines on the Environmental Dimension of Antimicrobial Resistance in India: An Insight into the Key Facets through Review and SWOT Analysis.

BACKGROUND: Antimicrobial resistance (AMR) is a multidimensional phenomenon. The environment acts as a mixing pot of drug-resistant bacteria from many sources such as pharmaceutical, biomedical, veterinary, and agricultural sectors. In this study, we analysed the existing AMR-related policies/guidelines/legislations in India in the above domains and how the current practices are being guided by them. METHODS: We used a convergent parallel mix method design. Quantitative data were collected through a review of policies/guidelines/legislations in the said domains and analysed using the SWOT tool parallelly supported by key informant interviews of domain-specific stakeholders. RESULTS: Altogether, 19 existing AMR policies/guidelines/legislations were identified. The existence of few policies/guidelines in each domain indicated the evolving environment for policy interventions. However, the lack of capacity among farmers, inadequate provision for structured capacity building, high cost of alternatives to antimicrobials, and lack of provision of incentivisation in case of crop failure were identified as the major weaknesses prevalent across the domains. Opportunities for policy refinements/the introduction of new policies are ample. However, easy access to antimicrobials and injudicious use imposes threats to AMR containment in all sectors. CONCLUSIONS: Despite having a few policies for the containment of AMR, their implementation witnesses challenge due to the lack of collaborative approaches, the existence of policies disjointed from ground reality, infrastructural issues, and the lack of capacity and resources.

Development of lab score system for predicting COVID-19 patient severity: A retrospective analysis.

AIM: To develop an accurate lab score based on in-hospital patients' potent clinical and biological parameters for predicting COVID-19 patient severity during hospital admission. METHODS: To conduct this retrospective analysis, a derivation cohort was constructed by including all the available biological and clinical parameters of 355 COVID positive patients (recovered = 285, deceased = 70), collected in November 2020-September 2021. For identifying potent biomarkers and clinical parameters to determine hospital admitted patient severity or mortality, the receiver operating characteristics (ROC) curve and Fischer's test analysis was performed. Relative risk regression was estimated to develop laboratory scores for each clinical and routine biological parameter. Lab score was further validated by ROC curve analysis of the validation cohort which was built with 50 COVID positive hospital patients, admitted during October 2021-January 2022. RESULTS: Sensitivity vs. 1-specificity ROC curve (>0.7 Area Under the Curve, 95% CI) and univariate analysis (p<0.0001) of the derivation cohort identified five routine biomarkers (neutrophil, lymphocytes, neutrophil: lymphocytes, WBC count, ferritin) and three clinical parameters (patient age, pre-existing comorbidities, admitted with pneumonia) for the novel lab score development. Depending on the relative risk (p values and 95% CI) these clinical parameters were scored and attributed to both the derivation cohort (n = 355) and the validation cohort (n = 50). ROC curve analysis estimated the Area Under the Curve (AUC) of the derivation and validation cohort which was 0.914 (0.883-0.945, 95% CI) and 0.873 (0.778-0.969, 95% CI) respectively. CONCLUSION: The development of proper lab scores, based on patients' clinical parameters and routine biomarkers, would help physicians to predict patient risk at the time of their hospital admission and may improve hospital-admitted COVID-19 patients' survivability.

Epidemiological drivers of mother to child HIV transmission in West Bengal, India: A retrospective cohort study.

BACKGROUND: HIV transmission through vertical route can be reduced to a large extent with combination of medical interventions. Apart from maternal HIV status several other epidemiological attributes determine this transmission dynamics.Objective: The objective of this study was to identify various associated factors that determine and modify the risk of HIV transmission from a mother living with HIV to her child.Materials and method: A retrospective cohort-study was conducted with 518 HIV-positive pregnant women with delivering live babies between April 2016 - September 2018. The HIV status of the children was ascertained with polymerase chain reaction. A number of socio-demographic and medical attributes were compared between HIV-positive (41) and HIV-negative babies (477) using bivariate and multivariate methods to identify disease modifying factors. RESULTS: Maternal HIV detection during the postnatal period (AOR = 11.2; 5.2 - 23.8), low birth weight (AOR = 2.7; 1.2 - 5.9), and vaginal delivery (AOR = 2.8; 1.01 - 7.7) were significantly associated with vertical transmission of HIV. Lower duration of maternal antiretroviral treatment and higher maternal age (>25 years) were also associated in bivariate analysis. CONCLUSION: The battery of PPTCT (Prevention of Parent to Child Transmission) interventions should be tailored in such a way to address all the epidemiological attributes influencing vertical transmission.

A retrospective analysis of serological & molecular testing data on dengue fever in Kolkata & adjacent districts during 2016-2019.

Background & objectives: Regional Virus Research and Diagnostic Laboratory established at ICMR-National Institute of Cholera and Enteric Diseases (NICED) regularly receives samples for dengue screening and serotyping from patients of acute febrile illness (AFI) from Kolkata and adjacent districts. In this study, data over a three year period (August 2016-July 2019) was retrospectively analyzed to provide insight into the epidemiological trends of dengue fever in this region. Methods: Serological screening of dengue was performed by detection of NS1 antigen and/or immunoglobulin M (IgM) antibody. Dengue serotyping was done by conventional or real-time reverse transcriptase-PCR. The data were analyzed to describe the distribution of dengue with respect to age of patient, duration of fever on the day of blood collection and month of the year. Zip codes were used for spatial plotting. Results: Out of the 24,474 samples received from Kolkata and its adjacent districts (Hooghly, Howrah, North and South 24 Parganas), 38.3 per cent (95% confidence interval: 37.7-38.9%) samples were screened positive for dengue. The correlation between age and dengue positivity was found to be weak. A combination of dengue NS1 antigen and dengue IgM antibody detection may be a better option for detecting dengue positivity compared to a single test. Most AFI cases were tested from August to November during the study period, with maximum dengue positivity noted during September (45.9%). The predominant serotype of 2016, dengue virus serotype 1 (DENV-1), was almost entirely replaced by DENV-2 in 2017 and 2018. Interpretation & conclusions: Dengue continues to be an important cause of AFI in the region and round-the-year preventive measures are required for its control. Serotype switching is alarming and should be monitored routinely.

Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility.

Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a clade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutations reside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S2 domain, which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations of miRNA binding and structure were also predicted for these mutations. More importantly, the possible implications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of S protein have also been discussed. Results report for the first time a bird's eye view on the accumulation of mutations in SARS-CoV-2 genome in Eastern India.

Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis.

Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.

Molecular characterization of Influenza A pandemic H1N1 viruses circulating in eastern India during 2017-19: Antigenic diversity in comparison to the vaccine strains.

In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.