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Yadav PD, Sahay RR, Balakrishnan A, Mohandas S, Radhakrishnan C, Gokhale MD, Balasubramanian R, Abraham P, Gupta N, Sugunan AP, Khobragade R, George K, Shete A, Patil S, Thankappan UP, Dighe H, Koshy J, Vijay V, Gayathri R, Kumar PJ, Rahim A, Naveen A, Nair S, Rajendran VR, Jayasree V, Majumdar T, Jain R, Viswanathan P, Patil DY, Kumar A, Nyayanit DA, Sarkale P, Waghmare A, Baradkar S, Gawande P, Bodke P, Kalele K, Yemul J, Dhaigude S, Holepannawar M, Gopale S, Chopade G, Ray S, Waghmare P, Narayan J, Mathapati B, Kadam M, Kumar A, Suryawanshi A, Jose BP, Sivadas S, Akash NP, Vimisha TV, Keerthi KV. Nipah Virus Outbreak in Kerala State, India Amidst of COVID-19 Pandemic. Front Public Health 2022; 10:818545. [PMID: 35252095 PMCID: PMC8891450 DOI: 10.3389/fpubh.2022.818545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022] Open
Abstract
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 Pteropus medius (P. medius) and 37.73% of Rousettus leschenaultia (R. leschenaultia). Neutralizing antibodies against NiV could be detected in P. medius. 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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Affiliation(s)
- Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
- *Correspondence: Pragya D. Yadav
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Anukumar Balakrishnan
- Indian Council of Medical Research-National Institute of Virology, Kerala Unit, Alappuzha, India
| | | | | | - Mangesh D. Gokhale
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - R. Balasubramanian
- Indian Council of Medical Research-National Institute of Virology, Kerala Unit, Alappuzha, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nivedita Gupta
- Epidemiology and Communicable Diseases Division, Indian Council of Medical Research, New Delhi, India
| | - A. P. Sugunan
- Indian Council of Medical Research-National Institute of Virology, Kerala Unit, Alappuzha, India
| | - Rajan Khobragade
- Health and Family Welfare Department, Government of Kerala, Thiruvananthapuram, India
| | - Kalpana George
- Department of Microbiology, Government Medical College, Kozhikode, India
| | - Anita Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Hitesh Dighe
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jijo Koshy
- Indian Council of Medical Research-National Institute of Virology, Kerala Unit, Alappuzha, India
| | - Vivek Vijay
- Indian Council of Medical Research-National Institute of Virology, Kerala Unit, Alappuzha, India
| | - R. Gayathri
- Department of Medicine, Government Medical College, Kozhikode, India
| | - P. Jayesh Kumar
- Department of Medicine, Government Medical College, Kozhikode, India
| | - Asma Rahim
- Department of Community Medicine, Government Medical College, Kozhikode, India
| | - A. Naveen
- National Health Mission, Kozhikode, India
| | | | | | - V. Jayasree
- District Medical Office of Health, Health Department, Kozhikode, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Rajlaxmi Jain
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Deepak Y. Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Prasad Sarkale
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Ashwini Waghmare
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Shrikant Baradkar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pranita Gawande
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Poonam Bodke
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Kaumudi Kalele
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jyoti Yemul
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Sachin Dhaigude
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Sanjay Gopale
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Ganesh Chopade
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Shilpa Ray
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Priyanka Waghmare
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jitendra Narayan
- Epidemiology and Communicable Diseases Division, Indian Council of Medical Research, New Delhi, India
| | - Basavaraj Mathapati
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Manoj Kadam
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Abhimanyu Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | | | - Saritha Sivadas
- Department of Microbiology, Government Medical College, Kozhikode, India
| | - N. P. Akash
- Department of Microbiology, Government Medical College, Kozhikode, India
| | - T. V. Vimisha
- Department of Microbiology, Government Medical College, Kozhikode, India
| | - K. V. Keerthi
- Department of Microbiology, Government Medical College, Kozhikode, India
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Yadav P, Mohandas S, Sarkale P, Nyayanit D, Shete A, Sahay R, Potdar V, Baradkar S, Gupta N, Sapkal G, Abraham P, Panda S, Bhargava B. 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; 15:164-171. [PMID: 34959053 PMCID: PMC8690136 DOI: 10.1016/j.jiph.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/23/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022] Open
Abstract
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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Affiliation(s)
- Pragya Yadav
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India.
| | - Sreelekshmy Mohandas
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Prasad Sarkale
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Dimpal Nyayanit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Anita Shete
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Rima Sahay
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Shrikant Baradkar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India
| | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India
| | - Balram Bhargava
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India
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Sarkale P, Patil S, Yadav PD, Nyayanit DA, Sapkal G, Baradkar S, Lakra R, Shete-Aich A, Prasad S, Basu A, Dar L, Vipat V, Giri S, Potdar V, Choudhary ML, Praharaj I, Jain A, Malhotra B, Gawande P, Kalele K, Gupta N, Cherian SS, Abraham P. First isolation of SARS-CoV-2 from clinical samples in India. Indian J Med Res 2020; 151:244-250. [PMID: 32362649 PMCID: PMC7366528 DOI: 10.4103/ijmr.ijmr_1029_20] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Prasad Sarkale
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Dimpal A. Nyayanit
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Gajanan Sapkal
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Shrikant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Rajen Lakra
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sharda Prasad
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Atanu Basu
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Veena Vipat
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Varsha Potdar
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Manohar Lal Choudhary
- Influenza Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Ira Praharaj
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Amita Jain
- King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Bharati Malhotra
- Department of Microbiology, SMS Medical College, Jaipur 302 004, Rajasthan, India
| | - Pranita Gawande
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Kaumudi Kalele
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Sarah S. Cherian
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
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