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Bhardwaj P, Yadav V, Sharma A, Gulafshan S, Pragnya Behera S, Raj Dwivedi G, Deval H, Paluru V, Murhekar M, Singh R. Integration of IgM ELISA and 56 kDa gene PCR in management of pediatric acute encephalitis syndrome associated with scrub typhus. Infect Dis Now 2024; 54:104865. [PMID: 38350558 DOI: 10.1016/j.idnow.2024.104865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/15/2024]
Abstract
OBJECTIVES To identify the potential target genes for detection of Orientia tsutsugamushi (OT) in pediatric acute encephalitis syndrome (pAES). METHODS DNA was extracted from whole blood of 100 pAES cases having tested positive (n = 41) and negative (n = 59) for scrub typhus (ST) by IgM ELISA. These samples were subjected to standard PCR for 56 kDa, 47 kDa, 16 s rRNA, groEL, traD genes and the newly identified 27 kDa gene. RESULTS Among the selected gene targets, 56 kDa demonstrated its superiority for OT detection over the other tested genes. The presence of OT was confirmed via PCR targeting 56 kDa gene in 17 out of the 41 (41.4 %) IgM-positive ST AES cases and 38 out of the 59 (64.4 %) ST IgM negative cases. None of the other gene targets were amplified. CONCLUSION Integration of serological diagnosis with molecular diagnostics targeting the 56 kDa gene for routine testing of AES patients would facilitate detection of OT in AES endemic regions.
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Affiliation(s)
- Pooja Bhardwaj
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Vishal Yadav
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Alok Sharma
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Shahzadi Gulafshan
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Sthita Pragnya Behera
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Gaurav Raj Dwivedi
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Vijayachari Paluru
- ICMR-Regional Medical Research Centre, Port Blair, Dollygunj, Port Blair - 744103, Andaman & Nicobar Islands, India
| | - Manoj Murhekar
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, Uttar Pradesh, India.
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Bhardwaj P, Nanaware NS, Behera SP, Kulkarni S, Deval H, Kumar R, Dwivedi GR, Kant R, Singh R. CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus. Biosensors (Basel) 2023; 13:1021. [PMID: 38131781 PMCID: PMC10742217 DOI: 10.3390/bios13121021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 12/23/2023]
Abstract
Orientia tsutsugamushi is responsible for causing scrub typhus (ST) and is the leading cause of acute encephalitis syndrome (AES) in AES patients. A rapid and sensitive method to detect scrub typhus on-site is essential for the timely deployment of control measures. In the current study, we developed a rapid, sensitive, and instrument-free lateral flow assay (LFA) detection method based on CRISPR/Cas12a technology for diagnosing ST (named LoCIST). The method is completed in three steps: first, harnessing the ability of recombinase polymerase for isothermal amplification of the target gene; second, CRISPR/Cas12a-based recognition of the target; and third, end-point detection by LFA. The detection limit of LoCIST was found to be one gene copy of ST genomic DNA per reaction, and the process was complete within an hour. In 81 clinical samples, the assay showed no cross-reactivity with other rickettsial DNA and was 100% consistent with PCR detection of ST. LoCIST demonstrated 97.6% sensitivity and 100% specificity. Overall, the LoCIST offers a novel alternative for the portable, simple, sensitive, and specific detection of ST, and it may help prevent and control AES outbreaks due to ST. In conclusion, LoCIST does not require specialized equipment and poses a potential for future applications as a point-of-care diagnostic.
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Affiliation(s)
- Pooja Bhardwaj
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | | | - Sthita Pragnya Behera
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Smita Kulkarni
- ICMR-National AIDS Research Institute, Bhosari, Pune 411026, India; (N.S.N.); (S.K.)
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Rajesh Kumar
- RGSC, Department of Genetics and Plant Breeding, Banaras Hindu University, Varanasi 221005, India;
| | - Gaurav Raj Dwivedi
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Rajni Kant
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
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Behera SP, Singh R, Deval H, Bhardwaj P, Zaman K, Misra BR, Kumar N, Srivastava M, Pandey AK, Yadav R, Kavathekar A, Kant R, Bondre VP. Molecular detection of spotted fever group of Rickettsiae in acute encephalitis syndrome cases from eastern Uttar Pradesh region of India. Zoonoses Public Health 2023; 70:403-410. [PMID: 37086017 DOI: 10.1111/zph.13044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
The Eastern Uttar Pradesh region of India is known for its endemicity of acute encephalitis syndrome (AES). Decades of research have established that Orientia tsutsugamushi, a causative of scrub typhus, is a substantial contributor (>60%) for the AES cases besides other aetiology, but additional factors in the remaining proportion are still unidentified. Rickettsial infections are challenging to diagnose in clinical settings due to overlapping clinical symptoms, the absence of definitive indicators, a low index of suspicion, and the lack of low-cost, rapid diagnostic tools. Hence, the present study was designed to determine the load of rickettsial infections among AES cases. Furthermore, we aim to find out the prevalent rickettsial species in AES cases as well as in the vector population at this location. The study included the whole blood/cerebrospinal fluid of AES patients and arthropod specimens from rodents. The molecular identification was performed using the 23S-5S intergenic spacer region and ompB gene with genomic DNA obtained from studied specimens. We detected 5.34% (62/1160) of rickettsial infection in AES cases. Among these, phylogenetic analysis confirmed the presence of 54.8% Rickettsia conorii (n = 34) and 16.1% of Rickettsia felis (n = 10), while the rest proportion of the isolates was unidentified at the species level. Furthermore, R. felis was identified in one CSF sample from AES patients and three flea samples from Xenopsylla cheopis. Rickettsia spp. was also confirmed in one Ornithonyssus bacoti mite sample. The results of this investigation concluded the presence of spotted fever group Rickettsia spp. among AES identified cases as well as in the mite and flea vectors that infest rodents.
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Affiliation(s)
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Pooja Bhardwaj
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Kamran Zaman
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Brij Ranjan Misra
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Niraj Kumar
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Mitali Srivastava
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Ashok Kumar Pandey
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Rajaram Yadav
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Asif Kavathekar
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, India
| | - Vijay P Bondre
- ICMR-National Institute of Virology, Encephalitis Group, Pune, India
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Bhardwaj P, Behera SP, Nanaware N, Zaman K, Deval H, Kant R, Kulkarni S, Kumar R, Dwivedi GR, Singh R. Phylogenetic and immunological investigations of complete TSA56 ORF of Orientia tsutsugamushi present in acute encephalitis syndrome cases from eastern Uttar Pradesh, India. Arch Microbiol 2023; 205:178. [PMID: 37029825 PMCID: PMC10082565 DOI: 10.1007/s00203-023-03492-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 04/09/2023]
Abstract
Scrub typhus (ST) caused by Orientia tsutsugamushi (OT), has long been known to cause acute encephalitis syndrome (AES) and acute febrile illness (AFI). The immunodominant 56 kDa protein of OT, which is encoded by the 56 kDa gene (1600 bp encoding 516-541 amino acids) is a commonly studied antigen for genotype and serotype assignment. Previous studies from India have utilized partial type specific antigen (TSA) 56 kDa sequences for OT strain characterisation. On the other hand, understanding the antigenic diversity of current OT strains, is critical for developing specific diagnostic tests and vaccines against ST. As a result, the current study analyses antigenic variants using the entire TSA56 ORF of OT from AES cases. Phylogenetic investigation using complete TSA56 ORF sequences revealed Karp and Gilliam were the circulating predominant strains of OT. Furthermore, Immuno-informatical analysis demonstrated that the majority of high-binding affinity CD4 TCEs against the most prevalent Indian human leukocyte antigen alleles were present in the S-VDIII/IV and S-VDIV spacer regions of TSA56 ORF. TSA56 conserved spacer is crucial for OT immunological response investigations. Further, the pathophysiological effects of spacer domains in ST require further investigation. Furthermore, the characterization of the TSA56 spacer region of the OT from different parts of India is critical for developing region-specific ST diagnostic assays and vaccines.
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Affiliation(s)
- Pooja Bhardwaj
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Sthita Pragnya Behera
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Nikita Nanaware
- ICMR-National AIDS Research Institute, Bhosari, Pune, 411026, India
| | - Kamran Zaman
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnatka, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Smita Kulkarni
- ICMR-National AIDS Research Institute, Bhosari, Pune, 411026, India
| | - Rajesh Kumar
- RGSC, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Gaurav Raj Dwivedi
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur, 273013, India.
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Mishra T, Goswami S, Deval H, Vaid R, Kant R. Recent public health concerns of the high-altitude tribal population of Lahaul and Spiti, Himachal Pradesh. J Family Med Prim Care 2023; 12:660-665. [PMID: 37312771 PMCID: PMC10259537 DOI: 10.4103/jfmpc.jfmpc_1416_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 11/24/2022] [Indexed: 06/15/2023] Open
Abstract
Objective India has a tribal population of 8.6%. Health concerns of the high-altitude tribal population in India play a vital role in overall socio-economic development and health transformation of the country. Therefore, the aim of this study was to determine the current health problems among the tribal population of Lahaul and Spiti district of Himachal Pradesh. Material and Methods The study area encompasses one regional hospital (RH) in Keylong (the district headquarters), three community health centers (CHCs), and 16 primary health care centers (PHCs). In addition, the district has 37 sub-centers (SCs) and 21 Ayurveda dispensaries to serve the district. The data for this study were gathered over a 4-year period from records of daily out-patient department registration from the various health centers (RH, CHCs, and PHCs) from 2017 to 2020. Results In terms of communicable diseases, the population in the concerned region was more likely to have acute respiratory infection, enteric fever, tuberculosis, and typhoid. Hypertension, asthma, bronchitis, and diabetes mellitus type II were determined to be the most common non-communicable diseases. Conclusion Acute respiratory disease, hypertension, diarrhea, accidental injuries, and eye problems were shown to be prevalent in the study area. The population's position in relation to these five diseases indicates the community's sensitivity to a variety of common conditions. There is a need to review the needs and priorities of the concerned population and create goals and targets to meet those needs using validated public health measures.
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Affiliation(s)
- Tanuja Mishra
- Scientist-C, ICMR-RMRC Field Station, Keylong, Lahaul and Spiti, Himachal Pradesh, India
| | - Shweta Goswami
- Medical Scientist-B, Field Station, Keylong, Lahaul and Spiti, Himachal Pradesh, India
| | - Hirawati Deval
- Dr. Hirawati Deval, PhD, Scientist- D, ICMR- Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Ranjit Vaid
- District Program Officer and Immunization Officer, Regional Hospital Keylong, Lahaul and Spiti, Himachal Pradesh, India
| | - Rajni Kant
- Scientist G and Director, ICMR- Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
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Sharma S, Aggarwal S, Kulkarni R, Kumar D, Mishra BK, Dwivedi GR, Devi KR, Mamidi RS, Singh KJ, Singh L, Sahu D, Adhikari T, Nair S, Kumar A, Juneja A, Sharma A, Begum S, Surve S, Prusty RK, Kumar S, Geddam JJB, Meur G, Mummadi MK, Kailash U, Palo SK, Kanungo S, Kshatri JS, Behera AK, Swain S, Singh R, Zaman K, Deval H, Pandey AK, Sarkar A, Kant R, Narain K, D’Aquino L, Gaym A, Singh VV, Rao MVV. Challenges in Accessing and Delivering Maternal and Child Health Services during the COVID-19 Pandemic: A Cross-Sectional Rapid Survey from Six States of India. Int J Environ Res Public Health 2023; 20:1538. [PMID: 36674296 PMCID: PMC9865999 DOI: 10.3390/ijerph20021538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND/OBJECTIVES Globally, the COVID-19 pandemic and its prevention and control policies have impacted maternal and child health (MCH) services. This study documents the challenges faced by patients in accessing MCH services, and the experiences of health care providers in delivering those services during the COVID-19 outbreak, explicitly focusing on the lockdown period in India. METHODS A cross-sectional study (rapid survey) was conducted in 18 districts from 6 states of India during March to June, 2020. The sample size included 540 MCH patients, 18 gynaecologists, 18 paediatricians, 18 district immunisation officers and 108 frontline health workers. Bivariate analysis and multivariable analysis were used to assess the association between sociodemographic characteristics, and challenges faced by the patients. RESULTS More than one-third of patients (n = 212; 39%) reported that accessing MCH services was a challenge during the lockdown period, with major challenges being transportation-related difficulties (n = 99; 46%) unavailability of hospital-based services (n = 54; 23%) and interrupted outreach health services (n = 39; 18.4%). The supply-side challenges mainly included lack of infrastructural preparedness for outbreak situations, and a shortage of human resources. CONCLUSIONS/RECOMMENDATIONS A holistic approach is required that focuses on both preparedness and response to the outbreak, as well reassignment and reinforcement of health care professionals to continue catering to and maintaining essential MCH services during the pandemic.
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Affiliation(s)
- Saurabh Sharma
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Sumit Aggarwal
- Indian Council of Medical Research, Ansari Nagar, New Delhi 110029, India
| | - Ragini Kulkarni
- National Institute for Research in Reproductive Health, Mumbai 400012, India
| | - Dinesh Kumar
- National Institute for Research in Tribal Health, Jabalpur 482003, India
| | | | | | - K. Rekha Devi
- Regional Medical Research Centre, NE Region, Dibrugarh 751023, India
| | | | | | - Lucky Singh
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Damodar Sahu
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Tulsi Adhikari
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Saritha Nair
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Anil Kumar
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Atul Juneja
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Anshita Sharma
- National Institute of Medical Statistics, Ansari Nagar, New Delhi 110029, India
| | - Shahina Begum
- National Institute for Research in Reproductive Health, Mumbai 400012, India
| | - Suchitra Surve
- National Institute for Research in Reproductive Health, Mumbai 400012, India
| | - Ranjan Kumar Prusty
- National Institute for Research in Reproductive Health, Mumbai 400012, India
| | - Surendra Kumar
- National Institute for Research in Reproductive Health, Mumbai 400012, India
| | | | - Gargi Meur
- National Institute of Nutrition, Hyderabad 500007, India
| | | | - Uma Kailash
- National Institute of Nutrition, Hyderabad 500007, India
| | | | | | | | | | | | - Rajeev Singh
- Regional Medical Research Centre, Gorakhpur 273013, India
| | - Kamran Zaman
- Regional Medical Research Centre, Gorakhpur 273013, India
| | - Hirawati Deval
- Regional Medical Research Centre, Gorakhpur 273013, India
| | | | - Abu Sarkar
- Regional Medical Research Centre, NE Region, Dibrugarh 751023, India
| | - Rajni Kant
- Regional Medical Research Centre, Gorakhpur 273013, India
| | - Kanwar Narain
- Regional Medical Research Centre, NE Region, Dibrugarh 751023, India
| | | | - Asheber Gaym
- UNICEF, India Country Office, New Delhi 110003, India
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Behera SP, Bhardwaj P, Deval H, Srivastava N, Singh R, Misra BR, Agrawal A, Kavathekar A, Kant R. Co-circulation of all the four Dengue virus serotypes during 2018-2019: first report from Eastern Uttar Pradesh, India. PeerJ 2023; 11:e14504. [PMID: 36643644 PMCID: PMC9835713 DOI: 10.7717/peerj.14504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/11/2022] [Indexed: 01/17/2023] Open
Abstract
Dengue fever is an endemic disease in India, transmitted by an infected mosquito bite. In India, the number of concurrent infections and the circulation of multiple dengue virus (DENV) serotypes has increased in recent decades. Molecular surveillance among the DENV serotype is important to keep track of the circulating serotypes, evolutionary changes, and key mutations that can alter the diagnostics. The current study included patients admitted for dengue in the Eastern Uttar Pradesh (E-UP) region during 2018-2019. The genetic characterization of the circulating DENV was accomplished through partial CprM (511 bp) gene amplification via reverse transcriptase polymerase chain reaction and sequencing. Phylogenetic analysis revealed the circulation of all four DENV1-4 serotypes. DENV-2 was the most abundant serotype (44%, 27/61), followed by DENV-3 (32%, 20/61). DENV-1 had a 16% (10/61) predominance, while DENV-4 (6%, 4/61) was found to be the least abundant serotype. DENV-2 genotypes were distributed among lineages I (7.4%), II (85%) and III (7.4%) of genotype IV, DENV-3 to lineage III of genotype III, DENV-1 to genotype III; DENV-2 to lineage B (75%) and C (25%) of genotype I. This primary report on the co-circulation of DENV1-4 serotypes from the E-UP region highlights the requirement of continuous molecular surveillance for monitoring circulating DENV serotypes.
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Affiliation(s)
| | - Pooja Bhardwaj
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Neha Srivastava
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Brij Ranjan Misra
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Awdhesh Agrawal
- Division of Pathology, Gorakhnath Hospital, Gorakhpur, Uttar Pradesh, India
| | - Asif Kavathekar
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
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Zaman K, Shete AM, Mishra SK, Kumar A, Reddy MM, Sahay RR, Yadav S, Majumdar T, Pandey AK, Dwivedi GR, Deval H, Singh R, Behera SP, Kumar N, Patil S, Kumar A, Dudhmal M, Joshi Y, Shukla A, Gawande P, Kavathekar A, Kumar N, Kumar V, Kumar K, Singh RS, Kumar M, Tiwari S, Verma A, Yadav PD, Kant R. Omicron BA.2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India. Front Med (Lausanne) 2022; 9:955930. [PMID: 36405589 PMCID: PMC9666497 DOI: 10.3389/fmed.2022.955930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/03/2022] [Indexed: 01/25/2023] Open
Abstract
Background Recent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India. Methods Whole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7. Results The mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men. Conclusion The current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.
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Affiliation(s)
- Kamran Zaman
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Anita M Shete
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Abhinendra Kumar
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Mahendra M Reddy
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Rima R Sahay
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Shailendra Yadav
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Triparna Majumdar
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Ashok K Pandey
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Gaurav Raj Dwivedi
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Hirawati Deval
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Rajeev Singh
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Niraj Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Savita Patil
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Ashish Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Manisha Dudhmal
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Yash Joshi
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Aishwarya Shukla
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Pranita Gawande
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Asif Kavathekar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Nalin Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Vijay Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Kamlesh Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Ravi Shankar Singh
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Manoj Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Shashikant Tiwari
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Ajay Verma
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Pragya D Yadav
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Rajni Kant
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
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Srivastava N, Deval H, Mittal M, Deoshatwar A, Bondre VP, Kant R, Yadav R. Extent of disability among paediatric Japanese encephalitis survivors and predictors of poor outcome: a retrospective cohort study in North India. BMJ Open 2022; 12:e060795. [PMID: 36316071 PMCID: PMC9628649 DOI: 10.1136/bmjopen-2022-060795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To determine the Japanese encephalitis (JE)-associated long-term functional and neurological outcomes, the extent of reduced social participation and predictors of poor outcomes among paediatric JE survivors. DESIGN A retrospective cohort study. SETTING Laboratory-confirmed JE-positive paediatric cases (<16 years of age) hospitalised at the paediatric ward of Baba Raghav Das Medical College, Gorakhpur, India, between 1 January 2017 and 31 December 2017, were followed up after 6-12 months of hospital discharge. PARTICIPANTS 126 patients were included in the study; median age was 7.5 years (range: 1.5-15 years), and 74 (58.73%) were male. OUTCOME MEASURES Functional outcome defined by Liverpool Outcome Score (LOS) dichotomised into poor (LOS=1-2) and good (LOS=3-5) outcome groups compared for demographic, clinical and biochemical parameters for prognostic factors of poor outcomes. Social participation of patients scaled on Child and Adolescent Scale of Participation score 2-5. RESULTS About 94 of 126 (74.6%) children developed neurological sequelae at different levels of severity. Age-expected social participation was compromised in 90 out of 118 children. In multivariate logistic regression analysis, a combination of parameters, JE unvaccinated status (OR: 61.03, 95% CI (14.10 to 264); p<0.001), low Glasgow Coma Score (GCS) at admission (≤8) (OR: 8.6, 95% CI (1.3 to 57.1); p=0.026), malnutrition (OR: 13.56, 95% CI (2.77 to 66.46); p=0.001) and requirement of endotracheal intubation (OR: 5.43, 95% CI (1.20 to 24.44); p=0.027) statistically significantly predicted the poor outcome with 77.8% sensitivity and 94.6% specificity. The goodness-of-fit test showed that the model fit well (Hosmer-Lemeshow goodness-of-fit test) (χ 2=3.13, p=0.988), and area under the receiver operating characteristic curve was 0.950. CONCLUSION This study estimates the burden of JE-presenting post-discharge deaths (15.4%) and disability (63.08%). Those who did not receive JE vaccine, were suffering from malnutrition, had GCS ≤8 at admission and required endotracheal intubation had poorer outcomes.
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Affiliation(s)
- Neha Srivastava
- ICMR-Regional Medical Research Centre, Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre, Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Mahima Mittal
- Department of Pediatrics, All India Institute of Medical Sciences Gorakhpur, Gorakhpur, India
| | | | - Vijay P Bondre
- ICMR, National Institute of Virology, Pune, Maharashtra, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Rajaram Yadav
- ICMR-Regional Medical Research Centre, Gorakhpur, Gorakhpur, Uttar Pradesh, India
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Kumar N, Misra BR, Reddy MM, Deval H, Zaman K, Kant R. COVID‐19 transmission among vaccinated laboratory workers during the second wave in eastern Uttar Pradesh, India. J Med Virol 2022; 94:3512-3514. [PMID: 35434827 PMCID: PMC9088332 DOI: 10.1002/jmv.27788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022]
Affiliation(s)
- Niraj Kumar
- Indian Council of Medical Research – Regional Medical Research Centre (ICMR – RMRC)Gorakhpur
| | - Brij Ranjan Misra
- Indian Council of Medical Research – Regional Medical Research Centre (ICMR – RMRC)Gorakhpur
| | - Mahendra M Reddy
- Indian Council of Medical Research – Regional Medical Research Centre (ICMR – RMRC)Gorakhpur
| | - Hirawati Deval
- Indian Council of Medical Research – Regional Medical Research Centre (ICMR – RMRC)Gorakhpur
| | - Kamran Zaman
- Indian Council of Medical Research – Regional Medical Research Centre (ICMR – RMRC)Gorakhpur
| | - Rajni Kant
- Indian Council of Medical Research – Regional Medical Research Centre (ICMR – RMRC)Gorakhpur
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Srivastava N, Deval H, Mittal M, Kant R, Bondre VP. The Outbreaks of Acute Encephalitis Syndrome in Uttar Pradesh, India (1978–2020) and Its Effective Management: A Remarkable Public Health Success Story. Front Public Health 2022; 9:793268. [PMID: 35223759 PMCID: PMC8863615 DOI: 10.3389/fpubh.2021.793268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/11/2021] [Accepted: 12/31/2021] [Indexed: 11/21/2022] Open
Abstract
Introduction Acute encephalitis syndrome (AES) is a major public health enigma in India and the world. Uttar Pradesh (UP) is witnessing recurrent and extensive seasonal AES outbreaks since 1978. Government of India and UP state government have devised various mitigation measures to reduce AES burden and AES associated mortality, morbidity and disability in Uttar Pradesh. The aim of this study was to describe the public health measures taken in order to control seasonal outbreaks of AES in UP between 1978 and 2020. Methods We used literature review as a method of analysis, including the Indian government policy documents. This review utilized search engines such as PubMed, Google Scholar, Research Gate, Cochrane, Medline to retrieve articles and information using strategic keywords related to Acute Encephalitis Syndrome. Data was also collected from progress reports of government schemes and websites of Indian Council of Medical Research (ICMR), National Vector Borne Disease Control Programme (NVBDCP) and Integrated Disease Surveillance Programmes (IDSP). Results The incidence of AES cases in UP have declined from 18.2 per million population during 2005-2009 to 15 per million population during 2015-2019 [CI 12.6–20.6, P-value < 0.001] and case fatality rate (CFR) reduced from 33% during 1980-1984 to 12.6% during 2015-2019 [CI 17.4–30.98, P-value < 0.001]. AES incidence was 9 (2019) and 7 (2020) cases per million populations respectively and CFR was 5.8% (2019) and 5% (2020). This decline was likely due to active surveillance programs identifying aetiological agents and risk factors of AES cases. The identified etiologies of AES include Japanese encephalitis virus (5–20%), Enterovirus (0.1–33%), Orientia tsutsugamushi (45–60%) and other viral (0.2–4.2%), bacterial (0–5%) and Rickettsial (0.5–2%) causes. The aggressive immunization programs against Japanese encephalitis with vaccination coverage of 72.3% in UP helped in declining of JE cases in the region. The presumptive treatment of febrile cases with empirical Doxycycline and Azithromycin (EDA) caused decline in Scrub Typhus-AES cases. Decrease in incidence of vector borne diseases (Malaria, Dengue, Japanese Encephalitis and Kala Azar) i.e., 39.6/100,000 population in 2010 to 18/100,000 population in 2017 is highlighting the impact of vector control interventions. Strengthening healthcare infrastructure in BRD medical college and establishment of Encephalitis Treatment Centre (ETC) at peripheral health centres and emergency ambulance services (Dial 108) reduced the referral time and helped in early treatment and management of AES cases. The AES admissions increased at ETC centres to 60% and overall case fatality rate of AES declined to 3%. Under clean India mission and Jal Jeevan mission, proportion of population with clean drinking water increased from 74.3% in 1992 to 98.7% in 2020. The proportion of household having toilet facilities increased from 22.9% in 1992 to 67.4% in 2020. Provisions for better nutritional status under state and national nutrition mission helped in reducing the burden of stunting (52%) and wasting (53.4%) among under five children in 1992 to 38.8% (stunting) and 36.8% (wasting) in year 2018. These factors have all likely contributed to steady AES decline observed in UP. Conclusion There is a recent steady decline in AES incidence and CFR since implementation of intensive AES surveillance system and JE immunization campaigns which is highlighting the success of interventions made by central and state government to control seasonal AES outbreaks in UP. Currently, AES incidence is 9 cases per million population (in year 2019) and mortality is 5.8%.
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Affiliation(s)
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre, Gorakhpur, India
- Hirawati Deval
| | - Mahima Mittal
- Department of Pediatrics, All India Institute of Medical Sciences, Gorakhpur, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, India
- *Correspondence: Rajni Kant
| | - Vijay P. Bondre
- Encephalitis Group, National Institute of Virology, Pune, India
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12
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Deval H, Alagarasu K, Srivastava N, Bachal R, Mittal M, Agrawal A, Bote M, Gondhalekar A, Bondre VP, Kant R. Association of single nucleotide polymorphisms in the CD209, MMP9, TNFA and IFNG genes with susceptibility to Japanese encephalitis in children from North India. Gene 2022; 808:145962. [PMID: 34530082 DOI: 10.1016/j.gene.2021.145962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022]
Abstract
Japanese encephalitis (JE), an acute encephalitis syndrome disease caused by infection with JE virus (JEV), is an important mosquito borne disease in developing countries. The clinical outcomes of JEV infection show inter individual differences. Only in a minor percent of the infected subjects, the disease progresses into acute encephalitis syndrome. Single nucleotide polymorphisms in the host immune response related genes are known to affect susceptibility to JE. In the present study, 238 JE cases and 405 healthy controls (HCs) without any known history of encephalitis were investigated for SNPs in the CD209 MX1, TLR3, MMP9, TNFA and IFNG genes which are important in the immune response against JEV by PCR based methods. The results revealed higher frequencies of heterozygous genotypes of CD209 rs4804803, MMP9 rs17576, TNFA rs1800629 and IFNG rs2430561 in JE cases compared to HCs. These SNPs were associated with JE in an over-dominant genetic model (Odds ratio with 95% CI 1.51 (1.09-2.10) for CD209 rs4804803, 1.52 (1.09-2.11) for MMP9 rs17576, and 1.55 (1.12-2.15) for IFNG rs2430561). The association of G/A genotype of TNFA rs1800629 with JE was confirmed in a larger sample size. The results suggest the association of CD209 rs4804803, MMP9 rs17576, IFNG rs2430561 and TNFA rs1800629 polymorphisms with susceptibility to JE.
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Affiliation(s)
- Hirawati Deval
- ICMR-Regional Research Medical Centre, Gorakhpur, Uttar Pradesh, India.
| | | | - Neha Srivastava
- ICMR-Regional Research Medical Centre, Gorakhpur, Uttar Pradesh, India
| | - Rupali Bachal
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Mahima Mittal
- All India Institute of Medical Sciences, Gorakhpur, Uttar Pradesh, India
| | - Apoorv Agrawal
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Minal Bote
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Vijay P Bondre
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajni Kant
- ICMR-Regional Research Medical Centre, Gorakhpur, Uttar Pradesh, India
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13
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Deval H, Nyayanit DA, Mishra SK, Yadav PD, Zaman K, Shankar P, Misra BR, Behera SP, Kumar N, Kumar A, Bhardwaj P, Dwivedi GR, Singh R, Shete AM, Pandit P, Pandey AK, Yadav GK, Gupta S, Kumar M, Kavathekar A, Singh RS, Prajapati S, Kant R. Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Front Med (Lausanne) 2022; 8:781287. [PMID: 35071267 PMCID: PMC8777020 DOI: 10.3389/fmed.2021.781287] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes-49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.
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Affiliation(s)
- Hirawati Deval
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Pragya D. Yadav
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Prem Shankar
- All India Institute of Medical Sciences, Gorakhpur, India
| | - Brij R. Misra
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Niraj Kumar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Abhinendra Kumar
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Pooja Bhardwaj
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Gaurav Raj Dwivedi
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Anita M. Shete
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Priyanka Pandit
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Ashok K. Pandey
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Girijesh Kumar Yadav
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Shashi Gupta
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Manoj Kumar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Asif Kavathekar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Ravi Shankar Singh
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Sanjay Prajapati
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
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Das A, Srivastava N, Deval H, Khan N, Kant R. Decline of Japanese encephalitis in Eastern Uttar Pradesh, India, 2009-2019. ASIAN PAC J TROP MED 2022. [DOI: 10.4103/1995-7645.345940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Behera SP, Kumar N, Singh R, Deval H, Zaman K, Misra B, Pandey A, Kant R, Kavathekar A, Kumar S, Nuthakki MR, Bondre VP. Molecular Detection and Genetic Characterization of Orientia tsutsugamushi from Hospitalized Acute Encephalitis Syndrome Cases During Two Consecutive Outbreaks in Eastern Uttar Pradesh, India. Vector Borne Zoonotic Dis 2021; 21:747-752. [PMID: 34191633 DOI: 10.1089/vbz.2021.0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Seasonal outbreaks of acute encephalitis syndrome (AES) have been reported especially in the pediatric population with a high case fatality rate in Eastern Uttar Pradesh, India. Orientia tsutsugamushi (OT) is a causative agent of scrub typhus that has been recently identified as a major cause of AES. However, the specific genotypes of OT responsible for AES cases of this region are not known. Therefore, the present study was undertaken to understand the molecular epidemiology of OT prevailing in the AES endemic Eastern Uttar Pradesh region of India. Methods: The study was conducted on 2529 hospitalized AES cases from August 2016 to December 2017. The presence of antibodies against OT from cerebrospinal fluid (CSF) and serum samples were tested using OT IgM enzyme-linked immunosorbent assay (ELISA), whereas OT DNA was tested from whole blood and CSF specimens targeting the partial gene of 56 kDa using nested PCR. Phylogenetic analysis was conducted with sequences (n = 241) generated in this study. Findings: Among the studied AES cases, 50% were found positive for antibodies against OT, whereas 37% of cases were positive for OT DNA. The genetic analysis study revealed that Gilliam (93.8%) is the prevailing genotype of OT followed by Karp (6.16%) genotype in AES cases. Furthermore, the Gilliam strains of this study showed they were >99% identical to earlier reported Gilliam strains from AES cases. Conclusion: We observed the presence of two main OT genotypes in AES cases, among which the majority of OT genotypes fall under the Gilliam clade. The understanding of predominant genotype will be beneficial for its future implications in vaccine development strategies and the development of rapid diagnostic tests.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Madhava Rao Nuthakki
- ICMR-RMRC, Gorakhpur, India.,National Institute of Virology, Field Unit, Rajiv Gandhi Institute of Chest Disease Premises, Bangalore, India
| | - Vijay P Bondre
- ICMR-RMRC, Gorakhpur, India.,National Institute of Virology, Field Unit, Rajiv Gandhi Institute of Chest Disease Premises, Bangalore, India
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Murhekar MV, Bhatnagar T, Thangaraj JWV, Saravanakumar V, Kumar MS, Selvaraju S, Rade K, Kumar CPG, Sabarinathan R, Turuk A, Asthana S, Balachandar R, Bangar SD, Bansal AK, Chopra V, Das D, Deb AK, Devi KR, Dhikav V, Dwivedi GR, Khan SMS, Kumar MS, Laxmaiah A, Madhukar M, Mahapatra A, Rangaraju C, Turuk J, Yadav R, Andhalkar R, Arunraj K, Bharadwaj DK, Bharti P, Bhattacharya D, Bhat J, Chahal AS, Chakraborty D, Chaudhury A, Deval H, Dhatrak S, Dayal R, Elantamilan D, Giridharan P, Haq I, Hudda RK, Jagjeevan B, Kalliath A, Kanungo S, Krishnan NN, Kshatri JS, Kumar A, Kumar N, Kumar VGV, Lakshmi GGJN, Mehta G, Mishra NK, Mitra A, Nagbhushanam K, Nimmathota A, Nirmala AR, Pandey AK, Prasad GV, Qurieshi MA, Reddy SD, Robinson A, Sahay S, Saxena R, Sekar K, Shukla VK, Singh HB, Singh PK, Singh P, Singh R, Srinivasan N, Varma DS, Viramgami A, Wilson VC, Yadav S, Yadav S, Zaman K, Chakrabarti A, Das A, Dhaliwal RS, Dutta S, Kant R, Khan AM, Narain K, Narasimhaiah S, Padmapriyadarshini C, Pandey K, Pati S, Patil S, Rajkumar H, Ramarao T, Sharma YK, Singh S, Panda S, Reddy DCS, Bhargava B. SARS-CoV-2 seroprevalence among the general population and healthcare workers in India, December 2020-January 2021. Int J Infect Dis 2021; 108:145-155. [PMID: 34022338 PMCID: PMC8132496 DOI: 10.1016/j.ijid.2021.05.040] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Earlier serosurveys in India revealed seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) of 0.73% in May-June 2020 and 7.1% in August-September 2020. A third serosurvey was conducted between December 2020 and January 2021 to estimate the seroprevalence of SARS-CoV-2 infection among the general population and healthcare workers (HCWs) in India. METHODS The third serosurvey was conducted in the same 70 districts as the first and second serosurveys. For each district, at least 400 individuals aged ≥10 years from the general population and 100 HCWs from subdistrict-level health facilities were enrolled. Serum samples from the general population were tested for the presence of immunoglobulin G (IgG) antibodies against the nucleocapsid (N) and spike (S1-RBD) proteins of SARS-CoV-2, whereas serum samples from HCWs were tested for anti-S1-RBD. Weighted seroprevalence adjusted for assay characteristics was estimated. RESULTS Of the 28,598 serum samples from the general population, 4585 (16%) had IgG antibodies against the N protein, 6647 (23.2%) had IgG antibodies against the S1-RBD protein, and 7436 (26%) had IgG antibodies against either the N protein or the S1-RBD protein. Weighted and assay-characteristic-adjusted seroprevalence against either of the antibodies was 24.1% [95% confidence interval (CI) 23.0-25.3%]. Among 7385 HCWs, the seroprevalence of anti-S1-RBD IgG antibodies was 25.6% (95% CI 23.5-27.8%). CONCLUSIONS Nearly one in four individuals aged ≥10 years from the general population as well as HCWs in India had been exposed to SARS-CoV-2 by December 2020.
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Affiliation(s)
- Manoj V Murhekar
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu, India.
| | - Tarun Bhatnagar
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | | | - V Saravanakumar
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | | | - Sriram Selvaraju
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Kiran Rade
- WHO Country Office for India, New Delhi, India
| | - C P Girish Kumar
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - R Sabarinathan
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Alka Turuk
- Indian Council of Medical Research, New Delhi, India
| | - Smita Asthana
- ICMR National Institute of Cancer Prevention and Research, NOIDA, Uttar Pradesh, India
| | - Rakesh Balachandar
- ICMR National Institute of Occupational Health, Ahmedabad, Gujarat, India
| | | | - Avi Kumar Bansal
- ICMR National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Vishal Chopra
- State TB Training and Demonstration Centre, Patiala, Punjab, India
| | - Dasarathi Das
- ICMR Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Alok Kumar Deb
- ICMR National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Kangjam Rekha Devi
- ICMR Regional Medical Research Centre, N.E. Region, Dibrugarh, Assam, India
| | - Vikas Dhikav
- ICMR National Institute for Implementation Research on Non-Communicable Diseases, Jodhpur, Rajasthan, India
| | | | | | - M Sunil Kumar
- State TB Training and Demonstration Centre, Thiruvananthapuram, Kerala, India
| | - Avula Laxmaiah
- ICMR National Institute of Nutrition, Hyderabad, Telangana, India
| | - Major Madhukar
- ICMR Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | | | - Chethana Rangaraju
- National Tuberculosis Institute, Bangalore and Lady Willingdon State TB Centre, Bengaluru, Karnataka, India
| | | | - Rajiv Yadav
- ICMR National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Rushikesh Andhalkar
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - K Arunraj
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | - Pravin Bharti
- ICMR National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | | | - Jyothi Bhat
- ICMR National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | | | - Debjit Chakraborty
- ICMR National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Anshuman Chaudhury
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Hirawati Deval
- ICMR Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Sarang Dhatrak
- ICMR National Institute of Occupational Health, Ahmedabad, Gujarat, India
| | - Rakesh Dayal
- State TB Training and Demonstration Centre, Ranchi, Jharkhand, India
| | - D Elantamilan
- ICMR National Institute for Implementation Research on Non-Communicable Diseases, Jodhpur, Rajasthan, India
| | | | - Inaamul Haq
- Government Medical College Srinagar, Srinagar, Jammu, India
| | - Ramesh Kumar Hudda
- ICMR National Institute for Implementation Research on Non-Communicable Diseases, Jodhpur, Rajasthan, India
| | - Babu Jagjeevan
- ICMR National Institute of Nutrition, Hyderabad, Telangana, India
| | - Arshad Kalliath
- State TB Training and Demonstration Centre, Thiruvananthapuram, Kerala, India
| | - Srikanta Kanungo
- ICMR Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | | | | | - Alok Kumar
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Niraj Kumar
- ICMR Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - V G Vinoth Kumar
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | - Ganesh Mehta
- ICMR National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Nandan Kumar Mishra
- ICMR National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Anindya Mitra
- State TB Training and Demonstration Centre, Ranchi, Jharkhand, India
| | - K Nagbhushanam
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | - A R Nirmala
- National Tuberculosis Institute, Bangalore and Lady Willingdon State TB Centre, Bengaluru, Karnataka, India
| | | | | | | | | | - Aby Robinson
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Seema Sahay
- ICMR National AIDS Research Institute, Pune, Maharashtra, India
| | - Rochak Saxena
- State TB Training and Demonstration Centre, Raipur, Chhattisgarh, India
| | - Krithikaa Sekar
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | - Hari Bhan Singh
- ICMR National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Prashant Kumar Singh
- ICMR National Institute of Cancer Prevention and Research, NOIDA, Uttar Pradesh, India
| | - Pushpendra Singh
- ICMR National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Rajeev Singh
- ICMR Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Nivetha Srinivasan
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | - Ankit Viramgami
- ICMR National Institute of Occupational Health, Ahmedabad, Gujarat, India
| | | | - Surabhi Yadav
- ICMR National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Suresh Yadav
- ICMR National Institute for Implementation Research on Non-Communicable Diseases, Jodhpur, Rajasthan, India
| | - Kamran Zaman
- ICMR Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Amit Chakrabarti
- ICMR National Institute of Occupational Health, Ahmedabad, Gujarat, India
| | - Aparup Das
- ICMR National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - R S Dhaliwal
- ICMR National Institute for Implementation Research on Non-Communicable Diseases, Jodhpur, Rajasthan, India
| | - Shanta Dutta
- ICMR National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Rajni Kant
- ICMR Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - A M Khan
- Indian Council of Medical Research, New Delhi, India
| | - Kanwar Narain
- ICMR Regional Medical Research Centre, N.E. Region, Dibrugarh, Assam, India
| | - Somashekar Narasimhaiah
- National Tuberculosis Institute, Bangalore and Lady Willingdon State TB Centre, Bengaluru, Karnataka, India
| | | | - Krishna Pandey
- ICMR Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Sanghamitra Pati
- ICMR Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Shripad Patil
- ICMR National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | | | | | - Y K Sharma
- State TB Training and Demonstration Centre, Raipur, Chhattisgarh, India
| | - Shalini Singh
- ICMR National Institute of Cancer Prevention and Research, NOIDA, Uttar Pradesh, India
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi, India
| | - D C S Reddy
- Independent Consultant, Lucknow, Uttar Pradesh, India
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Deval H, Behera SP, Agrawal A, Singh R, Misra B, Janardhan V, Patil G, Sah K, Kumar N, Singh R, Bondre VP. Genetic characterization of dengue virus serotype 2 isolated from dengue fever outbreaks in eastern Uttar Pradesh and western Bihar, India. J Med Virol 2021; 93:3322-3329. [PMID: 32633814 DOI: 10.1002/jmv.26239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 01/23/2023]
Abstract
Dengue (DEN) is the most common cause of mosquito-borne endemic viral diseases in the tropical and subtropical countries. DEN outbreaks associated with multiple dengue virus (DV) serotypes have been regularly reported in different parts of India. This study was done during DEN outbreaks in 2015 to 2016 in UP and Bihar where DEN-2 was found as the only prevalent serotype. DV-2 was the only serotype amplified in serotype-specific reverse-transcription polymerase chain reaction from sera of 210 (65.21%) out of 322 DV NS1 antigen-positive patients. Further genetic analysis based on full-length envelope (E) protein sequence derived from patient's sera as well as DV isolate showed the circulation of lineages I and III of DV-2 cosmopolitan genotype during 2015 and lineage II during 2016. Finally, the phylogenetic analysis using the E gene sequence revealed that these DV-2 strains have a close genetic relationship with the recently reported DV-2 genotypes from DEN outbreaks reported from different parts of north India. These results showed the circulation of cosmopolitan genotype of DV-2 in eastern Uttar Pradesh and western Bihar, India. The genetic database generated on circulating DV strains in this study will be useful as reference for disease surveillance and strengthening laboratory diagnosis protocols.
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Affiliation(s)
- Hirawati Deval
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Sthita P Behera
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Awdhesh Agrawal
- Division of Pathology, Gorakhnath Hospital, Gorakhpur, Uttar Pradesh, India
| | - Rajeev Singh
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Brijranjan Misra
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Vanka Janardhan
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Gajanan Patil
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Kamlesh Sah
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Niraj Kumar
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Ravishankar Singh
- Molecular Virology, National Institute of Virology (Gorakhpur Unit), Gorakhpur, Uttar Pradesh, India
| | - Vijay P Bondre
- Encephalitis Group, ICMR-National Institute of Virology, Microbial Containment Complex, Pune, Maharashtra, India
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18
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Yadav PD, Nyayanit DA, Majumdar T, Patil S, Kaur H, Gupta N, Shete AM, Pandit P, Kumar A, Aggarwal N, Narayan J, Vijay N, Kalawat U, Sugunan AP, Munivenkatappa A, Sharma T, Devi S, Majumdar T, Jaryal S, Bakshi R, Joshi Y, Sahay R, Shastri J, Singh M, Kumar M, Rawat V, Dutta S, Yadav S, Krishnasamy K, Raut S, Biswas D, Borkakoty B, Verma S, Rani S, Deval H, Patel D, Turuk J, Malhotra B, Fomda B, Nag V, Jain A, Bhargava A, Potdar V, Cherian S, Abraham P, Gopal A, Panda S, Bhargava B. An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Viruses 2021; 13:v13050925. [PMID: 34067745 PMCID: PMC8156686 DOI: 10.3390/v13050925] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the ‘GH’ clade, whereas the southern part reported the ‘GR’, with a few exceptions. These sequences also revealed the presence of single independent mutations—E484Q and N440K—from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January–August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.
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Affiliation(s)
- Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Harmanmeet Kaur
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Nivedita Gupta
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
- Correspondence:
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Neeraj Aggarwal
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Jitendra Narayan
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Neetu Vijay
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Usha Kalawat
- Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, India;
| | | | | | - Tara Sharma
- VRDL Sikkim Government College of Nursing, Gangtok 737101, India;
| | - Sulochna Devi
- Regional Institute of Medical Sciences IMPHAL, Imphal 795004, India;
| | - Tapan Majumdar
- Government Medical College, Agartala, Tripura 799006, India;
| | - Subhash Jaryal
- Dr. Rajendra Prasad Government Medical College, (H.P.), Kangra 176001, India;
| | | | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Rima Sahay
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Jayanti Shastri
- Kasturba Hospital for Infectious Diseases, Mumbai 400034, India;
| | - Mini Singh
- Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India;
| | - Manoj Kumar
- Rajendra Institute of Medical Sciences, Ranchi 834009, India;
| | - Vinita Rawat
- Government Medical College, Haldwani 263129, India;
| | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata 700010, India;
| | - Sarita Yadav
- Bhagat Phool Singh Government Medical College, Sonipat 131305, India;
| | - Kaveri Krishnasamy
- King Institute of Preventive Medicine & Research, Chennai 600032, India;
| | - Sharmila Raut
- Indira Gandhi Government Medical College & Hospital, Nagpur 440018, India;
| | - Debasis Biswas
- All India Institute of Medical Sciences, Bhopal 462020, India;
| | | | - Santwana Verma
- Indira Gandhi Medical College & Hospital, Shimla 171001, India;
| | - Sudha Rani
- Osmania Medical College, Hyderabad 500095, India;
| | - Hirawati Deval
- Regional Medical Research Center Gorakhpur, Gorakhpur 273013, India;
| | - Disha Patel
- B.J. Medical College, Ahmedabad 380016, India;
| | | | | | - Bashir Fomda
- Sher-I-Kashmir Institute of Medical Sciences, Srinagar 190011, India;
| | | | - Amita Jain
- Department of Microbiology, King George’s Medical University, Lucknow 226003, India;
| | - Anudita Bhargava
- All India Institute of Medical Sciences, Raipur, Raipur 492099, India;
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Sarah Cherian
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Anjani Gopal
- Indian Institute of Science Education and Research, Pune 411008, India;
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Balram Bhargava
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
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Misra BR, Kumar N, Kant R, Deval H, Singh R, Pandey AK, Behera SP, Bondre VP. Abundance of Ticks (Acari: Ixodidae) and Presence of Rickettsia and Anaplasma in Ticks Infesting Domestic Animals From Northern India. J Med Entomol 2021; 58:1370-1375. [PMID: 33470412 DOI: 10.1093/jme/tjaa296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Indexed: 06/12/2023]
Abstract
Rickettsia and Anaplasma are bacteria that can be transmitted by hematophagous arthropods such as ticks infesting animals in close proximity to humans. The main objective of the present study was to investigate abundance of common tick species infesting domestic animals and presence of Rickettsia and Anaplasma in tick populations. Adult ticks were collected from domestic animals in rural areas and screened by molecular detection of bacterial DNA for these two genera of bacteria. A total of 1,778 adult ixodid tick specimens were collected from 200 cattle, 200 buffaloes, 200 goats, and 40 dogs. The collection consisted of four species of ixodid ticks, Rhipicephalus (Boophilus) microplus (Canestrini) (83.8%), Hyalomma kumari (Sharif) (7.1%), Rhipicephalus sanguineus (Latreille) (6.4%), and Dermacentor auratus (Supino) (2.7%) infesting the domestic animals. The prevalence of all the collected tick species was highest in the month of October. Anaplasma spp. was the most frequently identified bacteria (3.3%) in tested ticks. Of 17 positive tick pools for Anaplasma spp., 14 pools were from ticks infesting cattle, 2 pools of ticks collected from buffalo, and the remaining pool were ticks infesting a goat at the time of collection. Although 1.6% tick pools of R. microplus collected from cattle tested positive for Rickettsia spp., present investigation provides evidence of the most prevalent ixodid ticks infesting domestic animals and the presence of obligate intracellular bacteria, Rickettsia and Anaplasma, in these ticks collected in the Gorakhpur division of Northern India.
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Affiliation(s)
- Brij Ranjan Misra
- ICMR-Regional Medical Research Centre Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Niraj Kumar
- ICMR-Regional Medical Research Centre Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | - Ashok Kumar Pandey
- ICMR-Regional Medical Research Centre Gorakhpur, Gorakhpur, Uttar Pradesh, India
| | | | - Vijay P Bondre
- ICMR-National Institute of Virology, Pune, Maharashtra, India
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20
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Deval H, Kant R, Bondre V, Mittal M, Murhekar M, Thangaraj J, Zaman K, Pandey A, Singh R, Misra B, Behera S, Kumar N, Shankar P, Srivastava N. A decade of acute encephalitis syndrome (AES) cases in eastern Uttar Pradesh, India: etiological scenario and preventive strategies (2010–2019). Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.11.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Deoshatwar AR, Behera SP, Kumar N, Misra BR, Deval H, Bondre VP, Mittal M. Primary varicella zoster virus infection-related hemiparesis and fatal neurological complications in an immunocompetent girl. Natl Med J India 2019; 32:381-382. [PMID: 33380643 DOI: 10.4103/0970-258x.303630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Avinash R Deoshatwar
- Division of Encephalitis, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sthita Pragnya Behera
- Division of Encephalitis, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Niraj Kumar
- Division of Encephalitis, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Brij Ranjan Misra
- Division of Encephalitis, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Hirawati Deval
- Division of Encephalitis, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Vijay P Bondre
- Division of Encephalitis, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Mahima Mittal
- Department of Paediatrics, Baba Raghav Das Medical College, Gorakhpur, Uttar Pradesh, India
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22
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Deval H, Alagarasu K, Mittal M, Srivastava N, Bachal R, Gondhalekar A, Chaudhary U, Chowdhary D, Bondre VP. Association of single nucleotide polymorphisms in TNFA and CCR5 genes with Japanese Encephalitis: A study from an endemic region of North India. J Neuroimmunol 2019; 336:577043. [PMID: 31479868 DOI: 10.1016/j.jneuroim.2019.577043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 01/23/2023]
Abstract
TNFA, IL1B, HMGB1, IL10, CXCL8, CCL2 and CCR5 gene polymorphisms were investigated in 183 Japanese Encephalitis (JE) cases and 361 healthy controls from North India. Higher frequency of TNFA rs1800629 G/A, CCR5 rs1799987 genotypes with A allele and lower frequency of combination lacking TNFA rs1800629 A, CCR5 rs333 Δ32, andCCR5 rs1799987 A alleles and CCL2 rs1024611 G/G genotype was observed in JE cases. TNFA rs1800629 A and CCR5 rs1799987 A alleles were associated with susceptibility while combination lacking TNFA rs1800629 A, CCR5 rs333 Δ32, and rs1799987 A alleles and CCL2 rs1024611 G/G genotype was associated with protection to JE.
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Affiliation(s)
- Hirawati Deval
- ICMR-Regional Research Medical Centre, Gorakhpur, Uttar Pradesh, India.
| | | | - Mahima Mittal
- BRD Medical College, Gorakhpur, Uttar Pradesh, India
| | - Neha Srivastava
- ICMR-Regional Research Medical Centre, Gorakhpur, Uttar Pradesh, India
| | - Rupali Bachal
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | | | | | - Vijay P Bondre
- ICMR-National Institute of Virology, Pune, Maharashtra, India
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Mittal M, Bondre V, Murhekar M, Deval H, Rose W, Verghese VP, Mittal M, Patil G, Sabarinathan R, Vivian Thangaraj JW, Kanagasabai K, Prakash JAJ, Gupta N, Gupte MM, Gupte MD. Acute Encephalitis Syndrome in Gorakhpur, Uttar Pradesh, 2016: Clinical and Laboratory Findings. Pediatr Infect Dis J 2018; 37:1101-1106. [PMID: 29746378 DOI: 10.1097/inf.0000000000002099] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Seasonal outbreaks of acute encephalitis syndrome (AES) with high fatality have been occurring in Gorakhpur, Uttar Pradesh, India, for several years. We conducted investigations during the 2016 outbreak to identify the etiology. METHODS We included 407 hospitalized AES patients with cerebrospinal fluid pleocytosis (>5 cells/mm) in our study. These patients were clinically examined; their blood and cerebrospinal fluid samples were collected and investigated for scrub typhus (ST), Japanese encephalitis virus (JEV), dengue virus and spotted fever group of Rickettsia by serology and/or polymerase chain reaction. RESULTS Of the 407 AES patients, 266 (65.4%), 42 (10.3%) and 29 (7.1%) were diagnosed to have ST, JEV and dengue infection, respectively. Four patients were diagnosed to have spotted fever group of Rickettsia infection. A significantly higher proportion of ST patients with AES had hepatomegaly, splenomegaly and facial edema. The common hematologic and biochemical abnormalities among ST-positive patients include thrombocytopenia, raised liver enzymes and bilirubin levels. The case fatality ratio was significantly higher among ST-negative AES patients (36.2% vs. 15.2%; P < 0.05). CONCLUSIONS ST accounted for approximately two third of the AES case-patients. Efforts are required to identify the etiology of AES case-patients who are negative for ST, JEV and dengue fever.
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Affiliation(s)
| | - Vijay Bondre
- ICMR-National Institute of Virology, Gorakhpur Unit, Gorakhpur, Uttar Pradesh, India
| | - Manoj Murhekar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Hirawati Deval
- ICMR-National Institute of Virology, Gorakhpur Unit, Gorakhpur, Uttar Pradesh, India
| | - Winsley Rose
- Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | | | | | - Gajanan Patil
- ICMR-National Institute of Virology, Gorakhpur Unit, Gorakhpur, Uttar Pradesh, India
| | | | | | | | | | | | | | - Mohan D Gupte
- Indian Council of Medical Research, New Delhi, India
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Deval H, Katoch K, Chauhan DS, Tyagi AK, Gupta RK, Kamal R, Kumar A, Yadav VS, Katoch VM, Hussain T. TlyA protein of Mycobacterium leprae: a probable bio-marker of active infection. LEPROSY REV 2016. [DOI: 10.47276/lr.87.4.501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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25
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Deval H, Katoch K, Chauhan DS, Tyagi AK, Gupta RK, Kamal R, Kumar A, Yadav VS, Katoch VM, Hussain T. TlyA protein of Mycobacterium leprae: a probable bio-marker of active infection. LEPROSY REV 2016; 87:501-515. [PMID: 30226354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The extent of pathogenicity of the mycobacterial infections depends on virulence factors that mediate survival inside macrophages. Virulence factors are generally believed to be specific for pathogenic species and mutated/non-functional in nonpathogenic strains. Mycobacterial TlyA can modulate the phagolysosome maturation pathway, immediately after entry into macrophages. Over-expression of open reading frame (ORF) ML1358 (tlyA) in tissues of leprosy patients by partial DNA chip and real time PCR analysis during active infection attracted our interest to explore the properties of this gene at molecular and serological levels, to understand its role in the host. Molecular properties were studied by cloning and expression of the corresponding gene in pASK-iba 43(þ) expression vector in E. coli and bioinformatics tools while sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and ELISA were applied to investigate the serological significance of rTlyA protein in different clinical states of leprosy. We observed that TlyA has a close relation among mycobacteria with specific protein domains in slow growing intracellular adapted pathogenic species. The presence of trans-membrane domains indicates its association to the cell membrane. The study revealed its highly significant sero-reactivity (P value , 0·001) in borderline lepromatous (BL) patients, and those with reversal reaction (RR) and erythema nodosum leprosum (ENL). Its role in active infection, association with the cell membrane, presence in pathogenic species and high sero-reactivity, suggested the tlyA gene as a strong disease progression marker.
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