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Philomenadin FS, Singh MP, Shastri J, Phukan AC, Nagarajan M, Kaliaperumal S, Ratho RK, Ram J, Sathe MJ, Ingole A, Rathod DB, Nongrum B, Parvez R, Malik V, Dhodapkar R. Whole genome analysis of Human Mastadenovirus D causing Keratoconjunctivitis in India - A multicentre study. J Infect Dev Ctries 2024; 18:450-457. [PMID: 38635622 DOI: 10.3855/jidc.18905] [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: 07/17/2023] [Accepted: 09/07/2023] [Indexed: 04/20/2024] Open
Abstract
INTRODUCTION Human mastadenovirus (HAdV) types 8, 37, 64 have been considered the major contributors in Epidemic keratoconjunctivitis (EKC) epidemics, but recent surveillance data have shown the involvement of emerging recombinants, including HAdV-53, HAdV-54, and HAdV-56. In our initial work, positive samples for adenovirus revealed that our strains were closer to HAdV-54 than HAdV-8. Hence, the current study aimed to use whole genome technology to identify the HAdV strain correctly. METHODOLOGY Oxford Nanopore technique was used, wherein a Targeted sequencing approach using long-range PCR amplification was performed. Primers were designed using HAdV-54 (AB448770.2) and HAdV-8 (AB897885.1) as reference sequences. Amplicons were sequenced on the GridION sequencer. Sequences were annotated using Gatu software, and similarities with standard reference sequence was calculated using Bioedit software. The phylogenetic tree was built after alignment in MEGA v7.0 using Neighbour joining method for each of the genes: Penton, Hexon, and Fiber. The effect of novel amino acid changes was evaluated using the PROVEAN tool. The Recombination Detection Program (RDP) package Beta 4.1 was used to identify recombinant sequences. RESULTS Of the five samples sequenced, OL450401, OL540403, and OL540406 showed nucleotide similarity to HAdV-54 in the penton region. Additionally, OL450401 showed a statistically significant recombination event with HAdV-54 as minor and HAdV-8 as major parents. This was further supported by phylogenetic analysis as well. CONCLUSIONS In the present study, we have found evidence of a shift from HAdV-8 towards HAdV-54, thus stressing the need for surveillance of HAdVs and to stay updated on the rise of new recombinants.
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Affiliation(s)
| | - Mini P Singh
- Department of Virology, PGIMER, Chandigarh, India
| | - Jayanthi Shastri
- Department of Microbiology, TNMC & BYL Nair Hospital, Mumbai, India
| | - Anil C Phukan
- Department of Microbiology, NEIGRIHMS, Shillong, India
| | | | | | | | - Jagat Ram
- Department of Ophthalmology, PGIMER, Chandigarh, India
| | - Madhav J Sathe
- Department of Microbiology, TNMC & BYL Nair Hospital, Mumbai, India
| | - Avinash Ingole
- Department of Ophthalmology, BYL Nair Hospital & TNMC, Mumbai, India
| | - Darshana B Rathod
- Department of Ophthalmology, BYL Nair Hospital & TNMC, Mumbai, India
| | | | - Rehnuma Parvez
- Regional Medical Research Centre, Port Blair, A & N, India
| | - Vineeta Malik
- Regional Medical Research Centre, Port Blair, A & N, India
| | - Rahul Dhodapkar
- RVRDL, Department of Microbiology, JIPMER, Pondicherry, India
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2
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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Swami A, Mohanty A, Jamwal A, Turbadkar D, Baveja S, Shastri J, Chitalia V. A comparative analysis of the second and third wave of the Covid-19 pandemic: an experience from a tertiary care hospital in Western India. J Med Microbiol 2023; 72. [PMID: 37171852 DOI: 10.1099/jmm.0.001685] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Introduction. As the world was still recovering from the 2020 pandemic, the devastating impact of Covid-19 driven by the Delta variant shook the world in 2021. As the second wave was declining, there was an unusual surge in Covid-19 positive cases by the end of 2021 which led to global concern about the change in virus characteristics.Hypothesis/gap statement. Whole genome sequencing is critical for understanding a rapidly progressing pandemic.Aim. To provide an insight into the major differences encountered in the changing characteristics between the second and third waves of the pandemic at a tertiary care hospital in India.Methods. A retrospective observational cohort analysis was conducted on Covid-positive patients during the second wave of the Covid-19 pandemic (from March 2021 to April 2021) and the third wave of the Covid-19 pandemic (from December 2021 to January 2022).Results. Out of 303 Covid-19 positive cases, 52 samples were tested by whole genome sequencing during the second wave and 108 during the third wave. A decline of 18.5 % was observed in the case fatality rate from the second wave to the third wave. There was a 5 % decline in the number of patients admitted with ARDS and a 16.3 % decline in the number of patients with co-morbidities.In total, 51.9 percent of cases were due to the Delta variant during the second wave and 95 percent due to the Omicron variant during the third wave. We found that 36.5 % of Covid-positive patients during the second wave had been vaccinated compared to 40 % in the third wave.Conclusion. Whole genome sequencing of clinical samples from a wide range of individuals during a viral epidemic will enable us to develop a more rapid public health response to new variants and identify the required vaccine modifications more quickly.
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Affiliation(s)
- Anjali Swami
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ankita Mohanty
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ashima Jamwal
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Dilip Turbadkar
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Sujata Baveja
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, T.N.Medical college and B.Y.L Nair Charitable Hospital and Lab Director, Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Vidushi Chitalia
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
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Jacob JJ, Pragasam AK, Vasudevan K, Velmurugan A, Priya Teekaraman M, Priya Thirumoorthy T, Ray P, Gupta M, Kapil A, Bai SP, Nagaraj S, Saigal K, Chandola TR, Thomas M, Bavdekar A, Ebenezer SE, Shastri J, De A, Dutta S, Alexander AP, Koshy RM, Jinka DR, Singh A, Srivastava SK, Anandan S, Dougan G, John J, Kang G, Veeraraghavan B, Mutreja A. Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages. PLoS Pathog 2023; 19:e1010650. [PMID: 37115804 PMCID: PMC10171690 DOI: 10.1371/journal.ppat.1010650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/10/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new S. Paratyphi A lineages/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of S. Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since S. Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid S. Paratyphi A serovar becoming a public health threat similar to the S. Typhi of today.
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Affiliation(s)
| | | | - Karthick Vasudevan
- Christian Medical College, Vellore, India
- REVA University, Bangalore, India
| | | | | | | | - Pallab Ray
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Madhu Gupta
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi, India
| | | | | | | | | | | | | | | | - Jayanthi Shastri
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | - Anuradha De
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | - Shantha Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | | | - Dasaratha R Jinka
- Rural Development Trust Hospital, Bathalapalli, Andhra Pradesh, India
| | | | | | | | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jacob John
- Christian Medical College, Vellore, India
| | | | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Acharjee A, Ray A, Salkar A, Bihani S, Tuckley C, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray. Viruses 2023; 15:248. [PMID: 36680289 PMCID: PMC9866125 DOI: 10.3390/v15010248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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6
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Kumar A, Rajan LS, Sabarinath PS K, Shete AM, Sahay RR, Patil DY, Ingole N, K K, Padinakarai AC, GB S, Shastri J, Padukone S, Joshi Y, Patil S, Majumdar T, Verma A, Yemul J, Shende N, Kumari V, Vedpathak P, Sathe S, Gawande P, Yadav PD. First detection of Varicella Zoster Virus clade 9 cases in India during mpox surveillance. Ann Med 2023; 55:2253733. [PMID: 37672487 PMCID: PMC10484040 DOI: 10.1080/07853890.2023.2253733] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The multi-country mpox outbreak across the globe has led to the systematic surveillance of mpox cases in India. During the surveillance of mpox, we encountered cases of Varicella Zoster Virus (VZV) in suspected mpox cases amongst children & adults. This study focused on the genomic characterization of VZV in India. METHODS A total of 331 mpox suspected cases were tested for VZV through real-time PCR, and the positive samples were subjected to next-generation sequencing to retrieve the whole genome of VZV using CLC genomics software. Phylogenetic analysis has been done in MEGA 11.0 software to identify circulating clades. RESULT Of the 331 suspected cases, 28 cases with vesicular rashes were found to be positive for VZV. The maximum genome could be retrieved from the clinical specimens of 16 cases with coverage greater than 98% when mapped with reference strain Dumas (NC 001348). The phylogenetic analyses of these sequences determined the circulation of clades 1, 5, and 9 in India. Further, the sequence analysis demonstrated non-synonymous single nucleotide polymorphism (SNPs) among specific ORF of VZV including ORF 14, ORF 22, ORF 36, ORF 37 and ORF 51. Although clade 1 and 5 has been reported earlier, the circulation of clade 9 of VZV has been determined for the first time in India. CONCLUSION Although the circulation of different clades of VZV was reported from India, the presence of clade 9 was detected for the first time during the mpox surveillance.
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Affiliation(s)
- Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Lekshmi S. Rajan
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Rima R. Sahay
- 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
| | - Nayana Ingole
- Virus Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Kaveri K
- King Institute of Preventive Medicine and Research, Chennai, India
| | | | - Shantala GB
- Bangalore Medical College and Research Institute, Bengaluru, India
| | - Jayanthi Shastri
- Virus Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | | | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Ajay Verma
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jyoti Yemul
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nandini Shende
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Vaishnavi Kumari
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pratiksha Vedpathak
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Shubhangi Sathe
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pranita Gawande
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
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7
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Rajoria S, Nair D, Suvarna K, Pai MGJ, Salkar A, Palanivel V, Verma A, Barpanda A, Awasthi G, Doshi H, Dhara V, Burli A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai. Adv Exp Med Biol 2023; 1412:175-195. [PMID: 37378767 DOI: 10.1007/978-3-031-28012-2_9] [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] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gaurav Awasthi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Hastyn Doshi
- Department of Computer Science, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vivek Dhara
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ananya Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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8
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Shastri J, Yadav PD, Agrawal S, Shete AM, Nyayanit DA, Parikh S, Gomare M, Sahay RR, Patil DY, Dudhmal M, Kadam N. Community transmission of SARS-CoV-2 with B.1.1.7 lineage in Mumbai, India. J Microbiol Immunol Infect 2022; 55:1116-1121. [PMID: 34772636 PMCID: PMC8563497 DOI: 10.1016/j.jmii.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/27/2021] [Accepted: 10/20/2021] [Indexed: 12/27/2022]
Abstract
The B.1.1.7 (Alpha) variant has been detected in Mumbai, India during February 2021. Subsequently, we retrieved 43 sequences from specimens of 51 COVID-19 cases from Mumbai. The sequence analysis revealed that the cases were mainly affected with Alpha variant which suggests its role in community transmission of SARS-CoV-2 in Mumbai, India.
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Affiliation(s)
- Jayanthi Shastri
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, 400034, India,Corresponding author. Department of Microbiology T.N. Medical College & B. y. L. Nair Hospital i/c Molecular Diagnostic reference Laboratory Kasturba hospital for infectious diseases Mumbai, 400011, India. Fax: +91 22 23072663
| | - Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Sachee Agrawal
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, 400034, India
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Swapneil Parikh
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, 400034, India
| | - Mangala Gomare
- Public Health Department, Municipal Corporation of Greater Mumbai, Mumbai, Maharashtra, 400 001, India
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Deepak Y. Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Neelam Kadam
- Public Health Department, Municipal Corporation of Greater Mumbai, Mumbai, Maharashtra, 400 001, India
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9
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Yadav PD, Kumar G, Mukherjee A, Nyayanit DA, Shete AM, Sahay RR, Kumar A, Majumdar T, Patil S, Pandit P, Joshi Y, Dudhmal M, Panda S, Sharma LK, Yadav Ml K, Shastri J, Gangwar M, Munivenkattapa A, Potdar V, Nagamani K, Goyal K, Gadepalli R, Thomas M, Shukla S, Nagraj P, Gupta V, Dalela G, Umar N, Patel SM. Delta variant SARS-CoV-2 infections in pediatric cases during the second wave in India. J Microbiol Immunol Infect 2022; 55:1060-1068. [PMID: 35843834 PMCID: PMC9250235 DOI: 10.1016/j.jmii.2022.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/26/2022] [Accepted: 06/16/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND During October 2020, Delta variant was detected for the first time in India and rampantly spread across the globe. It also led to second wave of pandemic in India which affected millions of people. However, there is limited information pertaining to the SARS-CoV-2 strain infecting the children in India. METHODS Here, we assessed the SARS-CoV-2 lineages circulating in the pediatric population of India during the second wave of the pandemic. Clinical and demographic details linked with the nasopharyngeal/oropharyngeal swabs (NPS/OPS) collected from SARS-CoV-2 cases (n = 583) aged 0-18 year and tested positive by real-time RT-PCR were retrieved from March to June 2021. RESULTS Symptoms were reported among 37.2% of patients and 14.8% reported to be hospitalized. The E gene CT value had significant statistical difference at the point of sample collection when compared to that observed in the sequencing laboratory. Out of these 512 sequences 372 were VOCs, 51 were VOIs. Most common lineages observed were Delta, followed by Kappa, Alpha and B.1.36, seen in 65.82%, 9.96%, 6.83% and 4.68%, respectively in the study population. CONCLUSION Overall, it was observed that Delta strain was the leading cause of SARS-CoV-2 infection in Indian children during the second wave of the pandemic. We emphasize on the need of continuous genomic surveillance in SARS-CoV-2 infection even amongst children.
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Affiliation(s)
- Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India,Corresponding author
| | - Gunjan Kumar
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Aparna Mukherjee
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Lokesh Kumar Sharma
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Kala Yadav Ml
- Bowring and Lady Curzon Medical College, Bangalore 560001, Karnataka, India
| | - Jayanthi Shastri
- Kasturba Hospital of Infectious Diseases, Mumbai 400011, Maharashtra, India
| | - Mayank Gangwar
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Ashok Munivenkattapa
- Indian Council of Medical Research-National Institute of Virology, Bangalore 560029, India
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - K. Nagamani
- Gandhi Hospital, Secunderabad, Telangana 500003, India
| | - Kapil Goyal
- Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | | | - Maria Thomas
- Christian Medical College, Ludhiana, Punjab 141008, India
| | - Suruchi Shukla
- King George Medical University, Lucknow 226003, Uttar Pradesh, India
| | - P. Nagraj
- Gandhi Medical College, Bhopal 462001, Madhya Pradesh, India
| | - Vivek Gupta
- Government Institute of Medical Sciences, Noida 201310, Uttar Pradesh, India
| | - Gaurav Dalela
- Sawai Man Singh Medical College, Jaipur 302004, Rajasthan, India
| | - Nawaz Umar
- Gulbarga Institute of Medical Sciences, Rajiv Gandhi University of Health Sciences, Gulbarga 585105, Karnataka, India
| | - Sweety M. Patel
- Smt. NHL Municipal Medical College, Ahmedabad 380006, Gujarat, India
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10
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Mahilkar S, Agrawal S, Chaudhary S, Parikh S, Sonkar SC, Verma DK, Chitalia V, Mehta D, Koner BC, Vijay N, Shastri J, Sunil S. SARS-CoV-2 variants: Impact on biological and clinical outcome. Front Med (Lausanne) 2022; 9:995960. [PMID: 36438034 PMCID: PMC9685312 DOI: 10.3389/fmed.2022.995960] [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: 07/16/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was first identified in December 2019, in Wuhan, China was found to be the etiological agent for a novel respiratory infection that led to a Coronavirus Induced Disease named COVID-19. The disease spread to pandemic magnitudes within a few weeks and since then we have been dealing with several waves across the world, due to the emergence of variants and novel mutations in this RNA virus. A direct outcome of these variants apart from the spike of cases is the diverse disease presentation and difficulty in employing effective diagnostic tools apart from confusing disease outcomes. Transmissibility rates of the variants, host response, and virus evolution are some of the features found to impact COVID-19 disease management. In this review, we will discuss the emerging variants of SARS-CoV-2, notable mutations in the viral genome, the possible impact of these mutations on detection, disease presentation, and management as well as the recent findings in the mechanisms that underlie virus-host interaction. Our aim is to invigorate a scientific debate on how pathogenic potential of the new pandemic viral strains contributes toward development in the field of virology in general and COVID-19 disease in particular.
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Affiliation(s)
- Shakuntala Mahilkar
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sachee Agrawal
- Department of Microbiology, Topiwala National Medical College (TNMC) and Bai Yamunabai Laxman Nair (BYL) Charitable Hospital, Mumbai, Maharashtra, India
| | - Sakshi Chaudhary
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Swapneil Parikh
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Subash C. Sonkar
- Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi, India
| | - Dileep Kumar Verma
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Vidushi Chitalia
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Divya Mehta
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Bidhan Chandra Koner
- Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospital, New Delhi, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health and Family Welfare, New Delhi, India
| | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College (TNMC) and Bai Yamunabai Laxman Nair (BYL) Charitable Hospital, Mumbai, Maharashtra, India
| | - Sujatha Sunil
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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11
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Yadav PD, Sahay RR, Agrawal S, Shete A, Adsul B, Tripathy S, Nyayanit DA, Manrai M, Patil DY, Kumar S, Marwah V, Sapkal GN, Shastri J, Viswanathan R, Pandit P, Mishra Y, Chavan S, Joshi Y, Kumar TA, Majumdar T, Kumar A, Patil S, Munshi R, Desai U, Kaushal H, Suryawanshi A, Dudhmal M, Gawande P, Jain R, Waghmare A, Kalele K, Vedpathak P, Yemul J, Bodke P, Kore T, Kakrani AL, Athavale P, Suryawanshi P, Patsute S, Padbidri V, Awate P, Abraham P. Clinical, immunological and genomic analysis of the post vaccinated SARS-CoV-2 infected cases with Delta derivatives from Maharashtra, India, 2021. J Infect 2022; 85:e26-e29. [PMID: 35398410 PMCID: PMC8990527 DOI: 10.1016/j.jinf.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India.
| | - Rima R Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Anita Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Srikanth Tripathy
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
| | - Dimpal A Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Manish Manrai
- Armed Forces Medical College, Pune, Maharashtra, India
| | - Deepak Y Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Sanjay Kumar
- Command Hospital (South Command), Pune, Maharashtra, India
| | - Vikas Marwah
- Army Institute of Cardio Thoracic Sciences, Pune, Maharashtra, India
| | - Gajanan N Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | | | | | | | - Smita Chavan
- Seven Hills Hospital, Mumbai, Maharashtra, India
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - T Ajai Kumar
- Army Institute of Cardio Thoracic Sciences, Pune, Maharashtra, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Renuka Munshi
- Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Unnati Desai
- Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Himanshu Kaushal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pranita Gawande
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Rajlaxmi Jain
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Ashwini Waghmare
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Kaumudi Kalele
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pratiksha Vedpathak
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jyoti Yemul
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Poonam Bodke
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Tejashri Kore
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - A L Kakrani
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
| | - Prachi Athavale
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
| | - Poonam Suryawanshi
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
| | - Sudhir Patsute
- Naidu Infectious Diseases Hospital, Pune, Maharashtra, India
| | - Vikram Padbidri
- Department of Microbiology and Infection Control, Jehangir Hospital, Pune, Maharashtra, India
| | - Pradip Awate
- State Surveillance Officer, Integrated Disease Surveillance program, Pune, Maharashtra, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
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12
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Yadav PD, Sapkal GN, Sahay RR, Patil DY, Agrawal S, Adsul B, Tripathy S, Deshpande GR, Nyayanit DA, Shete AM, Shastri J, Abraham P. Reduced neutralizing antibody response in naïve Covishield vaccinees against Omicron emphasizes booster vaccination. J Infect 2022; 85:90-122. [PMID: 35461911 PMCID: PMC9021040 DOI: 10.1016/j.jinf.2022.04.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/08/2022]
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13
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Yadav PD, Nyayanit DA, Gupta N, Shastri J, Sahay RR, Patil DY, Shete AM, Razdan A, Agrawal S, Kumar A, Majumdar T, Patil S, Sarkale P, Baradkar S, Dudhmal M, Kaur H, Aggarwal N. Detection and isolation of SARS-CoV-2 Eta variant from the international travelers and local residents of India. J Med Virol 2022; 94:3404-3409. [PMID: 35211985 PMCID: PMC9088542 DOI: 10.1002/jmv.27676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/06/2022] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 11/25/2022]
Abstract
International travel has been the major source for the rapid spread of new SARS‐CoV‐2 variants across the globe. During SARS‐CoV‐2 genomic surveillance, a total of 212 SARS‐CoV‐2 positive clinical specimens were sequenced using next‐generation sequencing. A complete SARS‐CoV‐2 genome could be retrieved from 90 clinical specimens. Of them, 14 sequences belonged to the Eta variant from clinical specimens of international travelers (n = 12) and local residents (n = 2) of India, and 76 belonged to other SARS‐CoV‐2 variants. Of all the Eta‐positive specimens, the virus isolates were obtained from the clinical specimens of six international travelers. Many variants of interest have been found to cause substantial community transmission or cluster infections. The detection of this variant with lethal E484K mutation across the globe and India necessitates persistent genomic surveillance of the SARS‐CoV‐2 variants, which would aid in taking preventive action.
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Affiliation(s)
- Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Dimpal A Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India, 110029
| | - Jayanthi Shastri
- Molecular Diagnostic reference Laboratory, Kasturba hospital for infectious diseases, Mumbai, India, 400034
| | - Rima R Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Deepak Y Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Anita M Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Alpana Razdan
- Genestrings Diagnostic Centre Pvt. Ltd., 3, MMTC, Geetanjali Enclave, New Delhi, 110017
| | - Sachee Agrawal
- Molecular Diagnostic reference Laboratory, Kasturba hospital for infectious diseases, Mumbai, India, 400034
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Prasad Sarkale
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Shreekant Baradkar
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India, 411021
| | - Harmanmeet Kaur
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India, 110029
| | - Neeraj Aggarwal
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India, 110029
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14
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Singh AK, Kasarpalkar N, Bhowmick S, Paradkar G, Talreja M, Shah K, Tiwari A, Palav H, Kaginkar S, Kulkarni R, Patil A, Kalsurkar V, Agrawal S, Shastri J, Dere R, Bharmal R, Mahale SD, Bhor VM, Patel V. Opposing roles for sMAdCAM and IL‐15 in COVID‐19 associated cellular immune pathology. J Leukoc Biol 2022; 111:1287-1295. [PMID: 35075682 PMCID: PMC9015433 DOI: 10.1002/jlb.3covbcr0621-300r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 12/24/2021] [Accepted: 12/31/2021] [Indexed: 12/26/2022] Open
Abstract
Immune cell dysregulation and lymphopenia characterize COVID‐19 pathology in moderate to severe disease. While underlying inflammatory factors have been extensively studied, homeostatic and mucosal migratory signatures remain largely unexplored as causative factors. In this study, we evaluated the association of circulating IL‐6, soluble mucosal addressin cell adhesion molecule (sMAdCAM), and IL‐15 with cellular dysfunction characterizing mild and hypoxemic stages of COVID‐19. A cohort of SARS‐CoV‐2 infected individuals (n = 130) at various stages of disease progression together with healthy controls (n = 16) were recruited from COVID Care Centres (CCCs) across Mumbai, India. Multiparametric flow cytometry was used to perform in‐depth immune subset characterization and to measure plasma IL‐6 levels. sMAdCAM, IL‐15 levels were quantified using ELISA. Distinct depletion profiles, with relative sparing of CD8 effector memory and CD4+ regulatory T cells, were observed in hypoxemic disease within the lymphocyte compartment. An apparent increase in the frequency of intermediate monocytes characterized both mild as well as hypoxemic disease. IL‐6 levels inversely correlated with those of sMAdCAM and both markers showed converse associations with observed lympho‐depletion suggesting opposing roles in pathogenesis. Interestingly, IL‐15, a key cytokine involved in lymphocyte activation and homeostasis, was detected in symptomatic individuals but not in healthy controls or asymptomatic cases. Further, plasma IL‐15 levels negatively correlated with T, B, and NK count suggesting a compensatory production of this cytokine in response to the profound lymphopenia. Finally, higher levels of plasma IL‐15 and IL‐6, but not sMAdCAM, were associated with a longer duration of hospitalization.
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Affiliation(s)
- Amit Kumar Singh
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
| | - Nandini Kasarpalkar
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Shilpa Bhowmick
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
| | - Gaurav Paradkar
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Mayur Talreja
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Karan Shah
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Abhishek Tiwari
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
| | - Harsha Palav
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
| | - Snehal Kaginkar
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
| | - Rajiv Kulkarni
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Ashwini Patil
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Varsha Kalsurkar
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Sachee Agrawal
- Department of Microbiology BYL Nair Hospital Mumbai Maharashtra India
| | - Jayanthi Shastri
- Department of Microbiology BYL Nair Hospital Mumbai Maharashtra India
| | - Rajesh Dere
- BKC COVID Jumbo Facility Municipal Corporation of Greater Mumbai Maharashtra India
| | - Ramesh Bharmal
- Office of the Dean TN Medical College & BYL Nair Hospital Mumbai Maharashtra India
| | | | - Vikrant M. Bhor
- Department of Molecular Immunology & Microbiology ICMR‐NIRRH Mumbai Maharashtra India
| | - Vainav Patel
- Department of Biochemistry & Virology ICMR‐NIRRH Mumbai Maharashtra India
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15
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Lad SB, Roy S, George JE, Chakraborti H, Lalsare S, Barik B, Singh A, Zade A, Agrawal S, Shastri J, Chatterjee A, Das Gupta K, Paul D, Kondabagil K. Development of a PNA–DiSc 2 based portable absorbance platform for the detection of pathogen nucleic acids. Analyst 2022; 147:5306-5313. [DOI: 10.1039/d2an01351g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A PortAbs based pathogen nucleic acid detection system using peptide nucleic acid (PNA) and a cyanine dye, DiSc2(5). The shift is measured of the absorbance induced by binding of a PNA probe to a complementary DNA strand using a portable two-color absorption system.
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Affiliation(s)
- Shailesh B. Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shomdutta Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Jijo Easo George
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Himadri Chakraborti
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Saumitra Lalsare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Bikash Barik
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Arushi Singh
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Amrutraj Zade
- Haystack Analytics Pvt. Ltd. Society For Innovation & Entrepreneurship (SINE), Kanwal Rekhi Building, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Jayanthi Shastri
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Anirvan Chatterjee
- Haystack Analytics Pvt. Ltd. Society For Innovation & Entrepreneurship (SINE), Kanwal Rekhi Building, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kantimay Das Gupta
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Debjani Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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16
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Njarekkattuvalappil SK, Thomas M, Kapil A, Saigal K, Ray P, Anandan S, Nagaraj S, Shastri J, Perumal SPB, Jinka DR, Thankaraj S, Ismavel V, Zachariah P, Singh A, Gupta M, Ebenezer SE, Thomas MS, Ghosh D, Kataria K, Senger M, Balasubramanian S, Kang G, John J. Ileal Perforation and Enteric Fever: Implications for Burden of Disease Estimation. J Infect Dis 2021; 224:S522-S528. [PMID: 35238354 PMCID: PMC8914860 DOI: 10.1093/infdis/jiab258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Ileal perforation occurs in about 1% of enteric fevers as a complication, with a case fatality risk (CFR) of 20%–30% in the early 1990s that decreased to 15.4% in 2011 in South East Asia. We report nontraumatic ileal perforations and its associated CFR from a 2-year prospective enteric fever surveillance across India.
Methods
The Surveillance for Enteric Fever in India (SEFI) project established a multitiered surveillance system for enteric fever between December 2017 and March 2020. Nontraumatic ileal perforations were surveilled at 8 tertiary care and 6 secondary care hospitals and classified according to etiology.
Results
Of the 158 nontraumatic ileal perforation cases identified,126 were consented and enrolled. Enteric fever (34.7%), tuberculosis (19.0%), malignancy (5.8%), and perforation of Meckel diverticulum (4.9%) were the common etiology. In those with enteric fever ileal perforation, the CFR was 7.1%.
Conclusions
Enteric fever remains the most common cause of nontraumatic ileal perforation in India, followed by tuberculosis. Better modalities of establishing etiology are required to classify the illness, and frame management guidelines and preventive measures. CFR data are critical for comprehensive disease burden estimation and policymaking.
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Affiliation(s)
| | - Maria Thomas
- Christian Medical College and Hospital, Ludhiana, India
| | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Pallab Ray
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | - Jayanthi Shastri
- Topiwala National Medical College and BYL Nair Charitable Hospital, Mumbai, India
| | | | | | - Shajin Thankaraj
- Makunda Christian Leprosy and General Hospital, Bazaricherra, Assam, India
| | - Vijayanand Ismavel
- Makunda Christian Leprosy and General Hospital, Bazaricherra, Assam, India
| | | | - Ashita Singh
- Chinchpada Christian Hospital, Maharashtra, India
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | - Dhruva Ghosh
- Christian Medical College and Hospital, Ludhiana, India
| | - Kamal Kataria
- All India Institute of Medical Sciences, New Delhi, India
| | | | | | | | - Jacob John
- Christian Medical College, Vellore, India
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17
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Veeraraghavan B, Pragasam AK, Ray P, Kapil A, Nagaraj S, Perumal SPB, Saigal K, Thomas M, Gupta M, Rongsen-Chandola T, Jinka DR, Shastri J, Alexander AP, Koshy RM, De A, Singh A, Evelyn Ebenezer S, Dutta S, Bavdekar A, More D, Sanghavi S, Nayakanti RR, Jacob JJ, Amladi A, Anandan S, Abirami BS, Bakthavatchalam YD, Sethuvel DPM, John J, Kang G. Evaluation of Antimicrobial Susceptibility Profile in Salmonella Typhi and Salmonella Paratyphi A: Presenting the Current Scenario in India and Strategy for Future Management. J Infect Dis 2021; 224:S502-S516. [PMID: 35238369 PMCID: PMC8892543 DOI: 10.1093/infdis/jiab144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Background
Systematic studies to estimate the disease burden of typhoid and paratyphoid in India are limited. Therefore, a multicenter study on the Surveillance of Enteric Fever in India was carried out to estimate the incidence, clinical presentation, and antimicrobial resistance (AMR) trend. The data presented here represent the national burden of AMR in Salmonella Typhi and Salmonella Paratyphi A.
Methods
Antimicrobial susceptibility testing was performed for S. Typhi and S. Paratyphi A (n = 2373) isolates collected prospectively during a 2-year period from November 2017 to January 2020.
Results
Of 2373 Salmonella isolates, 2032 (85.6%) were identified as S. Typhi and 341 (14.4%) were S. Paratyphi A. Approximately 2% of S. Typhi were multidrug-resistant (MDR), whereas all 341 (100%) of S. Paratyphi A isolates were sensitive to the first-line antimicrobials. Among 98% of ciprofloxacin nonsusceptible isolates, resistance (minimum inhibitory concentration [MIC] >0.5 µg/mL) was higher in S. Typhi (37%) compared with S. Paratyphi A (20%). Azithromycin susceptibility was 99.9% and 100% with a mean MIC of 4.98 μg/mL for S. Typhi and 7.39 μg/mL for S. Paratyphi A respectively. Ceftriaxone was the only agent that retained 100% susceptibility. Moreover, beta-lactam/beta-lactamase inhibitors showed potent in vitro activity against the study isolates.
Conclusions
Data obtained from this systematic surveillance study confirms the declining trend of MDR Salmonella isolates from India. The higher prevalence of ciprofloxacin nonsusceptibility enforces to limit its use and adhere to the judicious usage of azithromycin and ceftriaxone for enteric fever management.
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Affiliation(s)
| | | | - Pallab Ray
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Arti Kapil
- All India Institute of Medical Sciences, Delhi, India
| | | | | | | | | | - Madhu Gupta
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | | | | | - Jayanthi Shastri
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | | | | | - Anuradha De
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | | | | | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Deepak More
- Centre for Health Research & Development-Society for Applied Studies, New Delhi, India
| | | | | | | | | | | | | | | | | | - Jacob John
- Christian Medical College, Vellore, India
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18
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Kumar D, Sharma A, Rana SK, Prinja S, Ramanujam K, Karthikeyan AS, Raju R, Njarekkattuvalappil SK, Premkumar PS, Chauhan AS, Mohan VR, Ebenezer SE, Thomas MS, Gupta M, Singh A, Jinka DR, Thankaraj S, Koshy RM, Dhas Sankhro C, Kapil A, Shastri J, Saigal K, Perumal SPB, Nagaraj S, Anandan S, Thomas M, Ray P, John J, Kang G. Cost of Illness Due to Severe Enteric Fever in India. J Infect Dis 2021; 224:S540-S547. [PMID: 35238366 PMCID: PMC8892542 DOI: 10.1093/infdis/jiab282] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Lack of robust data on economic burden due to enteric fever in India has made decision making on typhoid vaccination a challenge. Surveillance for Enteric Fever network was established to address gaps in typhoid disease and economic burden.
Methods
Patients hospitalized with blood culture-confirmed enteric fever and nontraumatic ileal perforation were identified at 14 hospitals. These sites represent urban referral hospitals (tier 3) and smaller hospitals in urban slums, remote rural, and tribal settings (tier 2). Cost of illness and productivity loss data from onset to 28 days after discharge from hospital were collected using a structured questionnaire. The direct and indirect costs of an illness episode were analyzed by type of setting.
Results
In total, 274 patients from tier 2 surveillance, 891 patients from tier 3 surveillance, and 110 ileal perforation patients provided the cost of illness data. The mean direct cost of severe enteric fever was US$119.1 (95% confidence interval [CI], US$85.8–152.4) in tier 2 and US$405.7 (95% CI, 366.9–444.4) in tier 3; 16.9% of patients in tier 3 experienced catastrophic expenditure.
Conclusions
The cost of treating enteric fever is considerable and likely to increase with emerging antimicrobial resistance. Equitable preventive strategies are urgently needed.
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Affiliation(s)
| | - Atul Sharma
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Saroj Kumar Rana
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Shankar Prinja
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | | | | | | | | | | | | | | | | | | | - Madhu Gupta
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Ashita Singh
- Chinchpada Christian Hospital, Maharashtra,India
| | | | - Shajin Thankaraj
- Makunda Christian Leprosy and General Hospital, Bazaricherra, Assam,India
| | - Roshine Mary Koshy
- Makunda Christian Leprosy and General Hospital, Bazaricherra, Assam,India
| | | | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi,India
| | - Jayanthi Shastri
- Topiwala National Medical College and BYL Nair Charitable Hospital, Mumbai,India
| | | | | | | | | | - Maria Thomas
- Christian Medical College and Hospital, Ludhiana,India
| | - Pallab Ray
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Jacob John
- Christian Medical College, Vellore,India
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19
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Suvarna K, Salkar A, Palanivel V, Bankar R, Banerjee N, Gayathri J Pai M, Srivastava A, Singh A, Khatri H, Agrawal S, Shrivastav O, Shastri J, Srivastava S. A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients. J Proteome Res 2021; 20:4667-4680. [PMID: 34379420 PMCID: PMC8370121 DOI: 10.1021/acs.jproteome.1c00215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 03/17/2021] [Indexed: 12/24/2022]
Abstract
Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC-MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
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Affiliation(s)
- Kruthi Suvarna
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Renuka Bankar
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Nirjhar Banerjee
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Alisha Srivastava
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
- University of Delhi, New
Delhi, Delhi 110021, India
| | - Avinash Singh
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Harsh Khatri
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious
Diseases, Chinchpokli, Mumbai, Maharashtra 400034,
India
| | - Om Shrivastav
- Kasturba Hospital for Infectious
Diseases, Chinchpokli, Mumbai, Maharashtra 400034,
India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious
Diseases, Chinchpokli, Mumbai, Maharashtra 400034,
India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
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20
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Gupta N, Kaur H, Yadav PD, Mukhopadhyay L, Sahay RR, Kumar A, Nyayanit DA, Shete AM, Patil S, Majumdar T, Rana S, Gupta S, Narayan J, Vijay N, Barde P, Nataraj G, B. AK, Kumari MP, Biswas D, Iravane J, Raut S, Dutta S, Devi S, Barua P, Gupta P, Borkakoty B, Kalita D, Dhingra K, Fomda B, Joshi Y, Goyal K, John R, Munivenkatappa A, Dhodapkar R, Pandit P, Devi S, Dudhmal M, Kinariwala D, Khandelwal N, Tiwari YK, Khatri PK, Gupta A, Khatri H, Malhotra B, Nagasundaram M, Dar L, Sheikh N, Shastri J, Aggarwal N, Abraham P. Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Viruses 2021; 13:v13091782. [PMID: 34578363 PMCID: PMC8472862 DOI: 10.3390/v13091782] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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: 07/09/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 02/04/2023] Open
Abstract
From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.
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Affiliation(s)
- Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Harmanmeet Kaur
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Pragya Dhruv Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
- Correspondence: ; Tel.: +91-20-2600-6111; Fax: +91-20-2612-2669
| | - Labanya Mukhopadhyay
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Salaj Rana
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Swati Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Jitendra Narayan
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Neetu Vijay
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Pradip Barde
- Viral Research and Diagnostic Laboratory, National Institute of Research in Tribal Health (NIRTH), Jabalpur 482003, India;
| | - Gita Nataraj
- Viral Research and Diagnostic Laboratory, Department of Microbiology, KEM Medical College, Mumbai 400012, India;
| | - Amrutha Kumari B.
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, India; (A.K.B.); (M.P.K.)
| | - Manasa P. Kumari
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, India; (A.K.B.); (M.P.K.)
| | - Debasis Biswas
- Viral Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India;
| | - Jyoti Iravane
- Viral Research and Diagnostic Laboratory, Government Medical College, Aurangabad 431001, India;
| | - Sharmila Raut
- Viral Research and Diagnostic Laboratory, Indira Gandhi Government Medical College, Nagpur 440012, India;
| | - Shanta Dutta
- Viral Research and Diagnostic Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India;
| | - Sulochana Devi
- Viral Research and Diagnostic Laboratory, Regional Institute of Medical Sciences, Imphal 795004, India;
| | - Purnima Barua
- Viral Research and Diagnostic Laboratory, Jorhat Medical College, Jorhat 785001, India;
| | - Piyali Gupta
- Viral Research and Diagnostic Laboratory, Mahatma Gandhi Memorial Medical College, Jamshedpur 831020, India;
| | - Biswa Borkakoty
- Viral Research and Diagnostic Laboratory, ICMR-Regional Medical Research Centre, Dibrugarh 786001, India;
| | - Deepjyoti Kalita
- Viral Research and Diagnostic Laboratory, All India Institutes of Medical Sciences, Rishikesh 249203, India;
| | - Kanwardeep Dhingra
- Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar 143001, India;
| | - Bashir Fomda
- Viral Research and Diagnostic Laboratory, Sher-i-Kashmir Institute of Medical Sciences, Srinagar 190011, India;
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Kapil Goyal
- Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India;
| | - Reena John
- Viral Research and Diagnostic Laboratory, Government Medical College, Thrissur 680596, India;
| | | | - Rahul Dhodapkar
- Viral Research and Diagnostic Laboratory, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India;
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Sarada Devi
- Viral Research and Diagnostic Laboratory, Government Medical College, Thiruvanthapuram 695011, India;
| | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
| | - Deepa Kinariwala
- Viral Research and Diagnostic Laboratory, B. J. Medical College, Ahmedabad 380016, India;
| | - Neeta Khandelwal
- Viral Research and Diagnostic Laboratory, Government Medical College, Surat 395001, India;
| | - Yogendra Kumar Tiwari
- Viral Research and Diagnostic Laboratory, Jhalawar Medical College, Jhalawar 326001, India;
| | - Prabhat Kiran Khatri
- Viral Research and Diagnostic Laboratory, Dr. Sampurnanand Medical College, Jodhpur 342003, India;
| | - Anjli Gupta
- Viral Research and Diagnostic Laboratory, Sarder Patel Medical College, Bikaner 334001, India;
| | - Himanshu Khatri
- Viral Research and Diagnostic Laboratory, Department of Microbiology, GMERS Medical College, Himmatnagar 383001, India;
| | - Bharti Malhotra
- Viral Research and Diagnostic Laboratory, Sawai Man Singh Medical College, Jaipur 302004, India;
| | - Mythily Nagasundaram
- Viral Research and Diagnostic Laboratory, Coimbatore Medical College, Coimbatore 641018, India;
| | - Lalit Dar
- Viral Research and Diagnostic Laboratory, All India Institute of Medical Sciences, Delhi 110029, India;
| | - Nazira Sheikh
- Viral Research and Diagnostic Laboratory, Dr. V.M Government Medical College, Solapur 413003, India;
| | - Jayanthi Shastri
- Viral Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai 400011, India;
| | - Neeraj Aggarwal
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India; (N.G.); (H.K.); (L.M.); (S.R.); (S.G.); (J.N.); (N.V.); (N.A.)
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (R.R.S.); (A.K.); (D.A.N.); (A.M.S.); (S.P.); (T.M.); (Y.J.); (P.P.); (M.D.); (P.A.)
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21
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Gupta N, Kaur H, Yadav PD, Mukhopadhyay L, Sahay RR, Kumar A, Nyayanit DA, Shete AM, Patil S, Majumdar T, Rana S, Gupta S, Narayan J, Vijay N, Barde P, Nataraj G, B AK, Kumari MP, Biswas D, Iravane J, Raut S, Dutta S, Devi S, Barua P, Gupta P, Borkakoty B, Kalita D, Dhingra K, Fomda B, Joshi Y, Goyal K, John R, Munivenkatappa A, Dhodapkar R, Pandit P, Devi S, Dudhmal M, Kinariwala D, Khandelwal N, Tiwari YK, Khatri PK, Gupta A, Khatri H, Malhotra B, Nagasundaram M, Dar L, Sheikh N, Shastri J, Aggarwal N, Abraham P. Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Viruses 2021. [PMID: 34578363 DOI: 10.1101/2021.07.13.21260273v1.full-text] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.
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Affiliation(s)
- Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Harmanmeet Kaur
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Pragya Dhruv Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Labanya Mukhopadhyay
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Rima R Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Dimpal A Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Anita M Shete
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Salaj Rana
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Swati Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Jitendra Narayan
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Neetu Vijay
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Pradip Barde
- Viral Research and Diagnostic Laboratory, National Institute of Research in Tribal Health (NIRTH), Jabalpur 482003, India
| | - Gita Nataraj
- Viral Research and Diagnostic Laboratory, Department of Microbiology, KEM Medical College, Mumbai 400012, India
| | - Amrutha Kumari B
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, India
| | - Manasa P Kumari
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, India
| | - Debasis Biswas
- Viral Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
| | - Jyoti Iravane
- Viral Research and Diagnostic Laboratory, Government Medical College, Aurangabad 431001, India
| | - Sharmila Raut
- Viral Research and Diagnostic Laboratory, Indira Gandhi Government Medical College, Nagpur 440012, India
| | - Shanta Dutta
- Viral Research and Diagnostic Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Sulochana Devi
- Viral Research and Diagnostic Laboratory, Regional Institute of Medical Sciences, Imphal 795004, India
| | - Purnima Barua
- Viral Research and Diagnostic Laboratory, Jorhat Medical College, Jorhat 785001, India
| | - Piyali Gupta
- Viral Research and Diagnostic Laboratory, Mahatma Gandhi Memorial Medical College, Jamshedpur 831020, India
| | - Biswa Borkakoty
- Viral Research and Diagnostic Laboratory, ICMR-Regional Medical Research Centre, Dibrugarh 786001, India
| | - Deepjyoti Kalita
- Viral Research and Diagnostic Laboratory, All India Institutes of Medical Sciences, Rishikesh 249203, India
| | - Kanwardeep Dhingra
- Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar 143001, India
| | - Bashir Fomda
- Viral Research and Diagnostic Laboratory, Sher-i-Kashmir Institute of Medical Sciences, Srinagar 190011, India
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Kapil Goyal
- Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Reena John
- Viral Research and Diagnostic Laboratory, Government Medical College, Thrissur 680596, India
| | | | - Rahul Dhodapkar
- Viral Research and Diagnostic Laboratory, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Sarada Devi
- Viral Research and Diagnostic Laboratory, Government Medical College, Thiruvanthapuram 695011, India
| | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Deepa Kinariwala
- Viral Research and Diagnostic Laboratory, B. J. Medical College, Ahmedabad 380016, India
| | - Neeta Khandelwal
- Viral Research and Diagnostic Laboratory, Government Medical College, Surat 395001, India
| | - Yogendra Kumar Tiwari
- Viral Research and Diagnostic Laboratory, Jhalawar Medical College, Jhalawar 326001, India
| | - Prabhat Kiran Khatri
- Viral Research and Diagnostic Laboratory, Dr. Sampurnanand Medical College, Jodhpur 342003, India
| | - Anjli Gupta
- Viral Research and Diagnostic Laboratory, Sarder Patel Medical College, Bikaner 334001, India
| | - Himanshu Khatri
- Viral Research and Diagnostic Laboratory, Department of Microbiology, GMERS Medical College, Himmatnagar 383001, India
| | - Bharti Malhotra
- Viral Research and Diagnostic Laboratory, Sawai Man Singh Medical College, Jaipur 302004, India
| | - Mythily Nagasundaram
- Viral Research and Diagnostic Laboratory, Coimbatore Medical College, Coimbatore 641018, India
| | - Lalit Dar
- Viral Research and Diagnostic Laboratory, All India Institute of Medical Sciences, Delhi 110029, India
| | - Nazira Sheikh
- Viral Research and Diagnostic Laboratory, Dr. V.M Government Medical College, Solapur 413003, India
| | - Jayanthi Shastri
- Viral Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Neeraj Aggarwal
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
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Shastri J, Parikh S, Aggarwal V, Agrawal S, Chatterjee N, Shah R, Devi P, Mehta P, Pandey R. Severe SARS-CoV-2 Breakthrough Reinfection With Delta Variant After Recovery From Breakthrough Infection by Alpha Variant in a Fully Vaccinated Health Worker. Front Med (Lausanne) 2021; 8:737007. [PMID: 34490316 PMCID: PMC8418387 DOI: 10.3389/fmed.2021.737007] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 01/16/2023] Open
Abstract
Background: Post infection immunity and post vaccination immunity both confer protection against COVID-19. However, there have been many whole genome sequencing proven reinfections and breakthrough infections. Both are most often mild and caused by Variants of Concern (VOC). Methods: The patient in our study underwent serial COVID-19 RT-PCR, blood tests for serology, acute phase reactants, and chest imaging as part of clinical care. We interviewed the patient for clinical history and retrieved reports and case papers. We retrieved stored RT-PCR positive samples for whole genome sequencing (WGS) of SARS-CoV-2 from the patient's breakthrough infections and the presumed index case. Findings: The patient had three RT-PCR confirmed SARS-CoV-2 infections. Two breakthrough infections occurred in quick succession with the first over 3 weeks after complete vaccination with COVISHIELD and despite post-vaccination seroconversion. The first breakthrough infection was due to the Alpha variant and the second due to the Delta variant. The Delta variant infection resulted in hypoxia, hospitalization, and illness lasting seven weeks. Serial serology, acute phase reactants, and chest imaging supported WGS in establishing distinct episodes of infection. WGS established a fully vaccinated family member as the index case. Interpretation: The patient had an Alpha variant breakthrough infection despite past infection, complete vaccination, and seroconversion. Despite boosting after this infection, the patient subsequently had a severe Delta variant breakthrough infection. This was also a WGS proven reinfection and, therefore, a case of breakthrough reinfection. The patient acquired the infection from a fully vaccinated family member.
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Affiliation(s)
| | | | - Veena Aggarwal
- IJCP Group & Heart Care Foundation of India, New Delhi, India
| | | | | | - Rajit Shah
- Kasturba Hospital for Infectious Disease, Mumbai, India
| | - Priti Devi
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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23
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Jagtap D, Bhor VM, Bhowmick S, Kasarpalkar N, Sagvekar P, Kulkarni B, Pathak M, Chatterjee N, Dolas P, Palav H, Kaginkar S, Bhagat S, Munshi I, Parikh S, Agrawal S, Pawar C, Kaneria M, Mahale SD, Shastri J, Patel V. sMAdCAM: IL-6 Ratio Influences Disease Progression and Anti-Viral Responses in SARS-CoV-2 Infection. Front Immunol 2021; 12:619906. [PMID: 34194420 PMCID: PMC8236632 DOI: 10.3389/fimmu.2021.619906] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
The role of sMAdCAM, an important gut immune migratory marker, remains unexplored in COVID-19 pathogenesis considering recent studies positing the gut as a sanctuary site for SARS-CoV-2 persistence. Thus, assimilating profiles of systemic inflammatory mediators with sMAdCAM levels may provide insights into the progression of COVID-19 disease. Also, the role of these markers in governing virus specific immunity following infection remains largely unexplored. A cohort (n = 84) of SARS-C0V-2 infected individuals included a group of in-patients (n = 60) at various stages of disease progression together with convalescent individuals (n = 24) recruited between April and June 2020 from Mumbai, India. Follow-up of 35 in-patients at day 7 post diagnosis was carried out. Th1/Th2/Th17 cytokines along with soluble MAdCAM (sMAdCAM) levels in plasma were measured. Also, anti-viral humoral response as measured by rapid antibody test (IgG, IgM), Chemiluminescent Immunoassay (IgG), and antibodies binding to SARS-CoV-2 proteins were measured by Surface Plasmon Resonance (SPR) from plasma. IL-6 and sMAdCAM levels among in-patients inversely correlated with one another. When expressed as a novel integrated marker—sMIL index (sMAdCAM/IL-6 ratio)—these levels were incrementally and significantly higher in various disease states with convalescents exhibiting the highest values. Importantly, sMAdCAM levels as well as sMIL index (fold change) correlated with peak association response units of receptor binding domain and fold change in binding to spike respectively as measured by SPR. Our results highlight key systemic and gut homing parameters that need to be monitored and investigated further to optimally guide therapeutic and prophylactic interventions for COVID-19.
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Affiliation(s)
- Dhanashree Jagtap
- Department of Structural Biology Division, ICMR-NIRRH, Mumbai, India
| | - Vikrant M Bhor
- Department of Molecular Immunology & Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Shilpa Bhowmick
- Department of Biochemistry & Virology, ICMR-NIRRH, Mumbai, India
| | - Nandini Kasarpalkar
- Department of Molecular Immunology & Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Pooja Sagvekar
- Department of Biochemistry & Virology, ICMR-NIRRH, Mumbai, India
| | | | - Manish Pathak
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | | | - Pranam Dolas
- Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Harsha Palav
- Department of Biochemistry & Virology, ICMR-NIRRH, Mumbai, India
| | - Snehal Kaginkar
- Department of Biochemistry & Virology, ICMR-NIRRH, Mumbai, India
| | - Sharad Bhagat
- Department of Biochemistry & Virology, ICMR-NIRRH, Mumbai, India
| | - Itti Munshi
- Department of Primate Biology, ICMR-NIRRH, Mumbai, India
| | - Swapneil Parikh
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Sachee Agrawal
- Department of Microbiology, BYL Nair Hospital, Mumbai, India
| | | | - Mala Kaneria
- Department of Microbiology, BYL Nair Hospital, Mumbai, India.,Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Smita D Mahale
- Department of Structural Biology Division, ICMR-NIRRH, Mumbai, India
| | - Jayanthi Shastri
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, India.,Department of Microbiology, BYL Nair Hospital, Mumbai, India
| | - Vainav Patel
- Department of Biochemistry & Virology, ICMR-NIRRH, Mumbai, India
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24
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Yadav R, Acharjee A, Salkar A, Bankar R, Palanivel V, Agrawal S, Shastri J, Sabnis SV, Srivastava S. Mumbai mayhem of COVID-19 pandemic reveals important factors that influence susceptibility to infection. EClinicalMedicine 2021; 35:100841. [PMID: 33937730 PMCID: PMC8068776 DOI: 10.1016/j.eclinm.2021.100841] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND COVID-19 severity is disproportionately high in the elderly and people with comorbidities. However, other factors that predispose individuals to increased chances of infection are unclear. METHODS Data from 18,600 people screened for COVID-19 in Mumbai during the outbreak's initial phase, March 7 to June 30, 2020, were used to assess risk factors associated with COVID-19 using the odds ratio analysis. FINDINGS Males aged ≥60 years having both diabetes and hypertension were at the highest risk of COVID-19 infection (M vs. F OR=2.5, 95% CI=1.34-4.67, p = 0.0049). People having both diabetes and hypertension in ≥20 years (OR=4.11, 95% CI=3.26-5.20, p <0.0001), diabetes and hypertension independently in 20-39 (OR=4.13, 95% CI=2.22-7.70, p <0.0001, OR=4.32, 95% CI=2.10-8.88, p = 0.0001) and ≥60 years (OR=2.69, 95% CI=1.87-3.87, p <0.0001, OR=2.03, 95% CI=1.46-2.82, p <0.0001), chronic renal disease in 20-39 years (OR=5.38, 95% CI=1.91-15.09, p = 0.0007) age groups had significantly higher risk of COVID-19 infection than those without comorbidity. Quarantined people had significantly lower positive odds (OR=0.59, 95% CI=0.53-0.66, p <0.001) than non-quarantined people. INTERPRETATION Our research indicates that the risk of getting COVID-19 disease is not equal. When considering sex, age, and comorbidity together, we found that males aged ≥60 years and having both diabetes and hypertension had a significantly high risk of COVID-19 infection. Therefore, remedial measures such as vaccination programs should be prioritized for at-risk individuals. FUNDING SERB, India: SB/S1/COVID-2/2020 and Seed grant RD/0520-IRCCHC0-006 from IRCC, IIT Bombay.
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Affiliation(s)
- Radha Yadav
- Department of Mathematics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Renuka Bankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Sanjeev V. Sabnis
- Department of Mathematics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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25
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Suvarna K, Biswas D, Pai MGJ, Acharjee A, Bankar R, Palanivel V, Salkar A, Verma A, Mukherjee A, Choudhury M, Ghantasala S, Ghosh S, Singh A, Banerjee A, Badaya A, Bihani S, Loya G, Mantri K, Burli A, Roy J, Srivastava A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential. Front Physiol 2021; 12:652799. [PMID: 33995121 PMCID: PMC8120435 DOI: 10.3389/fphys.2021.652799] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 01/13/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
The pestilential pathogen SARS-CoV-2 has led to a seemingly ceaseless pandemic of COVID-19. The healthcare sector is under a tremendous burden, thus necessitating the prognosis of COVID-19 severity. This in-depth study of plasma proteome alteration provides insights into the host physiological response towards the infection and also reveals the potential prognostic markers of the disease. Using label-free quantitative proteomics, we performed deep plasma proteome analysis in a cohort of 71 patients (20 COVID-19 negative, 18 COVID-19 non-severe, and 33 severe) to understand the disease dynamics. Of the 1200 proteins detected in the patient plasma, 38 proteins were identified to be differentially expressed between non-severe and severe groups. The altered plasma proteome revealed significant dysregulation in the pathways related to peptidase activity, regulated exocytosis, blood coagulation, complement activation, leukocyte activation involved in immune response, and response to glucocorticoid biological processes in severe cases of SARS-CoV-2 infection. Furthermore, we employed supervised machine learning (ML) approaches using a linear support vector machine model to identify the classifiers of patients with non-severe and severe COVID-19. The model used a selected panel of 20 proteins and classified the samples based on the severity with a classification accuracy of 0.84. Putative biomarkers such as angiotensinogen and SERPING1 and ML-derived classifiers including the apolipoprotein B, SERPINA3, and fibrinogen gamma chain were validated by targeted mass spectrometry-based multiple reaction monitoring (MRM) assays. We also employed an in silico screening approach against the identified target proteins for the therapeutic management of COVID-19. We shortlisted two FDA-approved drugs, namely, selinexor and ponatinib, which showed the potential of being repurposed for COVID-19 therapeutics. Overall, this is the first most comprehensive plasma proteome investigation of COVID-19 patients from the Indian population, and provides a set of potential biomarkers for the disease severity progression and targets for therapeutic interventions.
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Affiliation(s)
- Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Medha Gayathri J. Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Renuka Bankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Amrita Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Manisha Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Saicharan Ghantasala
- Centre for Research in Nanotechnology and Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Susmita Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Avinash Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Apoorva Badaya
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gaurish Loya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Krishi Mantri
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ananya Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Jyotirmoy Roy
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Alisha Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Genetics, University of Delhi, New Delhi, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Mumbai, India
| | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Potdar V, Vipat V, Ramdasi A, Jadhav S, Pawar-Patil J, Walimbe A, Patil SS, Choudhury ML, Shastri J, Agrawal S, Pawar S, Lole K, Abraham P, Cherian S. Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends. Indian J Med Res 2021; 153:166-174. [PMID: 33818474 PMCID: PMC8184080 DOI: 10.4103/ijmr.ijmr_3418_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/10/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND & OBJECTIVES Several phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India. METHODS The whole genomes of 330 SARS-CoV-2 samples were sequenced using next-generation sequencing (NGS). Phylogenetic and sequence analysis of a total of 3014 Indian SARS-CoV-2 sequences from 20 different States/Union Territories (January to September 2020) from the Global Initiative on Sharing All Influenza Data (GISAID) database was performed to observe the clustering of Nextstrain and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) lineages with the GISAID clades. The identification of mutational sites under selection pressure was performed using Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting methods available in the Datamonkey server. RESULTS Temporal data of the Indian SARS-CoV-2 genomes revealed that except for Uttarakhand, West Bengal and Haryana that showed the circulation of GISAID clade O even after July 2020, the rest of the States showed a complete switch to GR/GH clades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH clades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these clades were found to occur majorly in the non-structural proteins coded by ORF1a and ORF1b. INTERPRETATION & CONCLUSIONS This study interpreted the geographical and temporal dominance of SARS-CoV-2 strains in India over a period of nine months based on the GISAID classification. An integration of the GISAID, Nextstrain and Pangolin classifications is also provided. The emergence of new lineages B.1.1.8 and B.1.113 was indicative of host-specific evolution of the SARS-CoV-2 strains in India. The hotspot mutations such as those driven by positive selection need to be further characterized.
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Affiliation(s)
- Varsha Potdar
- Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Veena Vipat
- Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ashwini Ramdasi
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Santosh Jadhav
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Atul Walimbe
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sucheta S. Patil
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College & B.Y.L. Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Sachee Agrawal
- Department of Microbiology, Topiwala National Medical College & B.Y.L. Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Shailesh Pawar
- ICMR-National Institute of Virology, Mumbai Unit, Mumbai, Maharashtra, India
| | - Kavita Lole
- Hepatitis Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sarah Cherian
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
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Sriraman K, Shaikh A, Parikh S, Udupa S, Chatterjee N, Shastri J, Mistry N. Non-invasive adapted N-95 mask sampling captures variation in viral particles expelled by COVID-19 patients: Implications in understanding SARS-CoV2 transmission. PLoS One 2021; 16:e0249525. [PMID: 33844696 PMCID: PMC8041197 DOI: 10.1371/journal.pone.0249525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/21/2021] [Indexed: 01/12/2023] Open
Abstract
Infectious respiratory particles expelled by SARS-CoV-2 positive patients are attributed to be the key driver of COVID-19 transmission. Understanding how and by whom the virus is transmitted can help implement better disease control strategies. Here we have described the use of a noninvasive mask sampling method to detect and quantify SARS-CoV-2 RNA in respiratory particles expelled by COVID-19 patients and discussed its relationship to transmission risk. Respiratory particles of 31 symptomatic SARS-CoV-2 positive patients and 31 asymptomatic healthy volunteers were captured on N-95 masks layered with a gelatin membrane in a 30-minute process that involved talking/reading, coughing, and tidal breathing. SARS-CoV-2 viral RNA was detected and quantified using rRT-PCR in the mask and in concomitantly collected nasopharyngeal swab (NPS) samples. The data were analyzed with respect to patient demographics and clinical presentation. Thirteen of 31(41.9%) patients showed SARS-COV-2 positivity in both the mask and NPS samples, while 16 patients were mask negative but NPS positive. Two patients were both mask and NPS negative. All healthy volunteers except one were mask and NPS negative. The mask positive patients had significantly lower NPS Ct value (26) compared to mask negative patients (30.5) and were more likely to be rapid antigen test positive. The mask positive patients could be further grouped into low emitters (expelling <100 viral copies) and high emitters (expelling >1000 viral copies). The study presents evidence for variation in emission of SARS-CoV-2 virus particles by COVID-19 patients reflecting differences in infectivity and transmission risk among individuals. The results conform to reported secondary infection rates and transmission and also suggest that mask sampling could be explored as an effective tool to assess individual transmission risks, at different time points and during different activities.
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Affiliation(s)
| | - Ambreen Shaikh
- The Foundation for Medical Research, Mumbai, Maharashtra, India
| | - Swapneil Parikh
- Molecular Laboratory, Viral Research, and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Sane Guruji Marg, Mumbai, Maharashtra, India
| | - Shreevatsa Udupa
- Molecular Laboratory, Viral Research, and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Sane Guruji Marg, Mumbai, Maharashtra, India
| | - Nirjhar Chatterjee
- Molecular Laboratory, Viral Research, and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Sane Guruji Marg, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Molecular Laboratory, Viral Research, and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Sane Guruji Marg, Mumbai, Maharashtra, India
- Department of Microbiology, BYL Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Nerges Mistry
- The Foundation for Medical Research, Mumbai, Maharashtra, India
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28
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Jawade K, Sinha AY, Bhagat S, Bhowmick S, Chauhan B, Kaginkar S, Palav H, Kasarpalkar N, Devadiga P, Karandikar K, Agrawal S, Shastri J, Munne K, Bhor VM, Mahale SD, Bhowmik S, Jagtap D, Patel V. A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples. Int J Infect Dis 2021; 106:395-400. [PMID: 33852938 PMCID: PMC8036167 DOI: 10.1016/j.ijid.2021.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/04/2021] [Revised: 03/31/2021] [Accepted: 04/04/2021] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND India bears the second largest burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. A multitude of reverse transcription polymerase chain reaction (RT-PCR) detection assays with disparate gene targets, including automated high-throughput platforms, are available. Varying concordance and interpretation of diagnostic results in this setting can result in significant reporting delays, leading to suboptimal disease management. This article reports the development of a novel ORF1a-based SARS-CoV-2 RT-PCR assay - Viroselect - that shows high concordance with conventional assays and the ability to resolve inconclusive results generated during the peak of the epidemic in Mumbai, India. METHODS A unique target region within SARS-CoV-2 ORF1a - the non-structural protein 3 (nsp3) region - was used to design and develop the assay. This hypervariable region (1923-3956) between SARS-CoV-2, SARS-CoV-1 and Middle East respiratory syndrome coronavirus was utilized to design the primers and probes for the RT-PCR assay. The concordance of this assay with commonly used emergency use authorization (US Food and Drug Administration) manual kits and an automated high-throughput testing platform was evaluated. Further, a retrospective analysis was carried out using Viroselect on samples reported as 'inconclusive' between April and October 2020. RESULTS In total, 701 samples were tested. Concordance analysis of 477 samples demonstrated high overall agreement of Viroselect with both manual (87.6%) and automated (84.7%) assays. Also, in the retrospective analysis of 224 additional samples reported as 'inconclusive', Viroselect was able to resolve 100% (19/19) and 93.7% (192/205) of samples which had inconclusive results on manual and automated high-throughput platforms, respectively. CONCLUSION Viroselect had high concordance with conventional assays, both manual and automated, and has potential to resolve inconclusive samples.
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Affiliation(s)
- Ketki Jawade
- Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India
| | | | - Sharad Bhagat
- Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India
| | - Shilpa Bhowmick
- Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India
| | | | - Snehal Kaginkar
- Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India
| | - Harsha Palav
- Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India
| | - Nandini Kasarpalkar
- Department of Molecular Immunology and Microbiology, ICMR-NIRRH, Mumbai, India
| | - Pratik Devadiga
- Department of Molecular Immunology and Microbiology, ICMR-NIRRH, Mumbai, India
| | - Kalyani Karandikar
- Department of Molecular Immunology and Microbiology, ICMR-NIRRH, Mumbai, India
| | - Sachee Agrawal
- Molecular Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India; Department of Microbiology, BYL Nair Hospital, Mumbai, India
| | - Jayanthi Shastri
- Molecular Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India; Department of Microbiology, BYL Nair Hospital, Mumbai, India
| | - Kiran Munne
- Department of Clinical Research, ICMR-NIRRH, Mumbai, India
| | - Vikrant M Bhor
- Department of Molecular Immunology and Microbiology, ICMR-NIRRH, Mumbai, India
| | - Smita D Mahale
- Department of Structural Biology Division, ICMR-NIRRH, Mumbai, India
| | | | - Dhanashree Jagtap
- Department of Structural Biology Division, ICMR-NIRRH, Mumbai, India.
| | - Vainav Patel
- Department of Biochemistry and Virology, ICMR-NRRH, Mumbai, India.
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29
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Vedpathak M, Chatterjee N, Baradkar V, Shastri J. Ophthalmomyiasis externa: A case report. Trop Parasitol 2021; 10:147-149. [PMID: 33747884 PMCID: PMC7951074 DOI: 10.4103/tp.tp_2_20] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 08/25/2020] [Indexed: 11/06/2022] Open
Abstract
Ophthalmomyiasis is the infestation of ocular structures by fly larvae (maggots). Oestrus ovis is common among them. This is usually observed in rural areas, but a case presented here is from the urban areas. Depending on the species of larvae and ocular structure involved, manifestations vary from self-limiting condition to optic nerve involvement which may lead to blindness, and hence, identification and prompt management is necessary. This case report alerts the ophthalmologists from the urban areas to consider time management and also microbiologists for rapid identification.
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Affiliation(s)
- Manoj Vedpathak
- Department of Microbiology, Dr. V.M. Government Medical College, Solapur, Maharashtra, India
| | - Nirjhar Chatterjee
- Department of Microbiology, TNMC and BYL Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Vasant Baradkar
- Department of Microbiology, TNMC and BYL Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, TNMC and BYL Nair Ch. Hospital, Mumbai, Maharashtra, India
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30
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Bankar S, Tokbipi PR, Ranwadkar I, Shastri J. Pulmonary cystic echinococcosis: A case report from tertiary care hospital. Trop Parasitol 2021; 10:163-164. [PMID: 33747888 PMCID: PMC7951081 DOI: 10.4103/tp.tp_3_20] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/11/2020] [Accepted: 03/23/2020] [Indexed: 11/12/2022] Open
Abstract
Human echinococcosis is a zoonotic infection transmitted by dogs in livestock-raising areas. We present a case of a 30-year-old female with respiratory symptoms.
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Affiliation(s)
- Sheetal Bankar
- Department of Microbiology, Orchid Medical Centre, Ranchi, Jharkhand, India
| | | | - Isha Ranwadkar
- Department of Microbiology, Topiwala National Medical College, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College and B.Y.L. Nair Ch. Hospital, Mumbai, Maharashtra, India
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31
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Kasarpalkar NJ, Bhowmick S, Patel V, Savardekar L, Agrawal S, Shastri J, Bhor VM. Frequency of Effector Memory Cells Expressing Integrin α 4β 7 Is Associated With TGF-β1 Levels in Therapy Naïve HIV Infected Women With Low CD4 + T Cell Count. Front Immunol 2021; 12:651122. [PMID: 33828560 PMCID: PMC8019712 DOI: 10.3389/fimmu.2021.651122] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/28/2022] Open
Abstract
Integrin α4β7 expressing CD4+ T cells are preferred targets for HIV infection and are thought to be predictors of disease progression. Concurrent analysis of integrin α4β7 expressing innate and adaptive immune cells was carried out in antiretroviral (ART) therapy naïve HIV infected women in order to determine its contribution to HIV induced immune dysfunction. Our results demonstrate a HIV infection associated decrease in the frequency of integrin α4β7 expressing endocervical T cells along with an increase in the frequency of integrin α4β7 expressing peripheral monocytes and central memory CD4+ T cells, which are considered to be viral reservoirs. We report for the first time an increase in levels of soluble MAdCAM-1 (sMAdCAM-1) in HIV infected individuals as well as an increased frequency and count of integrin β7Hi CD8+ memory T cells. Correlation analysis indicates that the frequency of effector memory CD8+ T cells expressing integrin α4β7 is associated with levels of both sMAdCAM-1 and TGF-β1. The results of this study also suggest HIV induced alterations in T cell homeostasis to be on account of disparate actions of sMAdCAM-1 and TGF-β1 on integrin α4β7 expressing T cells. The immune correlates identified in this study warrant further investigation to determine their utility in monitoring disease progression.
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Affiliation(s)
- Nandini J Kasarpalkar
- Department of Molecular Immunology and Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Shilpa Bhowmick
- Department of Biochemistry and Virology, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Vainav Patel
- Department of Biochemistry and Virology, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Lalita Savardekar
- Woman's Health Clinic and Bone Health Clinic, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Sachee Agrawal
- Department of Microbiology, Topiwala National Medical College and Bai Yamunabai Laxman Nair Hospital, Mumbai, India
| | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College and Bai Yamunabai Laxman Nair Hospital, Mumbai, India
| | - Vikrant M Bhor
- Department of Molecular Immunology and Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
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32
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Bankar R, Suvarna K, Ghantasala S, Banerjee A, Biswas D, Choudhury M, Palanivel V, Salkar A, Verma A, Singh A, Mukherjee A, Pai MGJ, Roy J, Srivastava A, Badaya A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic investigation reveals dominant alterations of neutrophil degranulation and mRNA translation pathways in patients with COVID-19. iScience 2021; 24:102135. [PMID: 33558857 PMCID: PMC7857979 DOI: 10.1016/j.isci.2021.102135] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 09/22/2020] [Revised: 12/17/2020] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of nasopharyngeal swab samples from patients with COVID-19 to study the host response by employing simple extraction strategies. Few of the host proteins such as interleukin-6, L-lactate dehydrogenase, C-reactive protein, Ferritin, and aspartate aminotransferase were found to be upregulated only in COVID-19-positive patients using targeted multiple reaction monitoring studies. The most important pathways identified by enrichment analysis were neutrophil degranulation, interleukin-12 signaling pathways, and mRNA translation of proteins thus providing the detailed investigation of host response in COVID-19 infection. Thus, we conclude that mass spectrometry-detected host proteins have a potential for disease severity progression; however, suitable validation strategies should be deployed for the clinical translation. Furthermore, the in silico docking of potential drugs with host proteins involved in the interleukin-12 signaling pathway might aid in COVID-19 therapeutic interventions.
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Affiliation(s)
- Renuka Bankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Saicharan Ghantasala
- Centre for Research in Nanotechnology and Sciences, Indian Institute of Technology Bombay, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Manisha Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Avinash Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Amrita Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Medha Gayathri J. Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Jyotirmoy Roy
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Alisha Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
- University of Delhi, New Delhi, Delhi 110021, India
| | - Apoorva Badaya
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
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33
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Shastri J, Parikh S, Agrawal S, Chatterjee N, Pathak M, Chaudhary S, Sharma C, Kanakan A, A V, Srinivasa Vasudevan J, Maurya R, Fatihi S, Thukral L, Agrawal A, Pinto L, Pandey R, Sunil S. Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India. Front Med (Lausanne) 2021; 8:631769. [PMID: 33768104 PMCID: PMC7985553 DOI: 10.3389/fmed.2021.631769] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 11/30/2020] [Accepted: 02/10/2021] [Indexed: 01/18/2023] Open
Abstract
Background: SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection. Methods: Nasopharyngeal (NP), oropharyngeal (OP) and whole blood (WB) samples were collected from paired samples of four individuals who were suspected of SARS-CoV-2 reinfection based on distinct clinical episodes and RT-PCR tests. Details from their case record files and investigations were documented. RNA was extracted from the NP and OP samples and subjected to WGS, and the nucleotide and amino acid sequences were subjected to genome and protein-based functional annotation analyses. Serial serology was performed for Anti-N IgG, Anti- S1 RBD IgG, and sVNT (surrogate virus neutralizing test). Findings: Three patients were more symptomatic with lower Ct values and longer duration of illness. Seroconversion was detected soon after the second episode in three patients. WGS generated a genome coverage ranging from 80.07 to 99.7%. Phylogenetic analysis revealed sequences belonged to G, GR and “Other” clades. A total of 42mutations were identified in all the samples, consisting of 22 non-synonymous, 17 synonymous, two in upstream, and one in downstream regions of the SARS-CoV-2 genome. Comparative genomic and protein-based annotation analyses revealed differences in the presence and absence of specific mutations in the virus sequences from the two episodes in all four paired samples. Interpretation: Based on the criteria of genome variations identified by whole genome sequencing and supported by clinical presentation, molecular and serological tests, we were able to confirm reinfections in two patients, provide weak evidence of reinfection in the third patient and unable to rule out a prolonged infection in the fourth. This study emphasizes the importance of detailed analyses of clinical and serological information as well as the virus's genomic variations while assessing cases of SARS-CoV-2 reinfection.
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Affiliation(s)
| | | | | | | | - Manish Pathak
- Kasturba Hospital for Infectious Disease, Mumbai, India
| | | | - Chetan Sharma
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Akshay Kanakan
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Vivekanand A
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Janani Srinivasa Vasudevan
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Ranjeet Maurya
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Saman Fatihi
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Lipi Thukral
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Anurag Agrawal
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | | | - Rajesh Pandey
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sujatha Sunil
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Malani A, Shah D, Kang G, Lobo GN, Shastri J, Mohanan M, Jain R, Agrawal S, Juneja S, Imad S, Kolthur-Seetharam U. Seroprevalence of SARS-CoV-2 in slums versus non-slums in Mumbai, India. Lancet Glob Health 2020; 9:e110-e111. [PMID: 33197394 PMCID: PMC7836622 DOI: 10.1016/s2214-109x(20)30467-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Anup Malani
- Medical School and Law School, University of Chicago, Chicago, IL, USA
| | - Daksha Shah
- Brihanmumbai Municipal Corporation, Mumbai, India
| | - Gagandeep Kang
- Department of Gastrointestinal Sciences, Vellore Christian Medical College, Vellore, India
| | | | | | - Manoj Mohanan
- Sanford School of Public Policy, Duke University, Durham, NC, USA
| | | | - Sachee Agrawal
- Topiwala National Medical College and BYL Nair Charitable Hospital, Mumbai, India
| | - Sandeep Juneja
- School of Technology and Computer Science, Tata Institute for Fundamental Research, Mumbai, India
| | | | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute for Fundamental Research, Mumbai 400 005, India.
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Gupta N, Potdar V, Praharaj I, Giri S, Sapkal G, Yadav P, Choudhary ML, Dar L, Sugunan AP, Kaur H, Munivenkatappa A, Shastri J, Kaveri K, Dutta S, Malhotra B, Jain A, Nagamani K, Shantala GB, Raut S, Vegad MM, Sharma A, Choudhary A, Brijwa M, Balakrishnan A, Manjunatha J, Pathak M, Srinivasan S, Banu H, Sharma H, Jain P, Sunita P, Ambica R, Fageria B, Patel D, Rajbongshi G, Vijay N, Narayan J, Aggarwal N, Nagar A, Gangakhedkar RR, Abraham P. Authors' response. Indian J Med Res 2020; 151:496. [PMID: 32611921 PMCID: PMC7530453 DOI: 10.4103/0971-5916.286255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Nivedita Gupta
- 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 411 021, Maharashtra, India
| | - Ira Praharaj
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Gajanan Sapkal
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 021, Maharashtra, India
| | - Pragya Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 021, Maharashtra, India
| | - Manohar Lal Choudhary
- Influenza Group, ICMR-National Institute of Virology, Pune 411 021, Maharashtra, India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - A P Sugunan
- ICMR-National Institute of Virology Kerala Unit, Alappuzha 688 005, Kerala, India, IndiaZ
| | - Harmanmeet Kaur
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi 110 001, India
| | - Ashok Munivenkatappa
- ICMR-National Institute of Virology Bangalore Field Unit, Bengaluru 560 011, Karnataka, India
| | - Jayanthi Shastri
- Department of Microbiology, Kasturba Hospital for Infectious Diseases, Mumbai 400 034, India
| | - Krishnasamy Kaveri
- Department of Virology, King Institute of Preventive Medicine & Research, Chennai 600 032, Tamil Nadu, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera & Enteric Diseases, Kolkata 700 010, West Bengal, India
| | - Bharti Malhotra
- Department of Microbiology, Sawai Man Singh Medical College, Jaipur 302 004, Rajasthan, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Kammilli Nagamani
- Department of Microbiology, Gandhi Medical College & Hospital, Secunderabad 500 003, Telangana, India
| | - G B Shantala
- Bangalore Medical College & Research Institute, Bengaluru 560 002, Karnataka, India
| | - Sharmila Raut
- Department of Microbiology, Indira Gandhi Government Medical College & Hospital, Nagpur 440 018, Maharashtra, India
| | - M M Vegad
- Department of Microbiology, Byramjee Jeejeebhoy Medical College, Ahmedabad 380 016, Gujarat, India
| | - Ajanta Sharma
- Department of Microbiology, Gauhati Medical College & Hospital, Guwahati 781 032, Assam, India
| | - Aashish Choudhary
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Megha Brijwa
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | | | - Jayaswamy Manjunatha
- ICMR-National Institute of Virology Bangalore Field Unit, Bengaluru 560 011, Karnataka, India
| | - Manish Pathak
- Department of Microbiology, Kasturba Hospital for Infectious Diseases, Mumbai 400 034, India
| | - Sivasubramanian Srinivasan
- Department of Virology, King Institute of Preventive Medicine & Research, Chennai 600 032, Tamil Nadu, India
| | - Hasina Banu
- ICMR-National Institute of Cholera & Enteric Diseases, Kolkata 700 010, West Bengal, India
| | - Himanshu Sharma
- Department of Microbiology, Sawai Man Singh Medical College, Jaipur 302 004, Rajasthan, India
| | - Parul Jain
- Department of Microbiology, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Pakalpati Sunita
- Department of Microbiology, Gandhi Medical College & Hospital, Secunderabad 500 003, Telangana, India
| | - R Ambica
- Bangalore Medical College & Research Institute, Bengaluru 560 002, Karnataka, India
| | - Babita Fageria
- Department of Microbiology, Indira Gandhi Government Medical College & Hospital, Nagpur 440 018, Maharashtra, India
| | - Disha Patel
- Department of Microbiology, Byramjee Jeejeebhoy Medical College, Ahmedabad 380 016, Gujarat, India
| | - Gitika Rajbongshi
- Department of Microbiology, Gauhati Medical College & Hospital, Guwahati 781 032, Assam, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi 110 001, India
| | - Jitendra Narayan
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi 110 001, India
| | - Neeraj Aggarwal
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Anu Nagar
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi 110 001, India
| | - Raman R Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Priya Abraham
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
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Gupta N, Potdar V, Praharaj I, Giri S, Sapkal G, Yadav P, Choudhary ML, Dar L, Sugunan AP, Kaur H, Munivenkatappa A, Shastri J, Kaveri K, Dutta S, Malhotra B, Jain A, Nagamani K, Shantala GB, Raut S, Vegad MM, Sharma A, Choudhary A, Brijwal M, Balakrishnan A, Manjunatha J, Pathak M, Srinivasan S, Banu H, Sharma H, Jain P, Sunita P, Ambica R, Fageria B, Patel D, Rajbongshi G, Vijay N, Narayan J, Aggarwal N, Nagar A, Gangakhedkar RR, Abraham P. Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories. Indian J Med Res 2020; 151:216-225. [PMID: 32242875 PMCID: PMC7258754 DOI: 10.4103/ijmr.ijmr_594_20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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] [Indexed: 12/29/2022] Open
Abstract
Background & objectives: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. Methods: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. Results: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. Interpretation & conclusions: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.
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Affiliation(s)
- Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Varsha Potdar
- Influenza Group, ICMR-National Institute of Virology, Pune, India
| | - Ira Praharaj
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Gajanan Sapkal
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | - Pragya Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | | | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - A P Sugunan
- ICMR-National Institute of Virology Kerala Unit, Alappuzha, Kerala, India
| | - Harmanmeet Kaur
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Ashok Munivenkatappa
- ICMR-National Institute of Virology Bangalore Field Unit, Bengaluru, Karnataka, India
| | - Jayanthi Shastri
- Department of Microbiology, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Krishnasamy Kaveri
- Department of Virology, King Institute of Preventive Medicine & Research, Chennai, Tamil Nadu, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Bharti Malhotra
- Department of Microbiology, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Kammilli Nagamani
- Department of Microbiology, Gandhi Medical College & Hospital, Secunderabad, Telangana, India
| | - G B Shantala
- Bangalore Medical College & Research Institute, Bengaluru, Karnataka, India
| | - Sharmila Raut
- Department of Microbiology, Indira Gandhi Government Medical College & Hospital, Nagpur, Maharashtra, India
| | - M M Vegad
- Department of Microbiology, Byramjee Jeejeebhoy Medical College, Ahmedabad, Gujarat, India
| | - Ajanta Sharma
- Department of Microbiology, Gauhati Medical College & Hospital, Guwahati, Assam, India
| | - Aashish Choudhary
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Megha Brijwal
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Jayaswamy Manjunatha
- ICMR-National Institute of Virology Bangalore Field Unit, Bengaluru, Karnataka, India
| | - Manish Pathak
- Department of Microbiology, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | | | - Hasina Banu
- ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Himanshu Sharma
- Department of Microbiology, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Parul Jain
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Pakalpati Sunita
- Department of Microbiology, Gandhi Medical College & Hospital, Secunderabad, Telangana, India
| | - R Ambica
- Bangalore Medical College & Research Institute, Bengaluru, Karnataka, India
| | - Babita Fageria
- Department of Microbiology, Indira Gandhi Government Medical College & Hospital, Nagpur, Maharashtra, India
| | - Disha Patel
- Department of Microbiology, Byramjee Jeejeebhoy Medical College, Ahmedabad, Gujarat, India
| | - Gitika Rajbongshi
- Department of Microbiology, Gauhati Medical College & Hospital, Guwahati, Assam, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Jitendra Narayan
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Neeraj Aggarwal
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Anu Nagar
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Raman R Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Sapkal G, Shete-Aich A, Jain R, Yadav PD, Sarkale P, Lakra R, Baradkar S, Deshpande GR, Mali D, Tilekar BN, Majumdar T, Kaushal H, Gurav Y, Gupta N, Mohandas S, Deshpande K, Kaduskar O, Salve M, Patil S, Gaikwad S, Sugunan A, Ashok M, Giri S, Shastri J, Abraham P, Gangakhedkar RR. Development of indigenous IgG ELISA for the detection of anti-SARS-CoV-2 IgG. Indian J Med Res 2020; 151:444-449. [PMID: 32611915 PMCID: PMC7530443 DOI: 10.4103/ijmr.ijmr_2232_20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND & OBJECTIVES Since the beginning of the year 2020, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted humankind adversely in almost all spheres of life. The virus belongs to the genus Betacoronavirus of the family Coronaviridae. SARS-CoV-2 causes the disease known as coronavirus disease 2019 (COVID-19) with mild-to-severe respiratory illness. The currently available diagnostic tools for the diagnosis of COVID-19 are mainly based on molecular assays. Real-time reverse transcription-polymerase chain reaction is the only diagnostic method currently recommended by the World Health Organization for COVID-19. With the rapid spread of SARS-CoV-2, it is necessary to utilize other tests, which would determine the burden of the disease as well as the spread of the outbreak. Considering the need for the development of such a screening test, an attempt was made to develop and evaluate an IgG-based ELISA for COVID-19. METHODS A total of 513 blood samples (131 positive, 382 negative for SARS-CoV-2) were collected and tested by microneutralization test (MNT). Antigen stock of SARS-CoV-2 was prepared by propagating the virus in Vero CCL-81 cells. An IgG capture ELISA was developed for serological detection of anti-SARS-CoV-2 IgG in serum samples. The end point cut-off values were determined by using receiver operating characteristic (ROC) curve. Inter-assay variability was determined. RESULTS The developed ELISA was found to be 92.37 per cent sensitive, 97.9 per cent specific, robust and reproducible. The positive and negative predictive values were 94.44 and 98.14 per cent, respectively. INTERPRETATION & CONCLUSIONS This indigenously developed IgG ELISA was found to be sensitive and specific for the detection of anti-SARS-CoV-2 IgG in human serum samples. This assay may be used for determining seroprevalence of SARS-CoV-2 in a population exposed to the virus.
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Affiliation(s)
- Gajanan Sapkal
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajlaxmi Jain
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajen Lakra
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Srikant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Gururaj Rao Deshpande
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Deepak Mali
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Bipin N. Tilekar
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Himanshu Kaushal
- Human Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yogesh Gurav
- Epidemiology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ketki Deshpande
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ojas Kaduskar
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Malvika Salve
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Shivshankar Gaikwad
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A.P. Sugunan
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - M. Ashok
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Jayanthi Shastri
- Department of Microbiology, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Raman R. Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Venkatesh A, Aggarwal S, Kumar S, Rajyaguru S, Kumar V, Bankar S, Shastri J, Patankar S, Srivastava S. Comprehensive proteomics investigation of P. vivax-infected human plasma and parasite isolates. BMC Infect Dis 2020; 20:188. [PMID: 32122317 PMCID: PMC7053139 DOI: 10.1186/s12879-020-4885-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 04/24/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Background In recent times, Plasmodium vivax (P. vivax) has become a serious threat to public health due to its ability to cause severe infection with fatal outcomes. Its unique biology makes it resilient to control measures that are otherwise effective against P. falciparum. A deeper understanding of P. vivax biology and pathogenesis is, therefore, essential for developing the right control strategies. Proteomics of P. falciparum has been helpful in studying disease biology and elucidating molecular mechanisms involved in the development of disease. However, unlike P. falciparum, proteomics data for P. vivax infection is minimal due to the absence of a continuous culture system. The dependence on clinical samples and animal models has drastically limited P. vivax research, creating critical knowledge gaps in our understanding of the disease. This study describes an in-depth proteomics analysis of P. vivax-infected human plasma and parasite isolates, to understand parasite biology, pathogenesis, and to identify new diagnostic targets for P. vivax malaria. Methods A mass-spectrometry- (MS) based proteomics approach (Q Exactive) was applied to analyze human plasma and parasite isolates from vivax malaria patients visiting a primary health centre in India. Additionally, a targeted proteomics assay was standardized for validating unique peptides of most recurring parasite proteins. Results Thirty-eight P. vivax proteins were detected in human plasma with high confidence. Several glycolytic enzymes were found along with hypothetical, cytoskeletal, ribosomal, and nuclear proteins. Additionally, 103 highly abundant P. vivax proteins were detected in parasite isolates. This represents the highest number of parasite proteins to be reported from clinical samples so far. Interestingly, five of these; three Plasmodium exported proteins (PVX_003545, PVX_003555 and PVX_121935), a hypothetical protein (PVX_083555) and Pvstp1 (subtelomeric transmembrane protein 1, PVX_094303) were found in both plasma and parasite isolates. Conclusions A parasite proteomics investigation is essential to understand disease pathobiology and design novel interventions. Control strategies against P. vivax also depend on early diagnosis. This work provides deeper insights into the biology of P. vivax by identifying proteins expressed by the parasite during its complex life-cycle within the human host. The study also reports antigens that may be explored as diagnostic candidates.
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Affiliation(s)
- Apoorva Venkatesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shalini Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Swati Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Srushti Rajyaguru
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sheetal Bankar
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai, India
| | - Jayanthi Shastri
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Abstract
INTRODUCTION: Dengue virus (DENV) causes a wide range of diseases in humans, from acute febrile illness Dengue fever (DF) to life-threatening Dengue hemorrhagic fever (DHF) or Dengue shock syndrome (DSS). Factors believed to be responsible for spread of Dengue virus infection include explosive population growth, unplanned urban overpopulation with inadequate public health systems, poor standing water and vector control, climate changes and increased international recreational, business, military travel to endemic areas. All of these factors must be addressed to control the spread of Dengue and other mosquito-borne infections. The detection of Dengue virus RNA by reverse transcriptase PCR (RT-PCR) in human serum or plasma samples is highly indicative of acute Dengue fever. Moreover, the method is able to identify the Dengue virus serotype by demonstrating defined sequence homologies in the viral genomic RNA. METHODS AND RESULTS: During the nine year period of this study analysis, 6767 strongly suspected cases were tested by RT-PCR. 1685 (24.9%) were Dengue PCR positive and confirmed as Dengue cases. Observations on the seasonality were based on the nine year's data as the intensity of sampling was at its maximum during monsoon season. Dengue typing was done on 100 positive samples after storage of Dengue RNA at – 80°C. Dengue serotypes were detected in 69 samples of which Dengue 2 was most predominant. 576 samples were processed for NS1 antigen and PCR simultaneously. 19/576 were positive (3.3 %) for NS1 as well as by PCR. 23/576 samples were negative for NS1 antigen, but were positive by RT-PCR. The remaining 534 samples which were negative for NS1 antigen were also negative by Dengue RT-PCR. CONCLUSION: In this study we sought to standardize rapid, sensitive, and specific fluorogenic probe-based RT-PCR assay to screen and serotype a representative range of Dengue viruses that are found in and around Mumbai. Qualitative Dengue virus TaqMan assays could have tremendous utility for the epidemiological investigation of Dengue illness and especially for the study of the viremic response with candidate live-attenuated dengue virus vaccines.
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Affiliation(s)
- Jayanthi Shastri
- Department of Microbiology, B.Y.L.Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Manita Williamson
- Department of Microbiology, B.Y.L.Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Nilima Vaidya
- Kasturba Hospital of Infectious Diseases, Mumbai, Maharashtra, India
| | - Sachee Agrawal
- Department of Microbiology, B.Y.L.Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Om Shrivastav
- Kasturba Hospital of Infectious Diseases, Mumbai, Maharashtra, India
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Gupta S, Agrawal S, Shastri J. Dengue and Chikungunya Mono and Co-infections among Patients with Acute Febrile Illness. J Clin Diagn Res 2020. [DOI: 10.7860/jcdr/2020/43920.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introduction: Dengue and Chikungunya fever are arboviral diseases which are spread by a common vector. Being clinically indistinguishable, it is necessary to distinguish both either by molecular or serology testing. Aim: To estimate the seroprevalence of Dengue and Chikungunya mono-infection as well as dual infection in patients with acute febrile illness. Materials and Methods: Two hundred patients with acute febrile illness were enrolled from April 2015 to October 2016. Detailed clinical history was documented. Samples were collected and subjected to Polymerase Chain Reaction (PCR) and Enzyme Linked Immuno Sorbent Assay (ELISA) testing. For qualitative data, frequency percentage table was used and association was done using Chi-square test. Results: Out of 200 patients, 8.5% had Chikungunya mono-infection and 41.5% patients had Dengue mono-infection. Dengue and Chikungunya co-infection was found in 4.5% patients. Most affected age group was 18-60 years wherein male preponderance was seen. In Chikungunya fever, 82.4% had morning stiffness and 35.3% had joint swelling; elbow and knee were the most commonly affected joints. In Chikungunya fever, 76.5% patients had restricted joint movements and 52.9% had Visual Analog Score (VAS) of 6-10. In Dengue fever, myalgia (67.5%) and rash (20.5%) were common symptoms. A total of 61.4% patients of Dengue fever had low platelet count. All Chikungunya cases and 88.1% Dengue cases detected by PCR had fever duration of less than five days. 85% of Chikungunya and 69% of Dengue cases detected by IgM ELISA had fever duration of more than five days. Conclusion: Diagnostic algorithms of acute febrile illness cases should include testing by both molecular and serology for both the viruses, which is the absolute need of the hour.
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Lahiri S, Venkataraman R, Jagan A, Deshmukh G, Patra S, Reddy V, Sangeetha V, Solanki R, Gupta J, Patel K, De A, Mukhopadhyay C, Dias M, Kanungo R, Mendiratta D, Nawal P, Shastri J, Vemu L, Rangarajan R. Evaluation of LAMP-based assays for carbapenemase genes. J Med Microbiol 2019; 68:1431-1437. [DOI: 10.1099/jmm.0.001050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Surobhi Lahiri
- Vitas Pharma Research Private Limited, TBI, University of Hyderabad, Hyderabad, India
| | - Rasika Venkataraman
- Vitas Pharma Research Private Limited, TBI, University of Hyderabad, Hyderabad, India
| | - Akshaya Jagan
- Vitas Pharma Research Private Limited, TBI, University of Hyderabad, Hyderabad, India
| | - Gargi Deshmukh
- Vitas Pharma Research Private Limited, TBI, University of Hyderabad, Hyderabad, India
| | - Sudipta Patra
- Department of Microbiology, Kasturba Medical College, Manipal, India
| | - Vani Reddy
- Department of Microbiology, St. John’s Medical College, Bangalore, India
| | - V. Sangeetha
- Department of Microbiology, Pondicherry Institute of Medical Sciences, Puducherry, India
| | | | - Jyoti Gupta
- Department of Microbiology, Chirayu Medical College & Hospital, Bhopal, India
| | | | - Anuradha De
- Department of Microbiology, T. N. Medical College, Mumbai, India
| | | | - Mary Dias
- Department of Microbiology, St. John’s Medical College, Bangalore, India
| | - Reba Kanungo
- Department of Microbiology, Pondicherry Institute of Medical Sciences, Puducherry, India
| | - Deepak Mendiratta
- Department of Microbiology, Chirayu Medical College & Hospital, Bhopal, India
| | | | - Jayanthi Shastri
- Department of Microbiology, T. N. Medical College, Mumbai, India
| | - Lakshmi Vemu
- Department of Microbiology, Kamineni Academy of Medical Sciences & Research Centre, Hyderabad, India
| | - Radha Rangarajan
- Vitas Pharma Research Private Limited, TBI, University of Hyderabad, Hyderabad, India
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Sonawane AA, Shastri J, Bavdekar SB. Respiratory Pathogens in Infants Diagnosed with Acute Lower Respiratory Tract Infection in a Tertiary Care Hospital of Western India Using Multiplex Real Time PCR. Indian J Pediatr 2019; 86:433-438. [PMID: 30637585 PMCID: PMC7091426 DOI: 10.1007/s12098-018-2840-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 12/11/2018] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To determine the frequency of respiratory pathogens in infants diagnosed with acute lower respiratory tract infections. METHODS A prospective cross-sectional observational study was conducted in infants hospitalized with a diagnosis of acute lower respiratory tract infection (ALRTI), in a tertiary care hospital in a metropolitan city of Western India. Nasopharyngeal swabs were analyzed by multiplex real time polymerase chain reaction, for 18 viruses and 3 bacteria (H. influenzae type b, C. pneumoniae and M. pneumoniae). The entire data was entered in Microsoft excel sheet and frequencies were determined. RESULTS One hundred eligible infants were enrolled. Pathogens were detected in 82 samples, which included Respiratory syncytial viruses (RSV) A / B (35.4%), Human rhinovirus (25.6%), Adenovirus (22%), Human Parainfluenza viruses (11%), Human bocavirus (9.8), Human metapneumovirus A / B (8.5%), Influenza A (H1N1) pdm 09 (6.1%), Parechovirus (3.7%), Human coronaviruses (3.66%), Haemophilus influenzae type b (6.1%), Chlamydia pneumoniae (2.4%) and Mycoplasma pneumoniae (2.4%). Influenza A (other than H1N1), Influenza B, Human Coronavirus 229E and Enterovirus were not detected. The rate of coinfection was 34% and rhinovirus was the most common of the multiple pathogens. CONCLUSIONS Spectrum of viral etiologies of ALRTI is highlighted. Etiological diagnosis of ALRTI would enable specific antiviral therapy, restrict antibiotic use and help in knowing burden of disease.
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Affiliation(s)
- Anuja A Sonawane
- Department of Microbiology, T.N. Medical College & B.Y.L. Nair Hospital, Mumbai, Maharashtra, 400008, India.
| | - Jayanthi Shastri
- Department of Microbiology, T.N. Medical College & B.Y.L. Nair Hospital, Mumbai, Maharashtra, 400008, India
| | - Sandeep B Bavdekar
- Department of Pediatrics, T.N. Medical College & B.Y.L. Nair Hospital, Mumbai, India
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Abstract
Introduction The WHO endorsed Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay, has been evaluated for pulmonary TB in a number of studies but very few have investigated it for extrapulmonary specimens. The present study evaluates the performance of Xpert MTB/RIF assay in the diagnosis of extrapulmonary TB (EPTB). Aim and Objectives The aim of the study is to determine sensitivity and specificity of Xpert MTB/RIF assay for diagnosis of EPTB and RIF resistance in comparison to culture on Lowenstein-Jensen (LJ) medium and proportion method (PM), respectively. Materials and Methods A total of 738 specimens from clinically suspected cases of EPTB were subjected to Ziehl-Neelsen staining, Xpert MTB/RIF assay and culture on LJ medium. PM was done on MTB isolates. Results The sensitivity, specificity of Xpert MTB/RIF assay for diagnosis of EPTB were 84.91% (95% confidence interval [CI] 72.41%-93.25%) and 86.72% (95% CI 83.94%-89.17%) and for RIF resistance detection were 60.00% (95% CI 32.29%-83.66%) and 94.74% (95% CI 73.97%-99.87%), respectively. Among culture-positive cases, the sensitivity of Xpert MTB/RIF assay was 94.12% in smear positive and 80.56% in smear-negative cases. Xpert MTB/RIF showed maximum sensitivity of MTB detection from lymph node specimens (100% [95% CI 54.07%-100.00%]) and other body fluids (100% [95% CI 15.81%-100.00%]). Conclusion The present study establishes Xpert MTB/RIF assay as a promising tool in the rapid diagnosis of EPTB and detection of RIF resistance.
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Affiliation(s)
- Sheetal Bankar
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Reena Set
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Disha Sharma
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
| | - Daksha Shah
- City TB Officer, Mumbai District Tuberculosis Control Society, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, T.N. Medical College and B Y L Nair Ch. Hospital, Mumbai, Maharashtra, India
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Sahay RR, Yadav PD, Majumdar T, Patil S, Sarkale P, Shete AM, Chaubal G, Dange VR, Patil S, Nyayanit DA, Shastri J, Mourya DT. Clinico-epidemiological investigation on Varicella Zoster Virus indicates multiple clade circulation in Maharashtra state, India. Heliyon 2018; 4:e00757. [PMID: 30175265 PMCID: PMC6118100 DOI: 10.1016/j.heliyon.2018.e00757] [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: 12/15/2017] [Revised: 06/18/2018] [Accepted: 08/23/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Varicella Zoster Virus (VZV) is consistently in circulation and shows an increase in disease burden during the spring season. Due to a wide range of clinical presentation from a vesicular rash to bleeding or neurological complications, it makes the clinical diagnosis difficult. The present study aims to understand whether the same strain of virus is responsible for the increase in the seasonal outbreaks occurring in different parts of the country with reference to the samples from Maharashtra, Rajasthan and Gujarat states of India. MATERIALS AND METHODS This study reports the clinico-epidemiological and laboratory findings of suspected Varicella cases. To understand the circulating clade few representative real-time Polymerase Chain Reaction (PCR) positive were analyzed by conventional PCR and partial Open Reading Frame (ORF) 22, partial ORF 38 and partial ORF 54 were sequenced to identify single nucleotide polymorphisms responsible for clade determination. Further partial glycoprotein B gene was sequenced, and a phylogenetic tree was generated. RESULTS A total of 50 cases from Maharashtra (Mumbai district) and referred clinical samples of Rajasthan (Barmer district; n = 12) and Gujarat States (Gandhi Nagar, Surat districts; n = 17) were tested for the presence of VZV. Vesicular rash with fever was a common clinical presentation with 82% cases having contact history with VZV positive cases, suggesting higher secondary attack rate. The vesicular fluid of all 50 cases from Mumbai revealed the presence of VZV by real-time PCR. Urine, serum and throat swab samples showed positivity by real-time PCR. Healthcare provider's samples from Rajasthan showed 36.4% [4/11] positivity. Clinical samples from Gujarat had positivity of 41.2% [7/17]. CONCLUSIONS This study analyses the clade based circulation of VZV in three states in India and suggests different clades circulating in Maharashtra state. Health education amongst the general population is suggested to reduce the secondary cases by early diagnosis, effective isolation policies and vaccination to reduce the burden of disease.
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Affiliation(s)
- Rima R. Sahay
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Pragya D. Yadav
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Triparna Majumdar
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Swapnil Patil
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Prasad Sarkale
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Anita M. Shete
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Gouri Chaubal
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Vinay R. Dange
- Kasturba Infectious Disease Hospital, Saat Rasta, Arthur Road, Chinchpokli, Mumbai 400011, India
| | - Savita Patil
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Dimpal A. Nyayanit
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
| | - Jayanthi Shastri
- Kasturba Infectious Disease Hospital, Saat Rasta, Arthur Road, Chinchpokli, Mumbai 400011, India
| | - Devendra T. Mourya
- Microbial Containment Complex, ICMR- National Institute of Virology, Sus Road, Pashan, Pune 410021, India
- Corresponding author.
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Balaji V, Kapil A, Shastri J, Pragasam AK, Gole G, Choudhari S, Kang G, John J. Longitudinal Typhoid Fever Trends in India from 2000 to 2015. Am J Trop Med Hyg 2018; 99:34-40. [PMID: 30047367 PMCID: PMC6128365 DOI: 10.4269/ajtmh.18-0139] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A very high incidence of typhoid was described in studies conducted in urban locations on the Indian subcontinent at the end of the twentieth century. Despite their availability, licensed immunogenic conjugate typhoid vaccines have not been introduced in the national immunization program, in part, because of a lack of understanding of where and for whom prevention is most necessary. Uncertainty regarding the burden of disease is based on the lack of reliable, recent estimates of culture-confirmed typhoid and an observed trend of low isolations of Salmonella Typhi and fewer complications at large referral hospitals in India. In this article, we examine the trends of S. Typhi isolation at three large tertiary care centers across India over 15 years and describe trends of recognized risk factors for typhoid from published literature. There appears to be a decline in the isolation of S. Typhi in blood cultures, which is more apparent in the past 5 years. These trends are temporally related to economic improvement, female literacy, and the use of antibiotics such as cephalosporins and azithromycin. The analysis of trends of culture-confirmed typhoid may not accurately capture the typhoid incidence trends if antibiotic use confounds the burden of disease presenting to larger facilities. Emerging antimicrobial resistance may result in a resurgence of disease if the underlying incidence and transmission of typhoid are not adequately addressed through public health approaches.
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Affiliation(s)
| | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi, India
| | - Jayanthi Shastri
- TN Medical College & B Y L Nair Hospital, Mumbai, Maharashtra, India
| | | | - Geeta Gole
- TN Medical College & B Y L Nair Hospital, Mumbai, Maharashtra, India
| | | | - Gagandeep Kang
- Translational Health Sciences Technology Institute, Faridabad, Haryana, India
| | - Jacob John
- Christian Medical College, Vellore, Tamil Nadu, India
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Venkatesh A, Lahiri A, Reddy PJ, Shastri J, Bankar S, Patankar S, Srivastava S. Front Cover: Identification of Highly Expressed Plasmodium Vivax
Proteins from Clinical Isolates Using Proteomics. Proteomics Clin Appl 2018. [DOI: 10.1002/prca.201870030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Nagral N, Joshi V, Baria K, Parikh P, Nagral A, Shastri J, Pawar C. Prevalence of non A to E hepatitis in Mumbai, India. Rev Gastroenterol Peru 2018; 38:49-53. [PMID: 29791422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
INTRODUCTION Acute viral hepatitis is a common problem in India. World wide data shows that 5 to 20 percent of this is caused by non A-E hepatitis. There is no data in India regarding non A-E hepatitis. We carried out this study to evaluate the epidemiology, clinical features, risk factors and outcome of non A-E hepatitis. MATERIAL AND METHODS In this single centre study, we evaluated all patients admitted with features of acute viral hepatitis at our hospital between the period of February to July 2015. A detailed history about the epidemiology, risk factors and clinical features was done. Patients were evaluated with bilirubin, transaminases and prothrombin time. Each patient was investigated for IgM HAV, IgM HEV, HBsAg and Antibody against hepatitis C. Patients turning out negative were investigated for presence of autoimmune hepatitis or Wilson's disease. All viral markers were repeated a week later to confirm non A-E status. RESULTS A total 265 patients were included of which 41 (15.4%) patients were non A-E hepatitis. They had higher age (28.55 vs 34.99, p<0.05) but similar gender and sub urban location. Median SEC classification was A2 in hepatitis A/E group as compared to A3 in non A-E group. The duration of symptoms and clinical features between the two groups were similar with Anorexia, Malasie, Nausea/vomiting being most common. The risk factors between the two groups were similar. The bilirubin and transaminases were non significantly lower than hepatitis A/E patients while albumin levels were significantly lower. The outcomes of both groups were similar with no mortality or fulminant hepatitis. CONCLUSION Non A-E hepatitis patients tends to be older, lower SEC class and had lower albumin levels as compared to hepatitis A/E.
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Affiliation(s)
| | | | | | - Pathik Parikh
- Department of Gastroenterology, LTM Medical College. Mumbai, India
| | - Aabha Nagral
- Kasturba Hospital of Infectious Diseases. Mumbai, India
| | - Jayanthi Shastri
- Department of Microbiology, Kasturba and Nair Hospital. Mumbai, India
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Venkatesh A, Lahiri A, Reddy PJ, Shastri J, Bankar S, Patankar S, Srivastava S. Identification of Highly Expressed Plasmodium Vivax Proteins from Clinical Isolates Using Proteomics. Proteomics Clin Appl 2017; 12:e1700046. [PMID: 28841253 DOI: 10.1002/prca.201700046] [Citation(s) in RCA: 12] [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] [Received: 03/12/2017] [Revised: 07/08/2017] [Indexed: 12/11/2022]
Abstract
Plasmodium vivax is the most geographically widespread species responsible for malaria in humans. Our study focused on identifying highly expressed parasite proteins using a shotgun proteomics approach. Parasites (P. vivax) are isolated from seven patient samples using saponin lysis. Protein extracts from these parasites are processed and subjected to LC-MS/MS analysis. An overall proteome coverage of 605 P. vivax proteins along with 1670 human host proteins are obtained upon combining the data from LC-MS/MS runs. While a major proportion of the P. vivax proteins are either hypothetical or involved in basic cellular activities, few proteins such as tryptophan-rich antigen (Pv-fam-a; PVX_090265), Pv-fam-d protein (PVX_101520), Plasmodium exported protein (PVX_003545), Pvstp1 (PVX_094303) and hypothetical protein (PVX_083555) are detected in more than 80% of the clinical isolates and found to be unique to P. vivax without orthologs in P. falciparum. Our proteomics study on individual parasite isolates reveals highly expressed P. vivax proteins, few of which may be good candidates for vivax malaria diagnosis due to their abundance and absence in P. falciparum. This study represents the first step towards the identification of biomarkers for P. vivax malaria. In future, their clinical diagnostic values must be explored and validated on large patient cohorts.
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Affiliation(s)
- Apoorva Venkatesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anwesha Lahiri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Jayanthi Shastri
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai
| | - Sheetal Bankar
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Tonse R, Gupta T, Sridhar E, Shastri J, Jain A, Bano N, Jalali R. Impact of WHO 2016 update and molecular markers in pleomorphic xanthoastrocytoma. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx366.006] [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: 11/14/2022] Open
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Abstract
Dirofilariasis is a worldwide zoonotic filariasis. Human dirofilariasis is a zoonotic infection most commonly caused by Dirofilariarepens. Dirofilariasis, caused by Dirofilaria repens, has been reported to occur widely throughout Asia, Europe, and Africa. It has not been widely recognized in India; however, several cases have been reported in the last few years. Ease and frequency of international travel has probably contributed to the increase in the number of cases. There is probably a focus of human infection with D. repens in Kerala, India. We report a case of ocular dirofilariasis, from the Western part of India. Among the Indian case reports of human dirofilariasis caused by D. repens, majority had ocular infections and few had subcutaneous involvement of the face.
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Affiliation(s)
- Sachee Agrawal
- Assistant Professor, Department of Microbiology, B.Y.L. Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Rahul Agrawal
- Consultant Ophthalmologist, Rahul Eye Clinic, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Professor and Head, Department of Microbiology, B.Y.L. Nair Charitable Hospital, Mumbai, Maharashtra, India
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