Publications by authors named "Nivedita Gupta"

139 Publications

Experiences of sharing results of community based serosurvey with participants in a district of Maharashtra, India.

PLoS One 2022 4;17(8):e0271920. Epub 2022 Aug 4.

ICMR- National Institute for Research in Reproductive and Child Health, Mumbai, India.

A growing number of organisations, including medical associations, recommend that research subjects should be given the option of being informed about the general outcome and results of the study. We recently completed a study involving nine serosurveys from 2018 to 2020 in five districts of India among three age groups (children 9 months to < 5 years; 5 to < 15 years of age, and women 15 to < 50 years of age before and after the measles and rubella (MR) vaccination campaigns). In Palghar district of Maharashtra all individuals in 30 selected clusters were enumerated, and 13 individuals per age group were randomly sampled. We established the procedures to return the results to the respondents for each stage of the survey. Of the 1,166 individuals selected for the measles and rubella serosurvey, 971 (83%) agreed to participate and were enrolled. Participants were informed that they will only be contacted if they test seronegative for measles and/or rubella antibodies. Overall, 140 individuals enrolled in the survey tested seronegative for IgG antibodies to measles and/or rubella viruses; were provided the reports and informed to seek medical advice. Upon follow up by phone, 10% (14) of the 140 participants reported to have been vaccinated. In this paper we discuss the procedures, experiences and considerations in returning results to participants in a community-based measles and rubella serosurvey. Although the lessons learned are specific to post measles-rubella vaccine campaign serosurvey in India, they might be helpful to those contemplating sharing results to participants of large scale survey settings.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0271920PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9352079PMC
August 2022

Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines.

Indian J Med Res 2022 01;155(1):105-122

Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India.

The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.
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http://dx.doi.org/10.4103/ijmr.ijmr_2544_21DOI Listing
January 2022

Inter-laboratory testing as a strategy for external quality assessment for qualitative detection of SARS-CoV-2 by real-time RT-PCR testing in India.

Indian J Med Res 2022 01;155(1):86-90

Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India.

To implement the strategy of test, track and treat to tackle the ongoing COVID-19 pandemic, the number of real-time RT-PCR-based testing laboratories was increased for diagnosis of SARS-CoV-2 in the country. To ensure reliability of the laboratory results, the Indian Council of Medical Research initiated external quality assessment (EQA) by deploying inter-laboratory quality control (ILQC) activity for these laboratories by nominating 34 quality control (QC) laboratories. This report presents the results of this activity for a period of September 2020 till November 2020. A total of 597 laboratories participated in this activity and 86 per cent of these scored ≥90 per cent concordance with QC laboratories. This ILQC activity showcased India's preparedness in quality diagnosis of SARS-CoV-2.
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http://dx.doi.org/10.4103/ijmr.ijmr_2433_21DOI Listing
January 2022

Development of the India COVID-19 vaccine tracker.

Indian J Med Res 2022 Jul 21. Epub 2022 Jul 21.

Indian Council of Medical Research, New Delhi, India.

COVID-19 was declared a pandemic by the World Health Organization (WHO) on March 11, 2020. Since then, efforts were initiated to develop safe and effective vaccines. Till date, 11 vaccines have been included in the WHO's emergency use list. The emergence and spread of variant strains of SARS-CoV-2 has altered the disease transmission dynamics, thus creating a need for continuously monitoring the real-world effectiveness of various vaccines and assessing their overall impact on disease control. To achieve this goal, the Indian Council of Medical Research (ICMR) along with the Ministry of Health and Family Welfare, Government of India, took the lead to develop the India COVID-19 Vaccination Tracker by synergizing three different public health databases: National COVID-19 testing database, CoWIN vaccination database and the COVID-19 India portal. A Vaccine Data Analytics Committee (VDAC) was constituted to advise on various modalities of the proposed tracker. The VDAC reviewed the data related to COVID-19 testing, vaccination and patient outcomes available in the three databases and selected relevant data points for inclusion in the tracker, following which databases were integrated, using common identifiers, wherever feasible. Multiple data filters were applied to retrieve information of all individuals ≥18 yr who died after the acquisition of COVID-19 infection with or without vaccination, irrespective of the time between vaccination and test positivity. Vaccine effectiveness (VE) against the reduction of mortality and hospitalizations was initially assessed. As compared to the hospitalization data, mortality reporting was found to be much better in terms of correctness and completeness. Therefore, hospitalization data were not considered for analysis and presentation in the vaccine tracker. The vaccine tracker thus depicts VE against mortality, calculated by a cohort approach using person-time analysis. Incidence of COVID-19 deaths among one- and two-dose vaccine recipients was compared with that among unvaccinated groups, to estimate the rate ratios (RRs). VE was estimated as 96.6 and 97.5 per cent, with one and two doses of the vaccines, respectively, during the period of reporting. The India COVID-19 Vaccination Tracker was officially launched on September 9, 2021. The high VE against mortality, as demonstrated by the tracker, has helped aid in allaying vaccine hesitancy, augmenting and maintaining the momentum of India's COVID-19 vaccination drive.
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http://dx.doi.org/10.4103/ijmr.ijmr_3500_21DOI Listing
July 2022

Effectiveness of BBV152/Covaxin and AZD1222/Covishield vaccines against severe COVID-19 and B.1.617.2/Delta variant in India, 2021: A multi-centric hospital-based case-control study.

Int J Infect Dis 2022 Jul 14. Epub 2022 Jul 14.

All India Institute of Medical Sciences, Jodhpur, India.

Background: India introduced BBV152/Covaxin and AZD1222/Covishield vaccines from January 2021. We estimated effectiveness of these vaccines against severe Coronavirus disease 2019 (COVID-19) among individuals aged ≥45 years.

Methods: We did a multi-centric, hospital-based, case-control study between May and July 2021. Cases were severe COVID-19 patients and controls were COVID-19 negative individuals from 11 hospitals. Vaccine effectiveness (VE) was estimated for full (2 doses ≥14days) and partial (1 dose ≥21 days) vaccination; duration between two vaccine doses and against the Delta variant. We used a random effects logistic regression model to calculate adjusted odds ratios (aOR) with 95% CI after adjusting for relevant known confounders.

Results: We enrolled 1,143 cases and 2,541 controls. The VE of full vaccination was 85% (95% CI: 79%-89%) with AZD1222/Covishield and 71% (95% CI: 57%-81%) with BBV152/Covaxin. The VE was highest for an interval of 6-8 weeks between two doses of AZD1222/Covishield (94%, 95% CI: 86%-97%) and BBV152/Covaxin (93%, 95% CI: 34%-99%). The VE estimates were similar against the Delta strain and sub-lineages.

Conclusion: BBV152/Covaxin and AZD1222/Covishield were effective against severe COVID-19 among the Indian population during the period of dominance of highly transmissible Delta variant in second wave of pandemic. An escalation of two-dose coverage with COVID-19 vaccines is critical to reduce severe COVID-19 and further mitigate the pandemic in the country.
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http://dx.doi.org/10.1016/j.ijid.2022.07.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288262PMC
July 2022

Zika a Vector Borne Disease Detected in Newer States of India Amidst the COVID-19 Pandemic.

Front Microbiol 2022 10;13:888195. Epub 2022 Jun 10.

Indian Council of Medical Research, National Institute of Virology, Pune, India.

Background: During the second wave of the COVID-19 pandemic, outbreaks of Zika were reported from Kerala, Uttar Pradesh, and Maharashtra, India in 2021. The Dengue and Chikungunya negative samples were retrospectively screened to determine the presence of the Zika virus from different geographical regions of India.

Methods: During May to October 2021, the clinical samples of 1475 patients, across 13 states and a union territory of India were screened and re-tested for Dengue, Chikungunya and Zika by CDC Trioplex Real time RT-PCR. The Zika rRTPCR positive samples were further screened with anti-Zika IgM and Plaque Reduction Neutralization Test. Next generation sequencing was used for further molecular characterization.

Results: The positivity was observed for Zika (67), Dengue (121), and Chikungunya (10) amongst screened cases. The co-infections of Dengue/Chikungunya, Dengue/Zika, and Dengue/Chikungunya/Zika were also observed. All Zika cases were symptomatic with fever (84%) and rash (78%) as major presenting symptoms. Of them, four patients had respiratory distress, one presented with seizures, and one with suspected microcephaly at birth. The Asian Lineage of Zika and all four serotypes of Dengue were found in circulation.

Conclusion: Our study indicates the spread of the Zika virus to several states of India and an urgent need to strengthen its surveillance.
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http://dx.doi.org/10.3389/fmicb.2022.888195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9226610PMC
June 2022

Re-assessing the biosafety level requirement & defining surveillance need for Kyasanur forest disease virus: Changed paradigm.

Indian J Med Res 2022 May 20. Epub 2022 May 20.

Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India.

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http://dx.doi.org/10.4103/ijmr.IJMR_1757_19DOI Listing
May 2022

Retraction Note to: Epidemiology and molecular typing of Candida isolates from burn patients.

Mycopathologia 2022 Aug;187(4):425

Special Centre for Molecular Medicine, Membrane Biology Laboratory, New Delhi, India.

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http://dx.doi.org/10.1007/s11046-022-00641-wDOI Listing
August 2022

Identification of Human Case of Avian Influenza A(H5N1) Infection, India.

Emerg Infect Dis 2022 06;28(6):1269-1273

A 11-year-old boy with acute myeloid leukemia was brought for treatment of severe acute respiratory infection in the National Capital Region, New Delhi, India. Avian influenza A(H5N1) infection was laboratory confirmed. Complete genome analysis indicated hemagglutinin gene clade 2.3.2.1a. We found the strain to be susceptible to amantadine and neuraminidase inhibitors.
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http://dx.doi.org/10.3201/eid2806.212246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9155886PMC
June 2022

Safety and immunogenicity of the Rotavac and Rotasiil rotavirus vaccines administered in an interchangeable dosing schedule among healthy Indian infants: a multicentre, open-label, randomised, controlled, phase 4, non-inferiority trial.

Lancet Infect Dis 2022 08 16;22(8):1191-1199. Epub 2022 May 16.

Division of Epidemiology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India; Division of Bacteriology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India. Electronic address:

Background: Rotavirus is the leading cause of severe dehydrating gastroenteritis among children younger than 5 years in low-income and middle-income countries. Two vaccines-Rotavac and Rotasiil-are used in routine immunisation in India. The safety and immunogenicity of these vaccines administered in a mixed regimen is not documented. We therefore aimed to compare the safety and seroresponse of recipients of a mixed regimen versus a single regimen.

Methods: We did a multicentre, open-label, randomised, controlled, phase 4, non-inferiority trial at two sites in India. We recruited healthy infants aged 6-8 weeks. Infants with systemic disorders, weight-for-height Z scores of less than minus three SDs, or a history of persistent diarrhoea were excluded. Eligible infants were randomly allocated to six groups in equal numbers to receive either the single vaccine regimen (ie, Rotavac-Rotavac-Rotavac [group 1] or Rotasiil-Rotasiil-Rotasiil [group 2]) or the mixed vaccine regimen (ie, Rotavac-Rotasiil-Rotavac [group 3], Rotasiil-Rotavac-Rotasiil [group 4], Rotavac-Rotasiil-Rotasiil [group 5], or Rotasiil-Rotavac-Rotavac [group 6]). Randomisation was done using an online software by site in blocks of at least 12. The primary outcome was seroresponse to rotavirus vaccine, measured using rotavirus-specific serum IgA antibodies 4 weeks after the third dose. The seroresponse rates were compared between recipients of the four mixed vaccine regimens (consisting of various combinations of Rotavac and Rotasiil) with recipients of the single vaccine regimens (consisting of Rotavac or Rotasiil only for all three doses). The non-inferiority margin was set at 10%. Safety follow-ups were done for the duration of study participation. This trial was registered with the Clinical Trials Registry India, number CTRI/2018/08/015317.

Findings: Between March 25, 2019, and Jan 15, 2020, a total of 1979 eligible infants were randomly assigned to receive a single vaccine regimen (n=659; 329 in group 1 and 330 in group 2) or a mixed vaccine regimen (n=1320; 329 each in groups 3 and 4, and 331 each in groups 5 and 6). All eligible participants received the first dose, 1925 (97·3%) of 1979 received the second dose, and 1894 (95·7%) received all three doses of vaccine. 1852 (93·6%) of 1979 participants completed the follow-up. The immunogenicity analysis consisted of 1839 infants (1238 [67·3%] in the mixed vaccine regimen and 601 [32·7%] in the single vaccine regimen; 13 samples were insufficient in quantity) who completed vaccination and provided post-vaccination sera. The seroresponse rate in the mixed vaccine regimen group (33·5% [95% CI 30·9-36·2]) was non-inferior compared with the single vaccine regimen group (29·6% [26·1-33·4]); the seroresponse rate difference was 3·9% (95% CI -0·7 to 8·3). The proportion of participants with any type of solicited adverse events was 90·9% (95% CI 88·4-93·0) in the single vaccine regimen group and 91·1% (89·5-92·6) in the mixed vaccine regimen group. No vaccine-related serious adverse events or intussusception were reported during the study.

Interpretation: Rotavac and Rotasiil can be safely used in an interchangeable manner for routine immunisation since the seroresponse was non-inferior in the mixed vaccine regimen compared with the single vaccine regimen. These results allow for flexibility in administering the vaccines, helping to overcome vaccine shortages and supply chain issues, and targeting migrant populations easily.

Funding: Ministry of Health and Family Welfare, Government of India.

Translation: For the Hindi translation of the abstract see Supplementary Materials section.
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http://dx.doi.org/10.1016/S1473-3099(22)00161-XDOI Listing
August 2022

Global respiratory virus surveillance: strengths, gaps, and way forward.

Int J Infect Dis 2022 Aug 15;121:184-189. Epub 2022 May 15.

XX, Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi-110029. Electronic address:

Current Situation: The global influenza surveillance and response system (GISRS), coordinated by the World Health Organization (WHO), is a global framework for surveillance of influenza and other respiratory viruses, data collection, laboratory capacity building, genomic data submission and archival, standardization, and calibration of reagents and vaccine strains, production of seasonal influenza vaccines and creating a facilitatory regulatory environment for the same. GAPS: WHO-designated national influenza centers (NICs) are entrusted with establishing surveillance in their respective countries. National and subnational surveillance remains weak in most parts of the world because of varying capacities of the NICs, lack of funds, poor human and veterinary surveillance mechanisms, lack of intersectoral coordination, and varying commitments of the local government.

Way Forward: As influenza viruses have a wide variety of nonhuman hosts, it is critical to strengthen surveillance at local levels for timely detection of untypable or novel strains with potential to cause epidemics or pandemics. In this article, we have proposed possible strategies to strengthen and expand local capacities for respiratory virus surveillance through the designated NICs of the WHO.
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http://dx.doi.org/10.1016/j.ijid.2022.05.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9107382PMC
August 2022

SARS-CoV-2 Kappa Variant Shows Pathogenicity in a Syrian Hamster Model.

Vector Borne Zoonotic Dis 2022 05;22(5):289-296

Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India.

The emergence of SARS-CoV-2 lineage B.1.617 variants in India has been associated with a surge in the number of daily infections. We investigated the pathogenic potential of Kappa (B.1.617.1) variant in Syrian golden hamsters. Two groups of Syrian golden hamsters (18 each) were inoculated intranasally with SARS-CoV-2 isolates, B.1 (D614G) and Kappa variant, respectively. The animals were monitored daily for the clinical signs and body weight. Throat swab, nasal wash, and organ samples (lungs, nasal turbinate, trachea) were collected and screened using SARS-CoV-2-specific RT-qPCR. Histopathologic evaluation of the lung samples was performed. The hamsters infected with the Kappa variant demonstrated increased body weight loss compared to the B.1 lineage isolate. The highest viral RNA load was observed in the nasal turbinate and lung specimens of animals infected with both variants. A significantly higher sgRNA load was observed in the nasal swabs (7 DPI), trachea (3 DPI), and lungs (3 DPI) of hamsters infected with the Kappa variant. Neutralizing antibody response generated in the B.1 lineage-infected hamster sera were comparable against both B.1 and Kappa variant in contrast to Kappa variant-infected hamsters, which showed lower titers against B.1 lineage isolate. Gross and microscopic evaluation of the lung specimens showed severe lung lesions in hamsters infected with Kappa variant compared to B.1. The study demonstrates pathogenicity of Kappa variant in hamsters evident with reduced body weight, high viral RNA load in lungs, and pronounced lung lesions. Both Kappa variant- and B.1-infected hamsters produced neutralizing antibodies against both variants studied.
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http://dx.doi.org/10.1089/vbz.2021.0080DOI Listing
May 2022

Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines.

Indian J Med Res 2022 May 6. Epub 2022 May 6.

Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India.

The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.
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http://dx.doi.org/10.4103/ijmr.ijmr_2544_21DOI Listing
May 2022

Strengthening public health systems for diagnosing patients with acute encephalitis syndrome of unidentified cause.

Authors:
Nivedita Gupta

Lancet Glob Health 2022 05;10(5):e596-e597

Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India. Electronic address:

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http://dx.doi.org/10.1016/S2214-109X(22)00123-1DOI Listing
May 2022

Expansion of the measles and rubella laboratory network, India.

Bull World Health Organ 2022 Apr 3;100(4):247-255. Epub 2022 Feb 3.

Hassan Institute of Medical Sciences, Hassan, Karnataka, India.

Objective: To expand the measles and rubella laboratory network of India by integrating new laboratories.

Methods: In collaboration with the World Health Organization (WHO), the Indian government developed a 10-step scheme to systematically expand the number of laboratories performing serological and molecular testing for measles and rubella. The Indian Council of Medical Research and WHO identified suitable laboratories based on their geographical location, willingness, preparedness, past performance and adherence to national quality control and quality assurance mechanisms. The 10-step scheme was initiated with training on measles and rubella diagnostic assays followed by testing of both measles and rubella serology and molecular unknown panels, cross-verification with reference laboratories and ended with WHO on-site accreditation.

Findings: After extensive training, technical support, funding and monitoring, all six selected laboratories attained passing scores of 90.0% or more in serological and molecular proficiency testing of measles and rubella. Since 2018, the laboratories are a part of the measles and rubella network of India. Within 12 months of initiation of independent reporting, the six laboratories have tested 2287 serum samples and 701 throat or nasopharyngeal swabs or urine samples.

Conclusion: The process led to strengthening and expansion of the network. This proficient laboratory network has helped India in scaling up serological and molecular testing of measles and rubella while ensuring high quality testing. The collaborative model developed by the Indian government with WHO can be implemented by other countries for expanding laboratory networks for surveillance of measles and rubella as well as other infectious diseases.
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http://dx.doi.org/10.2471/BLT.21.286999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8958835PMC
April 2022

Use of COVID-19 Test Positivity Rate, Epidemiological, and Clinical Tools for Guiding Targeted Public Health Interventions.

Front Public Health 2022 16;10:821611. Epub 2022 Mar 16.

Indian Council of Medical Research, New Delhi, India.

India experienced a second wave of COVID-19 infection with an unprecedented upsurge in the number of cases. We have analyzed the effect of different restrictive measures implemented in six Indian states. Further, based on available national and international data on disease transmission and clinical presentation, we have proposed a decision-making matrix for planning adequate resources to combat the future waves of COVID-19. We conclude that pragmatic and well calibrated localized restrictions, tailored as per specific needs may achieve a decline in disease transmission comparable to drastic steps like national lockdowns. Additionally, we have underscored the critical need for countries to generate local epidemiological, clinical and laboratory data alongwith community perception and uptake of various non-pharmaceutical interventions, for effective planning and policy making.
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http://dx.doi.org/10.3389/fpubh.2022.821611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8965807PMC
April 2022

SARS-CoV-2 and Influenza Virus Co-Infection Cases Identified through ILI/SARI Sentinel Surveillance: A Pan-India Report.

Viruses 2022 03 17;14(3). Epub 2022 Mar 17.

Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi 110029, India.

SARS-CoV-2/influenza virus co-infection studies have focused on hospitalized patients who usually had grave sequelae. Here, we report SARS-CoV-2/influenza virus co-infection cases from both community and hospital settings reported through integrated ILI/SARI (Influenza Like Illness/Severe Acute Respiratory Infection) sentinel surveillance established by the Indian Council of Medical Research. We describe the disease progression and outcomes in these cases. Out of 13,467 samples tested from 4 July 2021-31 January 2022, only 5 (0.04%) were of SARS-CoV-2/influenza virus co-infection from 3 different sites in distinct geographic regions. Of these, three patients with extremes of age required hospital admission, but none required ICU admission or mechanical ventilation. No mortality was reported. The other two co-infection cases from community settings were managed at home. This is the first report on SARS-CoV-2/Influenza virus co-infection from community as well as hospital settings in India and shows that influenza viruses are circulating in the community even during COVID-19. The results emphasize the need for continuous surveillance for multiple respiratory pathogens for effective public health management of ILI/SARI cases in line with the WHO (World Health Organization) recommendations.
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http://dx.doi.org/10.3390/v14030627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954151PMC
March 2022

Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens.

Viruses 2022 02 24;14(3). Epub 2022 Feb 24.

Indian Council of Medical Research-National Institute of Virology, Pune 411021, India.

Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung specimens of both passages. The successful isolation of the virus from hamster specimens with Vero CCL-81 was observed with cytopathic effect in infected cells and high viral load in the cell suspension. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequences, suggesting intact pathogenicity of the virus isolate. Our data demonstrated successful isolation of the Omicron variant with the in vivo method first followed by in vitro method. The virus isolate could be used in the future to explore different aspects of the Omicron variant.
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http://dx.doi.org/10.3390/v14030461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8951364PMC
February 2022

Nipah Virus Outbreak in Kerala State, India Amidst of COVID-19 Pandemic.

Front Public Health 2022;10:818545. Epub 2022 Feb 17.

Indian Council of Medical Research-National Institute of Virology, Pune, India.

We report here a Nipah virus (NiV) outbreak in Kozhikode district of Kerala state, India, which had caused fatal encephalitis in a 12-year-old boy and the outbreak response, which led to the successful containment of the disease and the related investigations. Quantitative real-time reverse transcription (RT)-PCR, ELISA-based antibody detection, and whole genome sequencing (WGS) were performed to confirm the NiV infection. Contacts of the index case were traced and isolated based on risk categorization. Bats from the areas near the epicenter of the outbreak were sampled for throat swabs, rectal swabs, and blood samples for NiV screening by real-time RT-PCR and anti-NiV bat immunoglobulin G (IgG) ELISA. A plaque reduction neutralization test was performed for the detection of neutralizing antibodies. Nipah viral RNA could be detected from blood, bronchial wash, endotracheal (ET) secretion, and cerebrospinal fluid (CSF) and anti-NiV immunoglobulin M (IgM) antibodies from the serum sample of the index case. Rapid establishment of an onsite NiV diagnostic facility and contact tracing helped in quick containment of the outbreak. NiV sequences retrieved from the clinical specimen of the index case formed a sub-cluster with the earlier reported Nipah I genotype sequences from India with more than 95% similarity. Anti-NiV IgG positivity could be detected in 21% of () and 37.73% of (). Neutralizing antibodies against NiV could be detected in . Stringent surveillance and awareness campaigns need to be implemented in the area to reduce human-bat interactions and minimize spillover events, which can lead to sporadic outbreaks of NiV.
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http://dx.doi.org/10.3389/fpubh.2022.818545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8891450PMC
March 2022

Enablers and barriers towards ensuring routine immunization services during the COVID-19 pandemic: findings from a qualitative study across five different states in India.

Trans R Soc Trop Med Hyg 2022 Mar 2. Epub 2022 Mar 2.

Regional Medical Research Centre, Department of Epidemiology, Odisha 751023, India.

Background: The coronavirus disease 2019 (COVID-19) pandemic has led to disruption in delivering routine healthcare services including routine immunization (RI) worldwide. Understanding the enablers and barriers for RI services during a pandemic is critically important to develop context-appropriate strategies to ensure uninterrupted routine services.

Methods: A community-based, cross-sectional descriptive study was conducted in five different states of India, nested within an ongoing multicentric study on RI. Telephone in-depth interviews among 56 health workers were carried out and the data were analyzed using a content analysis method.

Results: During the COVID-19 pandemic, healthcare providers encountered many challenges at the health system, community and individual level when rendering RI services. Challenges like the limited availability of personal protective equipment and vaccines, deployment for COVID-19 duty at system level, the difficulty in mobilizing people in the community, fear among people at community level, mobility restrictions and limited family support, as well as the stress and stigma at individual level, were barriers to providing RI services. By contrast, the issuing of identification cards to health staff, engaging community volunteers, the support given to health workers by their families and training on COVID-19, were factors that enabled health workers to maintain RI services during the pandemic.

Conclusions: When addressing the COVID-19-related public health emergency, we should not lose sight of the importance of services like RI.
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http://dx.doi.org/10.1093/trstmh/trac011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8903434PMC
March 2022

Inter-laboratory testing as a strategy for external quality assessment for qualitative detection of SARS-CoV-2 by real-time RT-PCR testing in India.

Indian J Med Res 2022 Feb 28. Epub 2022 Feb 28.

Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India.

To implement the strategy of test, track and treat to tackle the ongoing COVID-19 pandemic, the number of real-time RT-PCR-based testing laboratories was increased for diagnosis of SARS-CoV-2 in the country. To ensure reliability of the laboratory results, the Indian Council of Medical Research initiated external quality assessment (EQA) by deploying inter-laboratory quality control (ILQC) activity for these laboratories by nominating 34 quality control (QC) laboratories. This report presents the results of this activity for a period of September 2020 till November 2020. A total of 597 laboratories participated in this activity and 86 per cent of these scored ≥90 per cent concordance with QC laboratories. This ILQC activity showcased India's preparedness in quality diagnosis of SARS-CoV-2.
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http://dx.doi.org/10.4103/ijmr.ijmr_2433_21DOI Listing
February 2022

Detection and isolation of SARS-CoV-2 Eta variant from the international travelers and local residents of India.

J Med Virol 2022 07 7;94(7):3404-3409. Epub 2022 Mar 7.

Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India.

International travel has been the major source for the rapid spread of new SARS-CoV-2 variants across the globe. During SARS-CoV-2 genomic surveillance, a total of 212 SARS-CoV-2 positive clinical specimens were sequenced using next-generation sequencing. A complete SARS-CoV-2 genome could be retrieved from 90 clinical specimens. Of them, 14 sequences belonged to the Eta variant from clinical specimens of international travelers (n = 12) and local residents (n = 2) of India, and 76 belonged to other SARS-CoV-2 variants. Of all the Eta-positive specimens, the virus isolates were obtained from the clinical specimens of six international travelers. Many variants of interest have been found to cause substantial community transmission or cluster infections. The detection of this variant with lethal E484K mutation across the globe and India necessitates persistent genomic surveillance of the SARS-CoV-2 variants, which would aid in taking preventive action.
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http://dx.doi.org/10.1002/jmv.27676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9088542PMC
July 2022

External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India.

PLoS One 2022 8;17(2):e0263736. Epub 2022 Feb 8.

National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India.

Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country. The molecular laboratory testing network was augmented expeditiously, and number of laboratories was increased from one in January 2020 to 2951 till mid-September, 2021. This rapid expansion warranted the need to have inbuilt systems of quality control/ quality assurance. In addition to the ongoing inter-laboratory quality control (ILQC), India implemented an External Quality Assurance Program (EQAP) with assistance from World Health Organization (WHO) and Royal College of Pathologists, Australasia. Out of the 953 open system rRTPCR laboratories in both public and private sector who participated in the first round of EQAP, 891(93.4%) laboratories obtained a passing score of > = 80%. The satisfactory performance of Indian COVID-19 testing laboratories has boosted the confidence of the public and policy makers in the quality of testing. ILQC and EQAP need to continue to ensure adherence of the testing laboratories to the desired quality standards.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263736PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8824319PMC
February 2022

Isolation and characterization of SARS-CoV-2 Beta variant from UAE travelers.

J Infect Public Health 2022 Feb 24;15(2):182-186. Epub 2021 Dec 24.

Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411021, India.

Background: The emergence of SARS-CoV-2 variants in places where the virus is uncontained poses a global threat from the perspective of public health and vaccine efficacy. Travel has been important factor for the easy spread of SARS-CoV-2 variants worldwide. India has also observed the importation of SARS-CoV-2 variants through international travelers.

Methods: In this study, we have collected the oropharyngeal and nasopharyngeal swab specimens from 58 individuals with travel history from United Arab Emirates (UAE), East, West and South Africa, Qatar, Ukraine and Saudi Arabia arrived in India during February-March 2021. The clinical specimens were initially screened for SARS-CoV-2 using Real time RT-PCR. All the specimens were inoculated on to Vero CCL-81 cells for virus isolation. The viral isolates were further sequenced using Next-Generation Sequencing.

Results: All 58 cases were tested positive for SARS-CoV-2 using Real time RT-PCR. Four specimens showed progressive infectivity with fusion of the infected cells with neighboring cells leading to large mass of cells. Replication competent virus was confirmed from culture supernatant of the passage 2 using Real time RT-PCR. Two plaque purified SARS-CoV-2 isolates demonstrated high viral RNA load of 3.8-7.5 × 10 and 1.1-1.6 × 10 at passage 4 and 5 respectively. Nucleotide variations along with amino acid changes were also observed among these two isolates at passage 2-5. All four cases were male with no symptoms and co-morbidity. The sequence analysis has shown two different clusters, first cluster with nucleotide deletions in the ORF1ab and the spike, while second cluster with deletions in spike region. The viral isolates demonstrated 99.88-99.96% nucleotide identity with the representative sequences of Beta variant (B.1.351).

Conclusion: These findings suggest easier transmission of SARS-CoV-2 variants with human mobility through international travel. The isolated Beta variant would be useful to determine the protective efficacy of the currently available and upcoming COVID-19 vaccines in India.
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http://dx.doi.org/10.1016/j.jiph.2021.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8704724PMC
February 2022

Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model.

J Infect Public Health 2022 Feb 21;15(2):164-171. Epub 2021 Dec 21.

Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India.

Background: Considering the potential threat from emerging Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) variants and the rising COVID-19 cases, SARS-CoV-2 genomic surveillance is ongoing in India. We report herewith the isolation of the P.2 variant (B.1.1.28.2) from international travelers and further its pathogenicity evaluation and comparison with D614G variant (B.1) in hamster model.

Methods: Virus isolation was performed in Vero CCL81 cells and genomic characterization by next generation sequencing. The pathogenicity and host immune response of the isolate was assessed in Syrian hamster model and compared with B.1 variant.

Results: B.1.1.28.2 variant was isolated from nasal/throat swabs of international travelers returned to India from United Kingdom and Brazil. The B.1.1.28.2 variant induced body weight loss, viral replication in the respiratory tract and caused severe lung pathology in infected Syrian hamster model in comparison, with B.1 variant infected hamsters. The sera from B.1.1.28.2 infected hamsters efficiently neutralized the D614G variant virus whereas 6-fold reduction in the neutralization was seen in case of D614G variant infected hamsters' sera with the B.1.1.28.2 variant.

Conclusions: B.1.1.28.2 lineage variant could be successfully isolated and characterization could be performed. Pathogenicity of the isolate was demonstrated in Syrian hamster model and the findings of neutralization reduction is of great concern and point towards the need for screening the vaccines for efficacy.
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http://dx.doi.org/10.1016/j.jiph.2021.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8690136PMC
February 2022
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