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Jakharia A, Borkakoty B, Pait S, Baruah G, Hazarika R, Biswas D. First isolation and characterization of SARS-CoV-2 from COVID-19 patient of North East India. INDIAN J PATHOL MICR 2024; 67:133-139. [PMID: 38358202 DOI: 10.4103/ijpm.ijpm_748_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) responsible for the current pandemic has resulted in over 5 million deaths globally. More than a year has passed, still SARS-CoV-2 panic the public life. Virus isolation is of paramount importance for development of vaccines, in-vitro screening of antiviral compounds, pathogenesis studies, etc., Many cell lines were studied for amplification and replication of SARS-CoV-2 and Vero cells were found to be ideal cell lines for isolation. In May 2020, ICMR-Regional Medical Research Centre, NE region, India, successfully established the SARS-CoV-2 culture system in Vero CCL-81 cell lines. Phylogenetic analyses of the whole genome sequences of the SARS-CoV-2 isolate (EPI_ISL_2501532 | 2020-05-19) showed monophyletic clade G and lineage B.1.1.
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Affiliation(s)
- Aniruddha Jakharia
- Indian Council of Medical Research- Regional Medical Research Centre, North East Region (ICMR-RMRCNE), Lahowal, Assam, India
| | - Biswajyoti Borkakoty
- Indian Council of Medical Research- Regional Medical Research Centre, North East Region (ICMR-RMRCNE), Lahowal, Assam, India
| | - Sumi Pait
- Indian Council of Medical Research- Regional Medical Research Centre, North East Region (ICMR-RMRCNE), Lahowal, Assam, India
| | - Gautam Baruah
- Indian Council of Medical Research- Regional Medical Research Centre, North East Region (ICMR-RMRCNE), Lahowal, Assam, India
| | - Rahul Hazarika
- Indian Council of Medical Research- Regional Medical Research Centre, North East Region (ICMR-RMRCNE), Lahowal, Assam, India
| | - Dipankar Biswas
- Indian Council of Medical Research- Regional Medical Research Centre, North East Region (ICMR-RMRCNE), Lahowal, Assam, India
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Saravanan V, Chagaleti BK, Narayanan PL, Anandan VB, Manoharan H, Anjana GV, Peraman R, Namasivayam SKR, Kavisri M, Arockiaraj J, Muthu Kumaradoss K, Moovendhan M. Discovery and development of COVID-19 vaccine from laboratory to clinic. Chem Biol Drug Des 2024; 103:e14383. [PMID: 37953736 DOI: 10.1111/cbdd.14383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/01/2023] [Accepted: 10/13/2023] [Indexed: 11/14/2023]
Abstract
The world has recently experienced one of the biggest and most severe public health disasters with severe acute respiratory syndrome coronavirus (SARS-CoV-2). SARS-CoV-2 is responsible for the coronavirus disease of 2019 (COVID-19) which is one of the most widespread and powerful infections affecting human lungs. Current figures show that the epidemic had reached 216 nations, where it had killed about 6,438,926 individuals and infected 590,405,710. WHO proclaimed the outbreak of the Ebola virus disease (EVD), in 2014 that killed hundreds of people in West Africa. The development of vaccines for SARS-CoV-2 becomes more difficult due to the viral mutation in its non-structural proteins (NSPs) especially NSP2 and NSP3, S protein, and RNA-dependent RNA polymerase (RdRp). Continuous monitoring of SARS-CoV-2, dynamics of the genomic sequence, and spike protein mutations are very important for the successful development of vaccines with good efficacy. Hence, the vaccine development for SARS-CoV-2 faces specific challenges starting from viral mutation. The requirement of long-term immunity development, safety, efficacy, stability, vaccine allocation, distribution, and finally, its cost is discussed in detail. Currently, 169 vaccines are in the clinical development stage, while 198 vaccines are in the preclinical development stage. The majority of these vaccines belong to the Ps-Protein subunit type which has 54, and the minor BacAg-SPV (Bacterial antigen-spore expression vector) type, at least 1 vaccination. The use of computational methods and models for vaccine development has revolutionized the traditional methods of vaccine development. Further, this updated review highlights the upcoming vaccine development strategies in response to the current pandemic and post-pandemic era, in the field of vaccine development.
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Affiliation(s)
- Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Pavithra Lakshmi Narayanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Vijay Babu Anandan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Haritha Manoharan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - G V Anjana
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Ramalingam Peraman
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur, Hajipur, India
| | - S Karthik Raja Namasivayam
- Department of Research & Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - M Kavisri
- Department of Civil Engineering, Saveetha School of Engineering, SIMATS Deemed University, Chennai, India
| | - Jesu Arockiaraj
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Kathiravan Muthu Kumaradoss
- Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, India
| | - Meivelu Moovendhan
- Centre for Ocean Research, Col. Dr. Jeppiar Research Park, Sathyabama Institute of Science and Technology, Chennai, India
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Nagendla NK, Subrahanyam SB, Konda S, Mudiam MKR. Development of liquid chromatography-triple quadrupole mass spectrometric method for the quantitative determination of a novel adjuvant, Imidazoquinoline gallamide in aluminum hydroxide gel-Imidazoquinoline gallamide and COVAXIN. J Sep Sci 2023; 46:e2300380. [PMID: 37609812 DOI: 10.1002/jssc.202300380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Imidazoquinoline gallamide is a toll-like receptor 7/8 agonist, belongs to the imidazoquinoline class, has the potential to activate antigen-presenting cells, and enhances immune response, primarily Th1 response. The COVAXIN is a whole virion inactivated Coronavirus disease 2019 vaccine formulated with this novel adjuvant called, aluminum hydroxide gel Imidazoquinoline gallamide, wherein, Imidazoquinoline gallamide is chemisorbed onto aluminum hydroxide gel. Herein, an analytical method based on liquid chromatography-tandem mass spectrometry was developed to identify and quantify Imidazoquinoline gallamide in aluminum hydroxide gel Imidazoquinoline gallamide and COVAXIN. The multiple reaction monitoring transitions were optimized for Imidazoquinoline gallamide quantification are [M+H]+ ions with 512.24→343.19 m/z (quantifier ion) and 512.24→360.22 m/z (qualifier ion). The developed method was validated as per the international conference on harmonization quality2 revison1 guidelines. The method was linear in the range of 0.025-10 µg/mL with a coefficient of determination of 0.9985 and the limit of quantification is 0.025 µg/mL. The accuracy was in the range of 82-121 % and intra- and inter-day precision was less than 7.1% and 5.39%, respectively. The expanded uncertainty results are 9.2% for Imidazoquinoline gallamide in the sample. The validated method was successfully applied to evaluate Imidazoquinoline gallamide concentration in every batch of COVAXIN.
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Affiliation(s)
- Narendra Kumar Nagendla
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- Department of Analytical and Structural Chemistry, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Seetha Bala Subrahanyam
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- Department of Analytical and Structural Chemistry, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Satyanand Konda
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- Department of Analytical and Structural Chemistry, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohana Krishna Reddy Mudiam
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- Department of Analytical and Structural Chemistry, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Bhardwaj P, Mishra SK, Behera SP, Zaman K, Kant R, Singh R. Genomic evolution of the SARS-CoV-2 Variants of Concern: COVID-19 pandemic waves in India. EXCLI JOURNAL 2023; 22:451-465. [PMID: 37534220 PMCID: PMC10390896 DOI: 10.17179/excli2023-6098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 08/04/2023]
Abstract
SARS-CoV-2 has mutated rapidly since its first case report in Wuhan, China, leading to the emergence of an indefinite number of variants. India has witnessed three waves of the COVID-19 pandemic. The country saw its first wave of SARS-CoV-2 illness from late January 2020 to February 2021. With a peak surge of cases in mid-September 2020, India recorded more than 11 million cases and a death toll of more than 0.165 million at this time. India faced a brutal second wave driven by the emergence of highly infectious SARS-CoV-2 variants B.1.617.2 (Delta variant) and the third wave with the leading cause of BA.2 (Omicron variant), which has led to an unprecedented rise in COVID-19 cases in the country. On September 14, 2022, India recorded a cumulative 44.51 million cases of COVID-19 with more than 0.528 million deaths. The discovery of common circulating mutants is facilitated by genome sequencing. The changes in the Spike surface glycoprotein recombinant binding domains served as the critical alterations, resulting in enhanced infectivity and transmissibility, with severe clinical effects. Further, the predominant mutation in the SARS-CoV-2 spike protein; the D614G strains served as a model for vaccine development. The mutation of the Wuhan strain to the Variant of Concern led to a significant increase in SARS-CoV-2 infections. In addition, there was a shift in the age group affected by SARS-CoV-2 variant infection. The current review summarized the COVID-19 pandemic's Variant of Concern and the advent of SARS-CoV-2 in India.
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Affiliation(s)
- Pooja Bhardwaj
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
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Yadav PD, Kumar S, Agarwal K, Jain M, Patil DR, Maithal K, Mathapati B, Giri S, Mohandas S, Shete A, Sapkal G, Patil DY, Dey A, Chandra H, Deshpande G, Gupta N, Abraham P, Kaushal H, Sahay RR, Tripathy A, Nyayanit D, Jain R, Kumar A, Sarkale P, Baradkar S, Rajanathan C, Raju HP, Patel S, Shah N, Dwivedi P, Singh D. Needle-free injection system delivery of ZyCoV-D DNA vaccine demonstrated improved immunogenicity and protective efficacy in rhesus macaques against SARS-CoV-2. J Med Virol 2023; 95:e28484. [PMID: 36625386 DOI: 10.1002/jmv.28484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/12/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
The apprehension of needles related to injection site pain, risk of transmitting bloodborne pathogens, and effective mass immunization have led to the development of a needle-free injection system (NFIS). Here, we evaluated the efficacy of the NFIS and needle injection system (NIS) for the delivery and immunogenicity of DNA vaccine candidate ZyCoV-D in rhesus macaques against SARS-CoV-2 infection. Briefly, 20 rhesus macaques were divided into 5 groups (4 animals each), that is, I (1 mg dose by NIS), II (2 mg dose by NIS), III (1 mg dose by NFIS), IV (2 mg dose by NFIS) and V (phosphate-buffer saline [PBS]). The macaques were immunized with the vaccine candidates/PBS intradermally on Days 0, 28, and 56. Subsequently, the animals were challenged with live SARS-CoV-2 after 15 weeks of the first immunization. Blood, nasal swab, throat swab, and bronchoalveolar lavage fluid specimens were collected on 0, 1, 3, 5, and 7 days post infection from each animal to determine immune response and viral clearance. Among all the five groups, 2 mg dose by NFIS elicited significant titers of IgG and neutralizing antibody after immunization with enhancement in their titers postvirus challenge. Besides this, it also induced increased lymphocyte proliferation and cytokine response. The minimal viral load post-SARS-CoV-2 challenge and significant immune response in the immunized animals demonstrated the efficiency of NFIS in delivering 2 mg ZyCoV-D vaccine candidate.
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Affiliation(s)
- Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Sanjay Kumar
- Department of Neurosurgery, Command Hospital [Southern Command], Armed Forces Medical College [AFMC], Pune, India
| | - Kshitij Agarwal
- Department of Respiratory Medicine, University college of Medical Scieneces and Guru Teg Bahadur Hospital, University of Delhi, New Delhi, India
| | - Mukul Jain
- Zydus Research Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Dilip R Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Kapil Maithal
- Vaccine Technology Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Basavaraj Mathapati
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Suresh Giri
- Zydus Research Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Sreelekshmy Mohandas
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Deepak Y Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Ayan Dey
- Vaccine Technology Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Harish Chandra
- Vaccine Technology Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Gururaj Deshpande
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | | | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Himanshu Kaushal
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Rima R Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Anuradha Tripathy
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Dimpal Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Rajlaxmi Jain
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Abhimanyu Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Prasad Sarkale
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Shreekant Baradkar
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | | | - Hari Prasad Raju
- Vaccine Technology Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Satish Patel
- Zydus Research Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Niraj Shah
- Zydus Research Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Pankaj Dwivedi
- Zydus Research Centre, Cadila Healthcare Limited, Ahmedabad, Gujarat, India
| | - Dharmendra Singh
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
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Khare S, Niharika, Singh A, Hussain I, Singh NB, Singh S. SARS-CoV-2 Vaccines: Types, Working Principle, and Its Impact on Thrombosis and Gastrointestinal Disorders. Appl Biochem Biotechnol 2023; 195:1541-1573. [PMID: 36222988 PMCID: PMC9554396 DOI: 10.1007/s12010-022-04181-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
In the current scenario of the coronavirus pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), considerable efforts have been made to control the pandemic by the development of a strong immune system through massive vaccination. Just after the discovery of the genetic sequences of SARS-CoV-2, the development of vaccines became the prime focus of scientists around the globe. About 200 SARS-CoV-2 candidate vaccines have already been entered into preclinical and clinical trials. Various traditional and novel approaches are being utilized as a broad range of platforms. Viral vector (replicating and non-replicating), nucleic acid (DNA and RNA), recombinant protein, virus-like particle, peptide, live attenuated virus, an inactivated virus approaches are the prominent attributes of the vaccine development. This review article includes the current knowledge about the platforms used for the development of different vaccines, their working principles, their efficacy, and the impacts of COVID-19 vaccines on thrombosis. We provide a detailed description of the vaccines that are already approved by administrative authorities. Moreover, various strategies utilized in the development of emerging vaccines that are in the trial phases along with their mode of delivery have been discussed along with their effect on thrombosis and gastrointestinal disorders.
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Affiliation(s)
- Shubhra Khare
- grid.411343.00000 0001 0213 924XPlant Physiology Laboratory, Department of Botany, University of Allahabad, Prayagraj, 211002 U.P. India
| | - Niharika
- grid.411343.00000 0001 0213 924XPlant Physiology Laboratory, Department of Botany, University of Allahabad, Prayagraj, 211002 U.P. India
| | - Ajey Singh
- grid.411488.00000 0001 2302 6594Department of Botany, University of Lucknow, Lucknow, 226007 U.P. India
| | - Imtiyaz Hussain
- grid.412997.00000 0001 2294 5433Government Degree College, University of Ladakh, Dras, Ladakh India
| | - Narsingh Bahadur Singh
- grid.411343.00000 0001 0213 924XPlant Physiology Laboratory, Department of Botany, University of Allahabad, Prayagraj, 211002 U.P. India
| | - Subhash Singh
- grid.16416.340000 0004 1936 9174The Institute of Optics, University of Rochester, Rochester, NY-14627 USA
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Sunagar R, Prasad SD, Ella R, Vadrevu KM. Preclinical evaluation of safety and immunogenicity of a primary series intranasal COVID-19 vaccine candidate (BBV154) and humoral immunogenicity evaluation of a heterologous prime-boost strategy with COVAXIN (BBV152). Front Immunol 2022; 13:1063679. [PMID: 36569867 PMCID: PMC9773076 DOI: 10.3389/fimmu.2022.1063679] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Most if not all vaccine candidates developed to combat COVID-19 due to SARS-CoV-2 infection are administered parenterally. As SARS-CoV-2 is transmitted through infectious respiratory fluids, vaccine-induced mucosal immunity could provide an important contribution to control this pandemic. ChAd-SARS-CoV-2-S (BBV154), a replication-defective chimpanzee adenovirus (ChAd)-vectored intranasal (IN) COVID-19 vaccine candidate, encodes a prefusion-stabilized version of the SARS-CoV-2 spike protein containing two proline substitutions in the S2 subunit. We performed preclinical evaluations of BBV154 in mice, rats, hamsters and rabbits. Repeated dose toxicity studies presented excellent safety profiles in terms of pathology and biochemical analysis. IN administration of BBV154 elicited robust mucosal and systemic humoral immune responses coupled with Th1 cell-mediated immune responses. BBV154 IN vaccination also elicited potent variant (omicron) cross neutralization antibodies. Assessment of anti-vector (ChAd36) neutralizing antibodies following repeated doses of BBV154 IN administration showed insignificant titers of ChAd36 neutralizing antibodies. However, the immune sera derived from the same animals displayed significantly higher levels of SARS-CoV-2 virus neutralization (p<0.003). We also evaluated the safety and immunogenicity of heterologous prime-boost vaccination with intramuscular (IM) COVAXIN-prime followed by BBV154 IN administration. COVAXIN priming followed by BBV154 IN-booster showed an acceptable reactogenicity profile comparable to the homologous COVAXIN/COVAXIN or BBV154/BBV154 vaccination model. Heterologous vaccination of COVAXIN-prime and BBV154 booster also elicited superior (p<0.005) and cross variant (omicron) protective immune responses (p<0.013) compared with the homologous COVAXIN/COVAXIN schedule. BBV154 has successfully completed both homologous and heterologous combination schedules of human phase 3 clinical trials and received the restricted emergency use approval (in those aged above 18 years) from the Drugs Controller General of India (DCGI).
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Muacevic A, Adler JR, Kumar D, Purohit A, Garg M, Kanchan DT, Dutt N, Kothari N, Bhaskar S, Elhence P, Bhatia P, Nag VL, Garg MK, Misra S, Pandey A, Dhawan A. Ultrastructural Changes in Autopsy Tissues of COVID-19 Patients. Cureus 2022; 14:e31932. [PMID: 36582579 PMCID: PMC9794915 DOI: 10.7759/cureus.31932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2022] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION The COVID-19 pandemic resulted in substantial morbidity and mortality across the world. The prognosis was found to be poor in patients with co-morbidities such as diabetes, hypertension, interstitial lung disease, etc. Although biochemical studies were done in patient samples, no study has been reported from the Indian subcontinent about ultrastructural changes in the vital organs of COVID-19 patients. The present study was, therefore, conducted to understand the ultrastructural changes in the lung, liver, and brain of the deceased patients. METHODS The present study was conducted on samples obtained from reverse transcription-polymerase chain reaction (RT-PCR)-positive patients who were admitted to a tertiary care hospital in Western India. Core needle biopsies were done in eight fatal cases of COVID-19. The samples were taken from the lungs, liver, and brain and subjected to light microscopy, immunohistochemistry (IHC), and transmission electron microscopy (TEM). Clinical details and biochemical findings were also collected. Results: The study participants included seven males and one female. The presenting complaints included fever, breathlessness, and cough. Light microscopy revealed diffuse alveolar damage in the lungs. Further, a positive expression of SARS-CoV-2 nucleocapsid protein was observed in the pulmonary parenchyma of five patients. Also, the TEM microphotograph showed viral particles of size up to 80nm localized in alveolar epithelial cells. However, no viral particles were found in liver or brain samples. In the liver, macrovesicular steatosis and centrizonal congestion with loss of hepatocytes were observed in light microscopy. CONCLUSION This is the first study in the Indian population showing the in-situ presence of viral particles in core biopsies from fatal cases of COVID-19. As evident from the results, histology and ultrastructural changes in the lung correlated with the presence of viral particles. The study revealed a positive correlation between the damage in the lungs and the presence of viral particles.
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García-Machorro J, Ramírez-Salinas GL, Martinez-Archundia M, Correa-Basurto J. The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus. Vaccines (Basel) 2022; 10:1844. [PMID: 36366353 PMCID: PMC9693616 DOI: 10.3390/vaccines10111844] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 10/28/2023] Open
Abstract
After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - Marlet Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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11
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Joshi M, Mohandas S, Prasad S, Shinde M, Chavan N, Yadav PD, Lavania M. Lack of evidence of viability and infectivity of SARS-CoV-2 in the fecal specimens of COVID-19 patients. Front Public Health 2022; 10:1030249. [PMID: 36339137 PMCID: PMC9632423 DOI: 10.3389/fpubh.2022.1030249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 01/29/2023] Open
Abstract
SARS-CoV-2 can be shed in feces and can enter sewage systems. In order to implement effective control measures and identify new channels of transmission, it is essential to identify the presence of infectious virus particles in feces and sewage. In this study, we attempt to utilize Molecular techniques, cell cultures and animal models to find out the infectivity of SARS-CoV-2 in the feces of COVID-19 patients. Our findings exclude the presence of infectious virus particles, suggesting that fecal-oral transmission may not be the main mode of transmission. Larger-scale initiatives are nevertheless required, particularly considering the emergence of new viral strains.
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Affiliation(s)
- Madhuri Joshi
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Sreelekshmy Mohandas
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | - Sharda Prasad
- Electron Microscopy and Histopathology Group, ICMR-National Institute of Virology, Pune, India
| | - Manohar Shinde
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Nutan Chavan
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Pragya D. Yadav
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India,*Correspondence: Pragya D. Yadav
| | - Mallika Lavania
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India,Mallika Lavania
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12
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Dotiwala F, Upadhyay AK. A comprehensive review of BBV152 vaccine development, effectiveness, safety, challenges, and prospects. Front Immunol 2022; 13:940715. [PMID: 36177016 PMCID: PMC9513542 DOI: 10.3389/fimmu.2022.940715] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The world has responded to the COVID-19 pandemic with unprecedented speed and vigor in the mass vaccination campaigns, targeted to reduce COVID-19 severity and mortality, reduce the pressure on the healthcare system, re-open society, and reduction in disease mortality and morbidity. Here we review the preclinical and clinical development of BBV152, a whole virus inactivated vaccine and an important tool in the fight to control this pandemic. BBV152, formulated with a TLR7/8 agonist adjuvant generates a Th1-biased immune response that induces high neutralization efficacy against different SARS-CoV-2 variants of concern and robust long-term memory B- and T-cell responses. With seroconversion rates as high as 98.3% in vaccinated individuals, BBV152 shows 77.8% and 93.4% protection from symptomatic COVID-19 disease and severe symptomatic COVID-19 disease respectively. Studies in pediatric populations show superior immunogenicity (geometric mean titer ratio of 1.76 compared to an adult) with a seroconversion rate of >95%. The reactogenicity and safety profiles were comparable across all pediatric age groups between 2-18 yrs. as in adults. Like most approved vaccines, the BBV152 booster given 6 months after full vaccination, reverses a waning immunity, restores the neutralization efficacy, and shows synergy in a heterologous prime-boost study with about 3-fold or 300% increase in neutralization titers against multiple SARS-CoV-2 variants of concern. Based on the interim Phase III data, BBV152 received full authorization for adults and emergency use authorization for children from ages 6 to 18 years in India. It is also licensed for emergency use in 14 countries globally. Over 313 million vaccine doses have already been administered in India alone by April 18th, 2022.
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13
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Vadrevu KM, Ganneru B, Reddy S, Jogdand H, Raju D, Sapkal G, Yadav P, Reddy P, Verma S, Singh C, Redkar SV, Gillurkar CS, Kushwaha JS, Mohapatra S, Bhate A, Rai SK, Ella R, Abraham P, Prasad S, Ella K. Persistence of immunity and impact of third dose of inactivated COVID-19 vaccine against emerging variants. Sci Rep 2022; 12:12038. [PMID: 35835822 PMCID: PMC9281359 DOI: 10.1038/s41598-022-16097-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/04/2022] [Indexed: 12/30/2022] Open
Abstract
This is a comprehensive report on immunogenicity of COVAXIN® booster dose against ancestral and Variants of Concern (VOCs) up to 12 months. It is well known that neutralizing antibodies induced by COVID-19 vaccines wane within 6 months of vaccination leading to questions on the effectiveness of two-dose vaccination against breakthrough infections. Therefore, we assessed the persistence of immunogenicity up to 6 months after a two or three-dose with BBV152 and the safety of a booster dose in an ongoing phase 2, double-blind, randomized controlled trial (ClinicalTrials.gov: NCT04471519). We report persistence of humoral and cell mediated immunity up to 12 months of vaccination, despite decline in the magnitude of antibody titers. Administration of a third dose of BBV152 increased neutralization titers against both homologous (D614G) and heterologous strains (Alpha, Beta, Delta, Delta Plus and Omicron) with a slight increase in B cell memory responses. Thus, seronversion rate remain high in boosted recipients compared to non-booster, even after 6 months, post third dose against variants. No serious adverse events observed, except pain at the injection site, itching and redness. Hence, these results indicate that a booster dose of BBV152 is safe and necessary to ensure persistent immunity to minimize breakthrough infections of COVID-19, due to newly emerging variants. Trial registration: Registered with the Clinical Trials Registry (India) No. CTRI/2021/04/032942, dated 19/04/2021 and on Clinicaltrials.gov: NCT04471519.
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Affiliation(s)
| | - Brunda Ganneru
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, India
| | - Siddharth Reddy
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, India
| | - Harsh Jogdand
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, India
| | - Dugyala Raju
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, India
| | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Savita Verma
- Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, India
| | | | | | | | | | | | | | | | - Raches Ella
- Independent Clinical Development Consultant, Cambridge, USA
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Sai Prasad
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, India
| | - Krishna Ella
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, India
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14
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Nunes DR, Braconi CT, Ludwig-Begall LF, Arns CW, Durães-Carvalho R. Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. PLoS One 2022; 17:e0268389. [PMID: 35609034 PMCID: PMC9129020 DOI: 10.1371/journal.pone.0268389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/28/2022] [Indexed: 02/06/2023] Open
Abstract
Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of previously unreported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: (i) the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution, and (ii) a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains.
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Affiliation(s)
- Danilo Rosa Nunes
- Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
- * E-mail: (CTB); (RDC)
| | - Louisa F. Ludwig-Begall
- Department of Infectious and Parasitic Diseases, Veterinary Virology and Animal Viral Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Clarice Weis Arns
- Laboratory of Virology, University of Campinas, Campinas, SP, Brazil
| | - Ricardo Durães-Carvalho
- Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
- * E-mail: (CTB); (RDC)
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15
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Yadav PD, Mohandas S, Shete AM, Nyayanit DA, Gupta N, Patil DY, Sapkal GN, Potdar V, Kadam M, Kumar A, Kumar S, Suryavanshi D, Mote CS, Abraham P, Panda S, Bhargava B. SARS-CoV-2 Kappa Variant Shows Pathogenicity in a Syrian Hamster Model. Vector Borne Zoonotic Dis 2022; 22:289-296. [PMID: 35580212 DOI: 10.1089/vbz.2021.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Objectives: The emergence of SARS-CoV-2 lineage B.1.617 variants in India has been associated with a surge in the number of daily infections. We investigated the pathogenic potential of Kappa (B.1.617.1) variant in Syrian golden hamsters. Methods: Two groups of Syrian golden hamsters (18 each) were inoculated intranasally with SARS-CoV-2 isolates, B.1 (D614G) and Kappa variant, respectively. The animals were monitored daily for the clinical signs and body weight. Throat swab, nasal wash, and organ samples (lungs, nasal turbinate, trachea) were collected and screened using SARS-CoV-2-specific RT-qPCR. Histopathologic evaluation of the lung samples was performed. Results: The hamsters infected with the Kappa variant demonstrated increased body weight loss compared to the B.1 lineage isolate. The highest viral RNA load was observed in the nasal turbinate and lung specimens of animals infected with both variants. A significantly higher sgRNA load was observed in the nasal swabs (7 DPI), trachea (3 DPI), and lungs (3 DPI) of hamsters infected with the Kappa variant. Neutralizing antibody response generated in the B.1 lineage-infected hamster sera were comparable against both B.1 and Kappa variant in contrast to Kappa variant-infected hamsters, which showed lower titers against B.1 lineage isolate. Gross and microscopic evaluation of the lung specimens showed severe lung lesions in hamsters infected with Kappa variant compared to B.1. Conclusions: The study demonstrates pathogenicity of Kappa variant in hamsters evident with reduced body weight, high viral RNA load in lungs, and pronounced lung lesions. Both Kappa variant- and B.1-infected hamsters produced neutralizing antibodies against both variants studied.
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Affiliation(s)
- Pragya D Yadav
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Sreelekshmy Mohandas
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Anita M Shete
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Dimpal A Nyayanit
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - Deepak Y Patil
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Gajanan N Sapkal
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Varsha Potdar
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Manoj Kadam
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Abhimanyu Kumar
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Sanjay Kumar
- Department of Neurosurgery, Command Hospital (Southern Command), Armed Forces Medical College (AFMC), Pune, India
| | - Deepak Suryavanshi
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Chandrashekhar S Mote
- Department of Veterinary Pathology, Krantisinh Nana Patil College of Veterinary Science, Shirwal, India
| | - Priya Abraham
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - Balram Bhargava
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
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16
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Lavania M, Joshi MS, Ranshing SS, Potdar VA, Shinde M, Chavan N, Jadhav SM, Sarkale P, Mohandas S, Sawant PM, Tikute S, Padbidri V, Patwardhan S, Kate R. Prolonged Shedding of SARS-CoV-2 in Feces of COVID-19 Positive Patients: Trends in Genomic Variation in First and Second Wave. Front Med (Lausanne) 2022; 9:835168. [PMID: 35372453 PMCID: PMC8965355 DOI: 10.3389/fmed.2022.835168] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/04/2022] [Indexed: 01/08/2023] Open
Abstract
The main route of the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are through respiratory pathways and close contact of human-to-human. While information about other modes of transmission is comparatively less, some published literature supporting the likelihood of a fecal-oral mode of transmission has been accumulating. The diagnosis of SARS-COV-2 infected cases is based on the real-time reverse transcription-PCR (RT-PCR). The fecal excretion of SARS-COV-2 has been reported frequently, however, the role of fecal viral load with the severity of disease is not yet clear. Our study focused on the investigation of SARS-CoV-2 shedding in the fecal samples of patients with coronavirus disease 2019 (COVID-19). A total of 280 RT-PCR-positive patients were enrolled, among them 15.4% had gastrointestinal (GI) symptoms. It was shown that 62% of the patients were positive for SARS-CoV-2 RNA in fecal specimens. This positivity was not related to the presence of GI symptoms and the severity of disease. The next generation sequencing [NGS] of SARS-CoV-2 from fecal samples of patients was performed to analyze mutational variations. Findings from this study not only emphasized the potential presence of SARS-CoV-2 in feces, but also its continuing mutational changes and its possible role in fecal-oral transmission.
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Affiliation(s)
- Mallika Lavania
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Madhuri S Joshi
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Sujata S Ranshing
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Varsha A Potdar
- National Influenza Centre, ICMR-National Institute of Virology, Pune, India
| | - Manohar Shinde
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Nutan Chavan
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Santosh M Jadhav
- Bioinformatics and Data Management Group, ICMR-National Institute of Virology, Pune, India
| | - Prasad Sarkale
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | - Sreelekshmy Mohandas
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | - Pradeep M Sawant
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | | | - Vikram Padbidri
- Microbiology and Infection Control Jehangir Hospital, Pune, India
| | - Sampada Patwardhan
- Microbiology and Hospital Infection Control, Deenanath Mangeshkar Hospital and Research Center, Pune, India
| | - Rohan Kate
- Department of Medicine, Lokmanya Hospital Chinchwad, Pune, India
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17
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Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. Viruses 2022; 14:v14030461. [PMID: 35336868 PMCID: PMC8951364 DOI: 10.3390/v14030461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung specimens of both passages. The successful isolation of the virus from hamster specimens with Vero CCL-81 was observed with cytopathic effect in infected cells and high viral load in the cell suspension. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequences, suggesting intact pathogenicity of the virus isolate. Our data demonstrated successful isolation of the Omicron variant with the in vivo method first followed by in vitro method. The virus isolate could be used in the future to explore different aspects of the Omicron variant.
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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] [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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19
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Yadav PD, Sapkal GN, Abraham P, Ella R, Deshpande G, Patil DY, Nyayanit DA, Gupta N, Sahay RR, Shete AM, Panda S, Bhargava B, Mohan VK. Neutralization of Variant Under Investigation B.1.617.1 With Sera of BBV152 Vaccinees. Clin Infect Dis 2022; 74:366-368. [PMID: 33961693 DOI: 10.1093/cid/ciab411] [Citation(s) in RCA: 134] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Gajanan N Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Raches Ella
- Bharat Biotech International Limited, Genome Valley, Hyderabad, India
| | - Gururaj Deshpande
- 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
| | - Dimpal A Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - Rima R Sahay
- 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
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - Balram Bhargava
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - V Krishna Mohan
- Bharat Biotech International Limited, Genome Valley, Hyderabad, India
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Pawar SD, Kode SS, Keng SS, Tare DS, Diop OM, Abraham P, Sharma DK, Sangal L, Yadav PD, Potdar VA. Replication of SARS-CoV-2 in cell lines used in public health surveillance programmes with special emphasis on biosafety. Indian J Med Res 2022; 155:129-135. [PMID: 35859439 PMCID: PMC9552391 DOI: 10.4103/ijmr.ijmr_1448_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background & objectives Polio, measles, rubella, influenza and rotavirus surveillance programmes are of great public health importance globally. Virus isolation using cell culture is an integral part of such programmes. Possibility of unintended isolation of SARS-CoV-2 from clinical specimens processed in biosafety level-2 (BSL-2) laboratories during the above-mentioned surveillance programmes, cannot be ruled out. The present study was conducted to assess the susceptibility of different cell lines to SARS-CoV-2 used in these programmes. Methods Replication of SARS-CoV-2 was studied in RD and L20B, Vero/hSLAM, MA-104 and Madin-Darby Canine Kidney (MDCK) cell lines, used for the isolation of polio, measles, rubella, rotavirus and influenza viruses, respectively. SARS-CoV-2 at 0.01 multiplicity of infection was inoculated and the viral growth was assessed by observation of cytopathic effects followed by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Vero CCL-81 cell line was used as a positive control. Results SARS-CoV-2 replicated in Vero/hSLAM, and MA-104 cells, whereas it did not replicate in L20B, RD and MDCK cells. Vero/hSLAM, and Vero CCL-81 showed rounding, degeneration and detachment of cells; MA-104 cells also showed syncytia formation. In qRT-PCR, Vero/hSLAM and MA-104 showed 106 and Vero CCL-81 showed 107 viral RNA copies per μl. The 50 per cent tissue culture infectious dose titres of Vero/hSLAM, MA-104 and Vero CCL-81 were 105.54, 105.29 and 106.45/ml, respectively. Interpretation & conclusions Replication of SARS-CoV-2 in Vero/hSLAM and MA-104 underscores the possibility of its unintended isolation during surveillance procedures aiming to isolate measles, rubella and rotavirus. This could result in accidental exposure to high titres of SARS-CoV-2, which can result in laboratory acquired infections and community risk, highlighting the need for revisiting biosafety measures in public health laboratories.
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Affiliation(s)
- Shailesh D Pawar
- Poliovirus Group, ICMR-National Institute of Virology, Pune; ICMR-National Institute of Virology-Mumbai Unit, Mumbai, Maharashtra, India
| | - Sadhana S Kode
- Poliovirus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sachin S Keng
- Poliovirus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Deeksha S Tare
- Poliovirus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ousmane M Diop
- World Health Organization Headquarters, Geneva, Switzerland
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Deepa K Sharma
- ICMR-National Institute of Virology-Mumbai Unit, Mumbai, Maharashtra, India
| | - Lucky Sangal
- Regional Office for South-East Asia, World Health Organization, New Delhi, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Varsha A Potdar
- Human Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
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Kant R, Dwivedi G, Zaman K, Sahay RR, Sapkal G, Kaushal H, Nyayanit DA, Yadav PD, Deshpande G, Singh R, Chaowdhary S, Gupta N, Kumar S, Abraham P, Panda S, Bhargava B. Immunogenicity and safety of a heterologous prime-boost COVID-19 vaccine schedule: ChAdOx1 vaccine Covishield followed by BBV152 Covaxin. J Travel Med 2021; 28:6397775. [PMID: 34652440 PMCID: PMC8524638 DOI: 10.1093/jtm/taab166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/21/2022]
Abstract
The evidence for effectiveness of heterologous priming of COVID-19 vaccine is very limited. Here, we studied eighteen participants who received heterologous vaccination regimen of AstraZeneca’s ChAdOx1-nCov-19 followed by inactivated whole virion BBV152. Heterologous group participant doesn’t report any adverse event following immunization and demonstrated high humoral and neutralizing antibody response.
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Affiliation(s)
- Rajni Kant
- Indian Council of Medical Research-Regional Medical Research Centre (RMRC), Gorakhpur, Uttar Pradesh, 273013, India
| | - Gaurav Dwivedi
- Indian Council of Medical Research-Regional Medical Research Centre (RMRC), Gorakhpur, Uttar Pradesh, 273013, India
| | - Kamran Zaman
- Indian Council of Medical Research-Regional Medical Research Centre (RMRC), Gorakhpur, Uttar Pradesh, 273013, India
| | - Rima R Sahay
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Himanshu Kaushal
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Dimpal A Nyayanit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Gururaj Deshpande
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Rajeev Singh
- Indian Council of Medical Research-Regional Medical Research Centre (RMRC), Gorakhpur, Uttar Pradesh, 273013, India
| | - Sandeep Chaowdhary
- Chief Medical Officer, Community Health Centre, Siddarthnagar, Uttar Pradesh, 272207, India
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India
| | - Sanjay Kumar
- Command Hospital (Southern Command), Armed Forces Medical College, Pune, Maharashtra, 411040, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra, 411021, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India
| | - Balram Bhargava
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, 110029, India
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22
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Isolation and characterization of SARS-CoV-2 Beta variant from UAE travelers. J Infect Public Health 2021; 15:182-186. [PMID: 34974274 PMCID: PMC8704724 DOI: 10.1016/j.jiph.2021.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/25/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background The emergence of SARS-CoV-2 variants in places where the virus is uncontained poses a global threat from the perspective of public health and vaccine efficacy. Travel has been important factor for the easy spread of SARS-CoV-2 variants worldwide. India has also observed the importation of SARS-CoV-2 variants through international travelers. Methods In this study, we have collected the oropharyngeal and nasopharyngeal swab specimens from 58 individuals with travel history from United Arab Emirates (UAE), East, West and South Africa, Qatar, Ukraine and Saudi Arabia arrived in India during February–March 2021. The clinical specimens were initially screened for SARS-CoV-2 using Real time RT-PCR. All the specimens were inoculated on to Vero CCL-81 cells for virus isolation. The viral isolates were further sequenced using Next-Generation Sequencing. Results All 58 cases were tested positive for SARS-CoV-2 using Real time RT-PCR. Four specimens showed progressive infectivity with fusion of the infected cells with neighboring cells leading to large mass of cells. Replication competent virus was confirmed from culture supernatant of the passage 2 using Real time RT-PCR. Two plaque purified SARS-CoV-2 isolates demonstrated high viral RNA load of 3.8–7.5 × 1011 and 1.1–1.6 × 1011 at passage 4 and 5 respectively. Nucleotide variations along with amino acid changes were also observed among these two isolates at passage 2–5. All four cases were male with no symptoms and co-morbidity. The sequence analysis has shown two different clusters, first cluster with nucleotide deletions in the ORF1ab and the spike, while second cluster with deletions in spike region. The viral isolates demonstrated 99.88–99.96% nucleotide identity with the representative sequences of Beta variant (B.1.351). Conclusion These findings suggest easier transmission of SARS-CoV-2 variants with human mobility through international travel. The isolated Beta variant would be useful to determine the protective efficacy of the currently available and upcoming COVID-19 vaccines in India.
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Ella R, Reddy S, Blackwelder W, Potdar V, Yadav P, Sarangi V, Aileni VK, Kanungo S, Rai S, Reddy P, Verma S, Singh C, Redkar S, Mohapatra S, Pandey A, Ranganadin P, Gumashta R, Multani M, Mohammad S, Bhatt P, Kumari L, Sapkal G, Gupta N, Abraham P, Panda S, Prasad S, Bhargava B, Ella K, Vadrevu KM. Efficacy, safety, and lot-to-lot immunogenicity of an inactivated SARS-CoV-2 vaccine (BBV152): interim results of a randomised, double-blind, controlled, phase 3 trial. Lancet 2021; 398:2173-2184. [PMID: 34774196 PMCID: PMC8584828 DOI: 10.1016/s0140-6736(21)02000-6] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/17/2021] [Accepted: 08/25/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND We report the clinical efficacy against COVID-19 infection of BBV152, a whole virion inactivated SARS-CoV-2 vaccine formulated with a toll-like receptor 7/8 agonist molecule adsorbed to alum (Algel-IMDG) in Indian adults. METHODS We did a randomised, double-blind, placebo-controlled, multicentre, phase 3 clinical trial in 25 Indian hospitals or medical clinics to evaluate the efficacy, safety, and immunological lot consistency of BBV152. Adults (age ≥18 years) who were healthy or had stable chronic medical conditions (not an immunocompromising condition or requiring treatment with immunosuppressive therapy) were randomised 1:1 with a computer-generated randomisation scheme (stratified for the presence or absence of chronic conditions) to receive two intramuscular doses of vaccine or placebo administered 4 weeks apart. Participants, investigators, study coordinators, study-related personnel, the sponsor, and nurses who administered the vaccines were masked to treatment group allocation; an unmasked contract research organisation and a masked expert adjudication panel assessed outcomes. The primary outcome was the efficacy of the BBV152 vaccine in preventing a first occurrence of laboratory-confirmed (RT-PCR-positive) symptomatic COVID-19 (any severity), occurring at least 14 days after the second dose in the per-protocol population. We also assessed safety and reactogenicity throughout the duration of the study in all participants who had received at least one dose of vaccine or placebo. This report contains interim results (data cutoff May 17, 2021) regarding immunogenicity and safety outcomes (captured on days 0 to 56) and efficacy results with a median of 99 days for the study population. The trial was registered on the Indian Clinical Trials Registry India, CTRI/2020/11/028976, and ClinicalTrials.gov, NCT04641481 (active, not recruiting). FINDINGS Between Nov 16, 2020, and Jan 7, 2021, we recruited 25 798 participants who were randomly assigned to receive BBV152 or placebo; 24 419 received two doses of BBV152 (n=12 221) or placebo (n=12 198). Efficacy analysis was dependent on having 130 cases of symptomatic COVID-19, which occurred when 16 973 initially seronegative participants had at least 14 days follow-up after the second dose. 24 (0·3%) cases occurred among 8471 vaccine recipients and 106 (1·2%) among 8502 placebo recipients, giving an overall estimated vaccine efficacy of 77·8% (95% CI 65·2-86·4). In the safety population (n=25 753), 5959 adverse events occurred in 3194 participants. BBV152 was well tolerated; the same proportion of participants reported adverse events in the vaccine group (1597 [12·4%] of 12 879) and placebo group (1597 [12·4%] of 12 874), with no clinically significant differences in the distributions of solicited, unsolicited, or serious adverse events between the groups, and no cases of anaphylaxis or vaccine-related deaths. INTERPRETATION BBV152 was highly efficacious against laboratory-confirmed symptomatic COVID-19 disease in adults. Vaccination was well tolerated with no safety concerns raised in this interim analysis. FUNDING Bharat Biotech International and Indian Council of Medical Research.
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Affiliation(s)
- Raches Ella
- Bharat Biotech International, Hyderabad, India
| | | | | | - Varsha Potdar
- National Institute of Virology, Indian Council of Medical Research, Pune, India
| | - Pragya Yadav
- National Institute of Virology, Indian Council of Medical Research, Pune, India
| | | | | | - Suman Kanungo
- National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research, Kolkatta, India
| | - Sanjay Rai
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Savita Verma
- Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, India
| | | | | | | | - Anil Pandey
- ESIC Medical College and Hospital, Faridabad, India
| | | | - Raghavendra Gumashta
- Department of Community Medicine, People's College of Medical Sciences and Research Centre, People's University, Bhopal, India
| | | | | | - Parul Bhatt
- GMERS Medical College and Civil Hospital, Ahmedabad, India
| | | | - Gajanan Sapkal
- National Institute of Virology, Indian Council of Medical Research, Pune, India
| | | | - Priya Abraham
- National Institute of Virology, Indian Council of Medical Research, Pune, India
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi, India
| | - Sai Prasad
- Bharat Biotech International, Hyderabad, India
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Coronavirus Diseases (COVID-19): Features, Epidemiology, Mutational variations and Treatments Across India. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses are a group of enveloped viruses with a longer, undivided single-stranded RNA genome, which cause diseases in a variety of animals and humans. In addition to infecting other economically important animals (such as pigs or chickens), six coronaviruses are known to infect human hosts, causing respiratory illness. Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic animal coronaviruses that have produced local, regional, and worldwide outbreaks. It is suspected that the current pandemic, caused by a similar coronavirus (SARS-CoVID-19). A new variant of B.1.617 lineage that causes worry about many countries has been identified first in the UK but it makes the worst scenario in India. This includes mutants with immune prolapse E484K and N501Y mutations. Some new variants recently discovered in India like double & triple mutation due to some specific climatic and environmental conditions. Because it creates a viral exodermis and contacts human cells due to mutations in peplomer proteins. The other type of protein is spike protein, are required to bind to receptors in human cells mutations. It can improve the affinity for human receptors and increase the virus, they can cause immune prolapse and reinfection. Moreover, these viruses are capable of adapting and mutating to the new environment. Our immune system is unable to distinguish them from previous infections due to changes in the structure of proteins. The rapid transmission of the COVID-19 around the world causing a severe mortality rate depends on mutation on their spike protein.
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25
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Perumal V, Narayanan V, Rajasekar SJS. Prediction of COVID Criticality Score with Laboratory, Clinical and CT Images using Hybrid Regression Models. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 209:106336. [PMID: 34403841 PMCID: PMC8352851 DOI: 10.1016/j.cmpb.2021.106336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVE Rapid and precise diagnosis of COVID-19 is very critical in hotspot regions. The main aim of this proposed work is to investigate the baseline, laboratory and CT features of COVID-19 affected patients of two groups (Early and Critical stages). The detection model for COVID-19 is built depending upon the manifestations that define the severity of the disease. METHODS The CT scan images are fed into the various deep learning, machine learning and hybrid learning models to mine the necessary features and predict CT Score. The predicted CT score along with other clinical, laboratory and CT scan image features are then passed to train the various Regression models for predicting the COVID Criticality (CC) Score. These baseline, laboratory and CT features of COVID-19 are reduced using Statistical analysis and Univariate logistic regression analysis. RESULTS When analysing the prediction of CT scores using images alone, AlexNet+Lasso yields better outcome with regression score of 0.9643 and RMSE of 0.0023 when compared with Decision tree (RMSE of 0.0034; Regression score of 0.9578) and GRU (RMSE of 0.1253; regression score of 0.9323). When analysing the prediction of CC scores using CT scores and other baseline, laboratory and CT features, VGG-16+Linear Regression yields better results with regression score of 0.9911 and RMSE of 0.0002 when compared with Linear SVR (RMSE of 0.0006; Regression score of 0.9911) and LSTM (RMSE of 0.0005; Regression score of 0.9877). The correlation analysis is performed to identify the significance of utilizing other features in prediction of CC Score. The correlation coefficient of CT scores with actual value is 0.93 and 0.92 for Early stage group and Critical stage group respectively. The correlation coefficient of CC scores with actual value is 0.96 for Early stage group and 0.95 for Critical stage group.The classification of COVID-19 patients are carried out with the help of predicted CC Scores. CONCLUSIONS This proposed work is carried out in the motive of helping radiologists in faster categorization of COVID patients as Early or Severe staged using CC Scores. The automated prediction of COVID Criticality Score using our diagnostic model can help radiologists and physicians save time for carrying out further treatment and procedures.
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Affiliation(s)
- Varalakshmi Perumal
- Department of Computer Technology, Madras Institute of Technology, Anna University, Chennai, India.
| | - Vasumathi Narayanan
- Department of Computer Technology, Madras Institute of Technology, Anna University, Chennai, India.
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Hemida MG. The next-generation coronavirus diagnostic techniques with particular emphasis on the SARS-CoV-2. J Med Virol 2021; 93:4219-4241. [PMID: 33751621 PMCID: PMC8207115 DOI: 10.1002/jmv.26926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/15/2022]
Abstract
The potential zoonotic coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) are of global health concerns. Early diagnosis is the milestone in their mitigation, control, and eradication. Many diagnostic techniques are showing great success and have many advantages, such as the rapid turnover of the results, high accuracy, and high specificity and sensitivity. However, some of these techniques have several pitfalls if samples were not collected, processed, and transported in the standard ways and if these techniques were not practiced with extreme caution and precision. This may lead to false-negative/positive results. This may affect the downstream management of the affected cases. These techniques require regular fine-tuning, upgrading, and optimization. The continuous evolution of new strains and viruses belong to the coronaviruses is hampering the success of many classical techniques. There are urgent needs for next generations of coronaviruses diagnostic assays that overcome these pitfalls. This new generation of diagnostic tests should be able to do simultaneous, multiplex, and high-throughput detection of various coronavirus in one reaction. Furthermore, the development of novel assays and techniques that enable the in situ detection of the virus on the environmental samples, especially air, water, and surfaces, should be given considerable attention in the future. These approaches will have a substantial positive impact on the mitigation and eradication of coronaviruses, including the current SARS-CoV-2 pandemic.
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Affiliation(s)
- Maged G. Hemida
- Department of Microbiology, College of Veterinary MedicineKing Faisal UniversityAl AhsaSaudi Arabia
- Department of Virology, Faculty of Veterinary MedicineKafrelsheikh UniversityKafr ElsheikhEgypt
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27
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Ella R, Reddy S, Jogdand H, Sarangi V, Ganneru B, Prasad S, Das D, Raju D, Praturi U, Sapkal G, Yadav P, Reddy P, Verma S, Singh C, Redkar SV, Gillurkar CS, Kushwaha JS, Mohapatra S, Bhate A, Rai S, Panda S, Abraham P, Gupta N, Ella K, Bhargava B, Vadrevu KM. Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBV152: interim results from a double-blind, randomised, multicentre, phase 2 trial, and 3-month follow-up of a double-blind, randomised phase 1 trial. THE LANCET. INFECTIOUS DISEASES 2021; 21:950-961. [PMID: 33705727 DOI: 10.1101/2020.12.21.20248643] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND BBV152 is a whole-virion inactivated SARS-CoV-2 vaccine (3 μg or 6 μg) formulated with a toll-like receptor 7/8 agonist molecule (IMDG) adsorbed to alum (Algel). We previously reported findings from a double-blind, multicentre, randomised, controlled phase 1 trial on the safety and immunogenicity of three different formulations of BBV152 (3 μg with Algel-IMDG, 6 μg with Algel-IMDG, or 6 μg with Algel) and one Algel-only control (no antigen), with the first dose administered on day 0 and the second dose on day 14. The 3 μg and 6 μg with Algel-IMDG formulations were selected for this phase 2 study. Herein, we report interim findings of the phase 2 trial on the immunogenicity and safety of BBV152, with the first dose administered on day 0 and the second dose on day 28. METHODS We did a double-blind, randomised, multicentre, phase 2 clinical trial to evaluate the immunogenicity and safety of BBV152 in healthy adults and adolescents (aged 12-65 years) at nine hospitals in India. Participants with positive SARS-CoV-2 nucleic acid and serology tests were excluded. Participants were randomly assigned (1:1) to receive either 3 μg with Algel-IMDG or 6 μg with Algel-IMDG. Block randomisation was done by use of an interactive web response system. Participants, investigators, study coordinators, study-related personnel, and the sponsor were masked to treatment group allocation. Two intramuscular doses of vaccine were administered on day 0 and day 28. The primary outcome was SARS-CoV-2 wild-type neutralising antibody titres and seroconversion rates (defined as a post-vaccination titre that was at least four-fold higher than the baseline titre) at 4 weeks after the second dose (day 56), measured by use of the plaque-reduction neutralisation test (PRNT50) and the microneutralisation test (MNT50). The primary outcome was assessed in all participants who had received both doses of the vaccine. Cell-mediated responses were a secondary outcome and were assessed by T-helper-1 (Th1)/Th2 profiling at 2 weeks after the second dose (day 42). Safety was assessed in all participants who received at least one dose of the vaccine. In addition, we report immunogenicity results from a follow-up blood draw collected from phase 1 trial participants at 3 months after they received the second dose (day 104). This trial is registered at ClinicalTrials.gov, NCT04471519. FINDINGS Between Sept 5 and 12, 2020, 921 participants were screened, of whom 380 were enrolled and randomly assigned to the 3 μg with Algel-IMDG group (n=190) or 6 μg with Algel-IMDG group (n=190). Geometric mean titres (GMTs; PRNT50) at day 56 were significantly higher in the 6 μg with Algel-IMDG group (197·0 [95% CI 155·6-249·4]) than the 3 μg with Algel-IMDG group (100·9 [74·1-137·4]; p=0·0041). Seroconversion based on PRNT50 at day 56 was reported in 171 (92·9% [95% CI 88·2-96·2] of 184 participants in the 3 μg with Algel-IMDG group and 174 (98·3% [95·1-99·6]) of 177 participants in the 6 μg with Algel-IMDG group. GMTs (MNT50) at day 56 were 92·5 (95% CI 77·7-110·2) in the 3 μg with Algel-IMDG group and 160·1 (135·8-188·8) in the 6 μg with Algel-IMDG group. Seroconversion based on MNT50 at day 56 was reported in 162 (88·0% [95% CI 82·4-92·3]) of 184 participants in the 3 μg with Algel-IMDG group and 171 (96·6% [92·8-98·8]) of 177 participants in the 6 μg with Algel-IMDG group. The 3 μg with Algel-IMDG and 6 μg with Algel-IMDG formulations elicited T-cell responses that were biased to a Th1 phenotype at day 42. No significant difference in the proportion of participants who had a solicited local or systemic adverse reaction in the 3 μg with Algel-IMDG group (38 [20·0%; 95% CI 14·7-26·5] of 190) and the 6 μg with Algel-IMDG group (40 [21·1%; 15·5-27·5] of 190) was observed on days 0-7 and days 28-35; no serious adverse events were reported in the study. From the phase 1 trial, 3-month post-second-dose GMTs (MNT50) were 39·9 (95% CI 32·0-49·9) in the 3μg with Algel-IMDG group, 69·5 (53·7-89·9) in the 6 μg with Algel-IMDG group, 53·3 (40·1-71·0) in the 6 μg with Algel group, and 20·7 (14·5-29·5) in the Algel alone group. INTERPRETATION In the phase 1 trial, BBV152 induced high neutralising antibody responses that remained elevated in all participants at 3 months after the second vaccination. In the phase 2 trial, BBV152 showed better reactogenicity and safety outcomes, and enhanced humoral and cell-mediated immune responses compared with the phase 1 trial. The 6 μg with Algel-IMDG formulation has been selected for the phase 3 efficacy trial. FUNDING Bharat Biotech International. TRANSLATION For the Hindi translation of the abstract see Supplementary Materials section.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Savita Verma
- Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, India
| | | | | | | | | | | | | | - Sanjay Rai
- All India Institute of Medical Sciences, New Delhi, India
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
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Shete A, Mohandas S, Jain R, Yadav PD. A qualitative IgG ELISA for detection of SARS-CoV-2-specific antibodies in Syrian hamster serum samples. STAR Protoc 2021; 2:100573. [PMID: 33997801 PMCID: PMC8108381 DOI: 10.1016/j.xpro.2021.100573] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This protocol describes an indirect enzyme-linked immunosorbent assay for qualitative detection of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Syrian hamster serum samples. We describe the preparation of inactivated virus antigens and the negative control antigen and the use of antigen-coated microtiter plates to detect SARS-CoV-2-specific antibodies from SARS-CoV-2-infected hamsters, including the criteria for differentiating positive versus negative reaction. The limited batch-to-batch variability of this assay has been verified with two batches of independently prepared antigens. For complete details on the use and execution of this protocol, please refer to Mohandas et al. (2021). Inactivated SARS-CoV-2 whole-virion-based IgG ELISA Qualitative detection of anti-SARS-CoV-2 IgG antibody in infected hamster serum samples Criteria for determination of cutoff values for the assay
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Affiliation(s)
- Anita Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411021, India
| | - Sreelekshmy Mohandas
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411021, India
| | - Rajlaxmi Jain
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411021, India
| | - Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411021, India
- Corresponding author
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Hamer SA, Pauvolid-Corrêa A, Zecca IB, Davila E, Auckland LD, Roundy CM, Tang W, Torchetti MK, Killian ML, Jenkins-Moore M, Mozingo K, Akpalu Y, Ghai RR, Spengler JR, Barton Behravesh C, Fischer RSB, Hamer GL. SARS-CoV-2 Infections and Viral Isolations among Serially Tested Cats and Dogs in Households with Infected Owners in Texas, USA. Viruses 2021; 13:v13050938. [PMID: 34069453 PMCID: PMC8159091 DOI: 10.3390/v13050938] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 12/23/2022] Open
Abstract
Understanding the ecological and epidemiological roles of pets in the transmission of SARS-CoV-2 is critical for animal and human health, identifying household reservoirs, and predicting the potential enzootic maintenance of the virus. We conducted a longitudinal household transmission study of 76 dogs and cats living with at least one SARS-CoV-2-infected human in Texas and found that 17 pets from 25.6% of 39 households met the national case definition for SARS-CoV-2 infections in animals. This includes three out of seventeen (17.6%) cats and one out of fifty-nine (1.7%) dogs that were positive by RT-PCR and sequencing, with the virus successfully isolated from the respiratory swabs of one cat and one dog. Whole-genome sequences of SARS-CoV-2 obtained from all four PCR-positive animals were unique variants grouping with genomes circulating among people with COVID-19 in Texas. Re-sampling showed persistence of viral RNA for at least 25 d-post initial test. Additionally, seven out of sixteen (43.8%) cats and seven out of fifty-nine (11.9%) dogs harbored SARS-CoV-2 neutralizing antibodies upon initial sampling, with relatively stable or increasing titers over the 2–3 months of follow-up and no evidence of seroreversion. The majority (82.4%) of infected pets were asymptomatic. ‘Reverse zoonotic’ transmission of SARS-CoV-2 from infected people to animals may occur more frequently than recognized.
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Affiliation(s)
- Sarah A. Hamer
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; (A.P.-C.); (I.B.Z.); (E.D.); (L.D.A.)
- Correspondence: ; Tel.: +1-979-847-5693
| | - Alex Pauvolid-Corrêa
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; (A.P.-C.); (I.B.Z.); (E.D.); (L.D.A.)
- Laboratory of Respiratory Viruses and Measles, SARS-CoV-2 National Reference Laboratory and Regional Reference Laboratory in the Americas (PAHO/WHO), Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Italo B. Zecca
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; (A.P.-C.); (I.B.Z.); (E.D.); (L.D.A.)
| | - Edward Davila
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; (A.P.-C.); (I.B.Z.); (E.D.); (L.D.A.)
| | - Lisa D. Auckland
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; (A.P.-C.); (I.B.Z.); (E.D.); (L.D.A.)
| | - Christopher M. Roundy
- Department of Entomology, Texas A&M University and AgriLife Research, College Station, TX 77843, USA; (C.M.R.); (W.T.); (G.L.H.)
| | - Wendy Tang
- Department of Entomology, Texas A&M University and AgriLife Research, College Station, TX 77843, USA; (C.M.R.); (W.T.); (G.L.H.)
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA 50010, USA; (M.K.T.); (M.L.K.); (M.J.-M.); (K.M.)
| | - Mary Lea Killian
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA 50010, USA; (M.K.T.); (M.L.K.); (M.J.-M.); (K.M.)
| | - Melinda Jenkins-Moore
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA 50010, USA; (M.K.T.); (M.L.K.); (M.J.-M.); (K.M.)
| | - Katie Mozingo
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA 50010, USA; (M.K.T.); (M.L.K.); (M.J.-M.); (K.M.)
| | - Yao Akpalu
- Brazos County Health Department, Bryan, TX 77803, USA;
| | - Ria R. Ghai
- National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.R.G.); (J.R.S.); (C.B.B.)
| | - Jessica R. Spengler
- National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.R.G.); (J.R.S.); (C.B.B.)
| | - Casey Barton Behravesh
- National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.R.G.); (J.R.S.); (C.B.B.)
| | | | - Gabriel L. Hamer
- Department of Entomology, Texas A&M University and AgriLife Research, College Station, TX 77843, USA; (C.M.R.); (W.T.); (G.L.H.)
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A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Comput Biol Med 2021; 132:104315. [PMID: 33705994 PMCID: PMC7935700 DOI: 10.1016/j.compbiomed.2021.104315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease (COVID-19) rapidly expands to a global pandemic and its impact on public health varies from country to country. It is caused by a new virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is imperative for relapsing current antiviral therapeutics owing to randomized genetic drift in global SARS-CoV-2 isolates. A molecular mechanism behind the emerging genomic variants is not yet understood for the prioritization of selective antivirals. The present computational study was aimed to repurpose existing antivirals for Indian SARS-CoV-2 isolates by uncovering a hijack mechanism based on structural and functional characteristics of protein variants. Forty-one protein mutations were identified in 12 Indian SARS-CoV-2 isolates by analysis of genome variations across 460 genome sequences obtained from 30 geographic sites in India. Two unique mutations such as W6152R and N5928H found in exonuclease of Surat (GBRC275b) and Gandhinagar (GBRC239) isolates. We report for the first time the impact of folding rate on stabilizing/retaining a sequence-structure-function-virulence link of emerging protein variants leading to accommodate hijack ability from current antivirals. Binding affinity analysis revealed the effect of point mutations on virus infectivity and the drug-escaping efficiency of Indian isolates. Emodin and artinemol suggested herein as repurposable antivirals for the treatment of COVID-19 patients infected with Indian isolates. Our study concludes that a protein folding rate is a key structural and evolutionary determinant to enhance the receptor-binding specificity and ensure hijack ability from the prevalent antiviral therapeutics.
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Ella R, Vadrevu KM, Jogdand H, Prasad S, Reddy S, Sarangi V, Ganneru B, Sapkal G, Yadav P, Abraham P, Panda S, Gupta N, Reddy P, Verma S, Kumar Rai S, Singh C, Redkar SV, Gillurkar CS, Kushwaha JS, Mohapatra S, Rao V, Guleria R, Ella K, Bhargava B. Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBV152: a double-blind, randomised, phase 1 trial. THE LANCET. INFECTIOUS DISEASES 2021; 21:637-646. [PMID: 33485468 PMCID: PMC7825810 DOI: 10.1016/s1473-3099(20)30942-7] [Citation(s) in RCA: 246] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 11/28/2020] [Accepted: 12/04/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND To mitigate the effects of COVID-19, a vaccine is urgently needed. BBV152 is a whole-virion inactivated SARS-CoV-2 vaccine formulated with a toll-like receptor 7/8 agonist molecule adsorbed to alum (Algel-IMDG) or alum (Algel). METHODS We did a double-blind, multicentre, randomised, controlled phase 1 trial to assess the safety and immunogenicity of BBV152 at 11 hospitals across India. Healthy adults aged 18-55 years who were deemed healthy by the investigator were eligible. Individuals with positive SARS-CoV-2 nucleic acid and/or serology tests were excluded. Participants were randomly assigned to receive either one of three vaccine formulations (3 μg with Algel-IMDG, 6 μg with Algel-IMDG, or 6 μg with Algel) or an Algel only control vaccine group. Block randomisation was done with a web response platform. Participants and investigators were masked to treatment group allocation. Two intramuscular doses of vaccines were administered on day 0 (the day of randomisation) and day 14. Primary outcomes were solicited local and systemic reactogenicity events at 2 h and 7 days after vaccination and throughout the full study duration, including serious adverse events. Secondary outcome was seroconversion (at least four-fold increase from baseline) based on wild-type virus neutralisation. Cell-mediated responses were evaluated by intracellular staining and ELISpot. The trial is registered at ClinicalTrials.gov (NCT04471519). FINDINGS Between July 13 and 30, 2020, 827 participants were screened, of whom 375 were enrolled. Among the enrolled participants, 100 each were randomly assigned to the three vaccine groups, and 75 were randomly assigned to the control group (Algel only). After both doses, solicited local and systemic adverse reactions were reported by 17 (17%; 95% CI 10·5-26·1) participants in the 3 μg with Algel-IMDG group, 21 (21%; 13·8-30·5) in the 6 μg with Algel-IMDG group, 14 (14%; 8·1-22·7) in the 6 μg with Algel group, and ten (10%; 6·9-23·6) in the Algel-only group. The most common solicited adverse events were injection site pain (17 [5%] of 375 participants), headache (13 [3%]), fatigue (11 [3%]), fever (nine [2%]), and nausea or vomiting (seven [2%]). All solicited adverse events were mild (43 [69%] of 62) or moderate (19 [31%]) and were more frequent after the first dose. One serious adverse event of viral pneumonitis was reported in the 6 μg with Algel group, unrelated to the vaccine. Seroconversion rates (%) were 87·9, 91·9, and 82·8 in the 3 μg with Algel-IMDG, 6 μg with Algel-IMDG, and 6 μg with Algel groups, respectively. CD4+ and CD8+ T-cell responses were detected in a subset of 16 participants from both Algel-IMDG groups. INTERPRETATION BBV152 led to tolerable safety outcomes and enhanced immune responses. Both Algel-IMDG formulations were selected for phase 2 immunogenicity trials. Further efficacy trials are warranted. FUNDING Bharat Biotech International.
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Affiliation(s)
| | - Krishna Mohan Vadrevu
- Bharat Biotech, Hyderabad, India,Correspondence to: Dr Krishna Mohan Vadrevu, Bharat Biotech, Genome Valley, Hyderabad 500 078, India
| | | | | | | | | | | | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi, India
| | | | | | - Savita Verma
- Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, India
| | | | | | | | | | | | | | - Venkat Rao
- Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
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Ella R, Vadrevu KM, Jogdand H, Prasad S, Reddy S, Sarangi V, Ganneru B, Sapkal G, Yadav P, Abraham P, Panda S, Gupta N, Reddy P, Verma S, Kumar Rai S, Singh C, Redkar SV, Gillurkar CS, Kushwaha JS, Mohapatra S, Rao V, Guleria R, Ella K, Bhargava B. Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBV152: a double-blind, randomised, phase 1 trial. THE LANCET. INFECTIOUS DISEASES 2021; 21:637-646. [PMID: 33485468 DOI: 10.1101/2020.12.11.20210419] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 11/28/2020] [Accepted: 12/04/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND To mitigate the effects of COVID-19, a vaccine is urgently needed. BBV152 is a whole-virion inactivated SARS-CoV-2 vaccine formulated with a toll-like receptor 7/8 agonist molecule adsorbed to alum (Algel-IMDG) or alum (Algel). METHODS We did a double-blind, multicentre, randomised, controlled phase 1 trial to assess the safety and immunogenicity of BBV152 at 11 hospitals across India. Healthy adults aged 18-55 years who were deemed healthy by the investigator were eligible. Individuals with positive SARS-CoV-2 nucleic acid and/or serology tests were excluded. Participants were randomly assigned to receive either one of three vaccine formulations (3 μg with Algel-IMDG, 6 μg with Algel-IMDG, or 6 μg with Algel) or an Algel only control vaccine group. Block randomisation was done with a web response platform. Participants and investigators were masked to treatment group allocation. Two intramuscular doses of vaccines were administered on day 0 (the day of randomisation) and day 14. Primary outcomes were solicited local and systemic reactogenicity events at 2 h and 7 days after vaccination and throughout the full study duration, including serious adverse events. Secondary outcome was seroconversion (at least four-fold increase from baseline) based on wild-type virus neutralisation. Cell-mediated responses were evaluated by intracellular staining and ELISpot. The trial is registered at ClinicalTrials.gov (NCT04471519). FINDINGS Between July 13 and 30, 2020, 827 participants were screened, of whom 375 were enrolled. Among the enrolled participants, 100 each were randomly assigned to the three vaccine groups, and 75 were randomly assigned to the control group (Algel only). After both doses, solicited local and systemic adverse reactions were reported by 17 (17%; 95% CI 10·5-26·1) participants in the 3 μg with Algel-IMDG group, 21 (21%; 13·8-30·5) in the 6 μg with Algel-IMDG group, 14 (14%; 8·1-22·7) in the 6 μg with Algel group, and ten (10%; 6·9-23·6) in the Algel-only group. The most common solicited adverse events were injection site pain (17 [5%] of 375 participants), headache (13 [3%]), fatigue (11 [3%]), fever (nine [2%]), and nausea or vomiting (seven [2%]). All solicited adverse events were mild (43 [69%] of 62) or moderate (19 [31%]) and were more frequent after the first dose. One serious adverse event of viral pneumonitis was reported in the 6 μg with Algel group, unrelated to the vaccine. Seroconversion rates (%) were 87·9, 91·9, and 82·8 in the 3 μg with Algel-IMDG, 6 μg with Algel-IMDG, and 6 μg with Algel groups, respectively. CD4+ and CD8+ T-cell responses were detected in a subset of 16 participants from both Algel-IMDG groups. INTERPRETATION BBV152 led to tolerable safety outcomes and enhanced immune responses. Both Algel-IMDG formulations were selected for phase 2 immunogenicity trials. Further efficacy trials are warranted. FUNDING Bharat Biotech International.
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Affiliation(s)
| | | | | | | | | | | | | | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi, India
| | | | | | - Savita Verma
- Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, India
| | | | | | | | | | | | | | - Venkat Rao
- Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
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Prasad S, Meena VK, Yadav PD, Sarkale P, Baradkar S, Cherian S, Abraham P, Basu A. Electron microscopy imaging of SARS-CoV-2 at different temperatures. Indian J Med Res 2021; 153:692-695. [PMID: 34145089 PMCID: PMC8555590 DOI: 10.4103/ijmr.ijmr_4264_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sharda Prasad
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Virendra Kumar Meena
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Pragya D. Yadav
- Maximum Containment Facility, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Facility, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Shreekant Baradkar
- Maximum Containment Facility, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Sarah Cherian
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
| | - Atanu Basu
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411 001, Maharashtra, India
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Ganneru B, Jogdand H, Daram VK, Das D, Molugu NR, Prasad SD, Kannappa SV, Ella KM, Ravikrishnan R, Awasthi A, Jose J, Rao P, Kumar D, Ella R, Abraham P, Yadav PD, Sapkal GN, Shete-Aich A, Desphande G, Mohandas S, Basu A, Gupta N, Vadrevu KM. Th1 skewed immune response of whole virion inactivated SARS CoV 2 vaccine and its safety evaluation. iScience 2021; 24:102298. [PMID: 33723528 PMCID: PMC7944858 DOI: 10.1016/j.isci.2021.102298] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/27/2021] [Accepted: 03/07/2021] [Indexed: 02/07/2023] Open
Abstract
We report the development and evaluation of safety and immunogenicity of a whole virion inactivated (WVI) SARS-CoV-2 vaccine (BBV152), adjuvanted with aluminum hydroxide gel (Algel), or TLR7/8 agonist chemisorbed Algel. We used a well-characterized SARS-CoV-2 strain and an established Vero cell platform to produce large-scale GMP-grade highly purified inactivated antigen. Product development and manufacturing process were carried out in a BSL-3 facility. Immunogenicity and safety were determined at two antigen concentrations (3μg and 6μg), with two different adjuvants, in mice, rats, and rabbits. Our results show that BBV152 vaccine formulations generated significantly high antigen-binding and neutralizing antibody titers (NAb), at both concentrations, in all three species with excellent safety profiles. The inactivated vaccine formulation contains TLR7/8 agonist adjuvant-induced Th1-biased antibody responses with elevated IgG2a/IgG1 ratio and increased levels of SARS-CoV-2-specific IFN-γ+ CD4+ T lymphocyte response. Our results support further development for phase I/II clinical trials in humans.
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Affiliation(s)
- Brunda Ganneru
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | - Harsh Jogdand
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | - Vijaya Kumar Daram
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | - Dipankar Das
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | | | - Sai D. Prasad
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | | | - Krishna M. Ella
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | | | - Amit Awasthi
- Translational Health Sciences and Technology Institute (THSTI), NCR Biotech Science Cluster, PO box #04, Faridabad, Haryana 121001, India
| | - Jomy Jose
- RCC Laboratories India Private Ltd, Hyderabad, Telangana 500 078, India
| | - Panduranga Rao
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | - Deepak Kumar
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | - Raches Ella
- Bharat Biotech International Ltd, Hyderabad (BBIL), Telangana 500 078, India
| | - Priya Abraham
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Pragya D. Yadav
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Gajanan N. Sapkal
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Anita Shete-Aich
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Gururaj Desphande
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Sreelekshmy Mohandas
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Atanu Basu
- National Institute of Virology-Indian Council of Medical Research (NIV-ICMR), Pune, Maharashtra 411021, India
| | - Nivedita Gupta
- Indian Council of Medical Research (ICMR), India, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi 110029, India
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Ghosh N, Sharma N, Saha I. Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes. INFECTION GENETICS AND EVOLUTION 2021; 92:104823. [PMID: 33819681 PMCID: PMC8017916 DOI: 10.1016/j.meegid.2021.104823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/23/2022]
Abstract
The surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in this work, we have performed genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries around the globe in order to identify the potential conserved regions for the development of peptide based synthetic vaccine viz. epitopes with high immunogenic and antigenic scores. In this regard, multiple sequence alignment technique viz. Clustal Omega is used to align the 10,664 SARS-CoV-2 virus genomes. Thereafter, entropy is computed for each genomic coordinate of the aligned genomes. The entropy values are then used to find the conserved regions. These conserved regions are refined based on the criteria that their lengths should be greater than or equal to 60 nt and their corresponding protein sequences are without any stop codons. Furthermore, Nucleotide BLAST is used to verify the specificity of the conserved regions. As a result, we have obtained 17 conserved regions that belong to NSP3, NSP4, NSP6, NSP8, RdRp, Helicase, endoRNAse, 2’-O-RMT, Spike glycoprotein, ORF3a protein, Membrane glycoprotein and Nucleocapsid protein. Finally, these conserved regions are used to identify the T-cell and B-cell epitopes with their corresponding immunogenic and antigenic scores. Based on these scores, the most immunogenic and antigenic epitopes are then selected for each of these 17 conserved regions. Hence, we have obtained 30 MHC-I and 24 MHC-II restricted T-cell epitopes with 14 and 13 unique HLA alleles and 21 B-cell epitopes for the 17 conserved regions. Moreover, for validating the relevance of these epitopes, the binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. Also, the physico-chemical properties of the epitopes are reported along with Ramchandran plots and Z-Scores and the population coverage is shown as well. Overall, the analysis shows that the identified epitopes can be considered as potential candidates for vaccine design.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
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Mahalingam S, Peter J, Xu Z, Bordoloi D, Ho M, Kalyanaraman VS, Srinivasan A, Muthumani K. Landscape of humoral immune responses against SARS-CoV-2 in patients with COVID-19 disease and the value of antibody testing. Heliyon 2021; 7:e06836. [PMID: 33898857 PMCID: PMC8052472 DOI: 10.1016/j.heliyon.2021.e06836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
A new pandemic is ongoing in several parts of the world. The agent responsible is the newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The symptoms associated with this virus are known as the coronavirus disease-2019 (COVID-19). In this review, we summarize the published data on virus specific antibodies in hospitalized patients with COVID-19 disease, patients recovered from the disease and the individuals who are asymptomatic with SARS-CoV-2 infections. The review highlights the following: i) an adjunct role of antibody tests in the diagnosis of COVID-19 in combination with RT-PCR; ii) status of antibodies from COVID-19 convalescent patients to select donors for plasma therapy; iii) the potential confounding effects of other coronaviruses, measles, mumps and rubella in antibody testing due to homology of certain viral genes; and iv) the role of antibody testing for conducting surveillance in populations, incidence estimation, contact tracing and epidemiologic studies.
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Affiliation(s)
- Sundarasamy Mahalingam
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - John Peter
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Ziyang Xu
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Devivasha Bordoloi
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Michelle Ho
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | | | | | - Kar Muthumani
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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Ella R, Reddy S, Jogdand H, Sarangi V, Ganneru B, Prasad S, Das D, Raju D, Praturi U, Sapkal G, Yadav P, Reddy P, Verma S, Singh C, Redkar SV, Gillurkar CS, Kushwaha JS, Mohapatra S, Bhate A, Rai S, Panda S, Abraham P, Gupta N, Ella K, Bhargava B, Vadrevu KM. Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBV152: interim results from a double-blind, randomised, multicentre, phase 2 trial, and 3-month follow-up of a double-blind, randomised phase 1 trial. THE LANCET. INFECTIOUS DISEASES 2021; 21:950-961. [PMID: 33705727 PMCID: PMC8221739 DOI: 10.1016/s1473-3099(21)00070-0] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/23/2022]
Abstract
Background BBV152 is a whole-virion inactivated SARS-CoV-2 vaccine (3 μg or 6 μg) formulated with a toll-like receptor 7/8 agonist molecule (IMDG) adsorbed to alum (Algel). We previously reported findings from a double-blind, multicentre, randomised, controlled phase 1 trial on the safety and immunogenicity of three different formulations of BBV152 (3 μg with Algel-IMDG, 6 μg with Algel-IMDG, or 6 μg with Algel) and one Algel-only control (no antigen), with the first dose administered on day 0 and the second dose on day 14. The 3 μg and 6 μg with Algel-IMDG formulations were selected for this phase 2 study. Herein, we report interim findings of the phase 2 trial on the immunogenicity and safety of BBV152, with the first dose administered on day 0 and the second dose on day 28. Methods We did a double-blind, randomised, multicentre, phase 2 clinical trial to evaluate the immunogenicity and safety of BBV152 in healthy adults and adolescents (aged 12–65 years) at nine hospitals in India. Participants with positive SARS-CoV-2 nucleic acid and serology tests were excluded. Participants were randomly assigned (1:1) to receive either 3 μg with Algel-IMDG or 6 μg with Algel-IMDG. Block randomisation was done by use of an interactive web response system. Participants, investigators, study coordinators, study-related personnel, and the sponsor were masked to treatment group allocation. Two intramuscular doses of vaccine were administered on day 0 and day 28. The primary outcome was SARS-CoV-2 wild-type neutralising antibody titres and seroconversion rates (defined as a post-vaccination titre that was at least four-fold higher than the baseline titre) at 4 weeks after the second dose (day 56), measured by use of the plaque-reduction neutralisation test (PRNT50) and the microneutralisation test (MNT50). The primary outcome was assessed in all participants who had received both doses of the vaccine. Cell-mediated responses were a secondary outcome and were assessed by T-helper-1 (Th1)/Th2 profiling at 2 weeks after the second dose (day 42). Safety was assessed in all participants who received at least one dose of the vaccine. In addition, we report immunogenicity results from a follow-up blood draw collected from phase 1 trial participants at 3 months after they received the second dose (day 104). This trial is registered at ClinicalTrials.gov, NCT04471519. Findings Between Sept 5 and 12, 2020, 921 participants were screened, of whom 380 were enrolled and randomly assigned to the 3 μg with Algel-IMDG group (n=190) or 6 μg with Algel-IMDG group (n=190). Geometric mean titres (GMTs; PRNT50) at day 56 were significantly higher in the 6 μg with Algel-IMDG group (197·0 [95% CI 155·6–249·4]) than the 3 μg with Algel-IMDG group (100·9 [74·1–137·4]; p=0·0041). Seroconversion based on PRNT50 at day 56 was reported in 171 (92·9% [95% CI 88·2–96·2] of 184 participants in the 3 μg with Algel-IMDG group and 174 (98·3% [95·1–99·6]) of 177 participants in the 6 μg with Algel-IMDG group. GMTs (MNT50) at day 56 were 92·5 (95% CI 77·7–110·2) in the 3 μg with Algel-IMDG group and 160·1 (135·8–188·8) in the 6 μg with Algel-IMDG group. Seroconversion based on MNT50 at day 56 was reported in 162 (88·0% [95% CI 82·4–92·3]) of 184 participants in the 3 μg with Algel-IMDG group and 171 (96·6% [92·8–98·8]) of 177 participants in the 6 μg with Algel-IMDG group. The 3 μg with Algel-IMDG and 6 μg with Algel-IMDG formulations elicited T-cell responses that were biased to a Th1 phenotype at day 42. No significant difference in the proportion of participants who had a solicited local or systemic adverse reaction in the 3 μg with Algel-IMDG group (38 [20·0%; 95% CI 14·7–26·5] of 190) and the 6 μg with Algel-IMDG group (40 [21·1%; 15·5–27·5] of 190) was observed on days 0–7 and days 28–35; no serious adverse events were reported in the study. From the phase 1 trial, 3-month post-second-dose GMTs (MNT50) were 39·9 (95% CI 32·0–49·9) in the 3μg with Algel-IMDG group, 69·5 (53·7–89·9) in the 6 μg with Algel-IMDG group, 53·3 (40·1–71·0) in the 6 μg with Algel group, and 20·7 (14·5–29·5) in the Algel alone group. Interpretation In the phase 1 trial, BBV152 induced high neutralising antibody responses that remained elevated in all participants at 3 months after the second vaccination. In the phase 2 trial, BBV152 showed better reactogenicity and safety outcomes, and enhanced humoral and cell-mediated immune responses compared with the phase 1 trial. The 6 μg with Algel-IMDG formulation has been selected for the phase 3 efficacy trial. Funding Bharat Biotech International. Translation For the Hindi translation of the abstract see Supplementary Materials section.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Savita Verma
- Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, India
| | | | | | | | | | | | | | - Sanjay Rai
- All India Institute of Medical Sciences, New Delhi, India
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, India
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Yadav PD, Ella R, Kumar S, Patil DR, Mohandas S, Shete AM, Vadrevu KM, Bhati G, Sapkal G, Kaushal H, Patil S, Jain R, Deshpande G, Gupta N, Agarwal K, Gokhale M, Mathapati B, Metkari S, Mote C, Nyayanit D, Patil DY, Sai Prasad BS, Suryawanshi A, Kadam M, Kumar A, Daigude S, Gopale S, Majumdar T, Mali D, Sarkale P, Baradkar S, Gawande P, Joshi Y, Fulari S, Dighe H, Sharma S, Gunjikar R, Kumar A, Kalele K, Srinivas VK, Gangakhedkar RR, Ella KM, Abraham P, Panda S, Bhargava B. Immunogenicity and protective efficacy of inactivated SARS-CoV-2 vaccine candidate, BBV152 in rhesus macaques. Nat Commun 2021; 12:1386. [PMID: 33654090 PMCID: PMC7925524 DOI: 10.1038/s41467-021-21639-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/04/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic is a global health crisis that poses a great challenge to the public health system of affected countries. Safe and effective vaccines are needed to overcome this crisis. Here, we develop and assess the protective efficacy and immunogenicity of an inactivated SARS-CoV-2 vaccine in rhesus macaques. Twenty macaques were divided into four groups of five animals each. One group was administered a placebo, while three groups were immunized with three different vaccine candidates of BBV152 at 0 and 14 days. All the macaques were challenged with SARS-CoV-2 fourteen days after the second dose. The protective response was observed with increasing SARS-CoV-2 specific IgG and neutralizing antibody titers from 3rd-week post-immunization. Viral clearance was observed from bronchoalveolar lavage fluid, nasal swab, throat swab and lung tissues at 7 days post-infection in the vaccinated groups. No evidence of pneumonia was observed by histopathological examination in vaccinated groups, unlike the placebo group which exhibited interstitial pneumonia and localization of viral antigen in the alveolar epithelium and macrophages by immunohistochemistry. This vaccine candidate BBV152 has completed Phase I/II (NCT04471519) clinical trials in India and is presently in phase III, data of this study substantiates the immunogenicity and protective efficacy of the vaccine candidates.
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Affiliation(s)
- Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Raches Ella
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, Telangana, India
| | - Sanjay Kumar
- Department of Neurosurgery, Command Hospital (Southern Command), Armed Forces Medical College (AFMC), Pune, 411040, Maharashtra, India
| | - Dilip R Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Sreelekshmy Mohandas
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Anita M Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Krishna M Vadrevu
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, Telangana, India
| | - Gaurav Bhati
- Army Institute of Cardio-Thoracic Sciences, Pune, 411040, Maharashtra, India
| | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Himanshu Kaushal
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Rajlaxmi Jain
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Gururaj Deshpande
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, 110029, India
| | - Kshitij Agarwal
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, 110029, India
| | - Mangesh Gokhale
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Basavaraj Mathapati
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Siddhanath Metkari
- ICMR-National Institute for Research in Reproductive Health, Mumbai, 400012, Maharashtra, India
| | - Chandrashekhar Mote
- Department of Veterinary Pathology, Krantisinh Nana Patil College of Veterinary Science, Shirwal, 412801, Maharashtra, India
| | - Dimpal Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Deepak Y Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - B S Sai Prasad
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, Telangana, India
| | - Annasaheb Suryawanshi
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Manoj Kadam
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Abhimanyu Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Sachin Daigude
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Sanjay Gopale
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Deepak Mali
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Prasad Sarkale
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Shreekant Baradkar
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Pranita Gawande
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Sidharam Fulari
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Hitesh Dighe
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Sharda Sharma
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Rashmi Gunjikar
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Kaumudi Kalele
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Vellimedu K Srinivas
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, Telangana, India
| | - Raman R Gangakhedkar
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, 110029, India
| | - Krishna M Ella
- Bharat Biotech International Limited, Genome Valley, Hyderabad, 500 078, Telangana, India
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, 411021, Maharashtra, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, 110029, India
| | - Balram Bhargava
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, 110029, India.
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Yadav PD, Nyayanit DA, Sahay RR, Sarkale P, Pethani J, Patil S, Baradkar S, Potdar V, Patil DY. Isolation and characterization of the new SARS-CoV-2 variant in travellers from the United Kingdom to India: VUI-202012/01 of the B.1.1.7 lineage. J Travel Med 2021; 28:6121695. [PMID: 33506252 PMCID: PMC7928800 DOI: 10.1093/jtm/taab009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 11/18/2022]
Abstract
We have isolated the new severe acute respiratory syndrome coronavirus-2 variant of concern 202 012/01 from the positive coronavirus disease 2019 cases that travelled from the UK to India in the month of December 2020. This emphasizes the need for the strengthened surveillance system to limit the local transmission of this new variant.
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Affiliation(s)
- Pragya D Yadav
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
| | - Dimpal A Nyayanit
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
| | - Rima R Sahay
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
| | - Prasad Sarkale
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
| | - Jayshri Pethani
- Department of Microbiology, Smt. Nathiba Hargovandas Lakhmichand, Municipal Medical College (NHLMMC), Ahmedabad, Gujarat, 380006, India
| | - Savita Patil
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
| | - Shreekant Baradkar
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
| | - Varsha Potdar
- Influenza Department, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 001, India
| | - Deepak Y Patil
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra 411 021, India
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Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates. GENE REPORTS 2021; 25:101044. [PMID: 33623833 PMCID: PMC7893251 DOI: 10.1016/j.genrep.2021.101044] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/25/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.
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Muttineni R, Kammili N, Bingi TC, Rao M. R, Putty K, Dholaniya PS, Puli RK, Pakalapati S, S. S, K. S, Doodipala MR, Upadhyay AA, Bosinger SE, Amara RR, Kondapi AK. Clinical and whole genome characterization of SARS-CoV-2 in India. PLoS One 2021; 16:e0246173. [PMID: 33529260 PMCID: PMC7853523 DOI: 10.1371/journal.pone.0246173] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.
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Affiliation(s)
| | - Nagamani Kammili
- Department of Microbiology, Gandhi Medical College and Hospital, Secunderabad, India
| | - Thrilok Chander Bingi
- Department of General Medicine, Gandhi Medical College and Hospital, Secunderabad, India
| | - Raja Rao M.
- Department of General Medicine, Gandhi Medical College and Hospital, Secunderabad, India
| | - Kalyani Putty
- Department of Veterinary Biotechnology, College of Veterinary Science, Rajendranagar, PVNR Telangana Veterinary University, Hyderabad, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ravi Kumar Puli
- Telangana State Council for Science and Technology, Government of Telangana, Hyderabad, India
| | - Sunitha Pakalapati
- Department of Microbiology, Gandhi Medical College and Hospital, Secunderabad, India
| | - Saritha S.
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Shekar K.
- Virus Research Laboratory, Department of Zoology, Osmania University, Hyderabad, India
| | | | - Amit A. Upadhyay
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Steven E. Bosinger
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Rama R. Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Anand K. Kondapi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Pattabiraman C, Habib F, P. K. H, Rasheed R, Prasad P, Reddy V, Dinesh P, Damodar T, Hosallimath K, George AK, Kiran Reddy NV, John B, Pattanaik A, Kumar N, Mani RS, Venkataswamy MM, Shahul Hameed SK, Kumar B. G. P, Desai A, Vasanthapuram R. Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka. PLoS One 2020; 15:e0243412. [PMID: 33332472 PMCID: PMC7746284 DOI: 10.1371/journal.pone.0243412] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/21/2020] [Indexed: 12/17/2022] Open
Abstract
Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 91 genomes of SARS-CoV-2 which clustered into seven lineages (Pangolin lineages-A, B, B.1, B.1.80, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 17 contact clusters and 24 cases with no known contacts. We found 14 of the 17 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (12/17) were contained within a single district, reflecting local spread. In most of the 17 clusters, the index case (12/17) and spreaders (11/17) were symptomatic. Of the 91 sequences, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contact, indicating ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka suggests multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response.
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Affiliation(s)
- Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Harsha P. K.
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Risha Rasheed
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Vijayalakshmi Reddy
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Prameela Dinesh
- Directorate of Health and Family Welfare Services, Government of Karnataka, Bengaluru, India
| | - Tina Damodar
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Kiran Hosallimath
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anson K. George
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Nakka Vijay Kiran Reddy
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Banerjee John
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Amrita Pattanaik
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Narendra Kumar
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Reeta S. Mani
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Shafeeq K. Shahul Hameed
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Prakash Kumar B. G.
- Directorate of Health and Family Welfare Services, Government of Karnataka, Bengaluru, India
| | - Anita Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
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Ghosh N, Sharma N, Saha I, Saha S. Genome-wide analysis of Indian SARS-CoV-2 genomes to identify T-cell and B-cell epitopes from conserved regions based on immunogenicity and antigenicity. Int Immunopharmacol 2020; 91:107276. [PMID: 33385714 PMCID: PMC7831793 DOI: 10.1016/j.intimp.2020.107276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/21/2020] [Accepted: 12/02/2020] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has a high transmission rate and shows frequent mutations, thus making vaccine development an arduous task. However, researchers around the globe are working hard to find a solution e.g. synthetic vaccine. Here, we have performed genome-wide analysis of 566 Indian SARS-CoV-2 genomes to extract the potential conserved regions for identifying peptide based synthetic vaccines, viz. epitopes with high immunogenicity and antigenicity. In this regard, different multiple sequence alignment techniques are used to align the SARS-CoV-2 genomes separately. Subsequently, consensus conserved regions are identified after finding the conserved regions from each aligned result of alignment techniques. Further, the consensus conserved regions are refined considering that their lengths are greater than or equal to 60nt and their corresponding proteins are devoid of any stop codons. Subsequently, their specificity as query coverage are verified using Nucleotide BLAST. Finally, with these consensus conserved regions, T-cell and B-cell epitopes are identified based on their immunogenic and antigenic scores which are then used to rank the conserved regions. As a result, we have ranked 23 consensus conserved regions that are associated with different proteins. This ranking also resulted in 34 MHC-I and 37 MHC-II restricted T-cell epitopes with 16 and 19 unique HLA alleles and 29 B-cell epitopes. After ranking, the consensus conserved region from NSP3 gene is obtained that is highly immunogenic and antigenic. In order to judge the relevance of the identified epitopes, the physico-chemical properties and binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Orissa, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
| | - Sudipto Saha
- Division of Bioinformatics Bose Institute, Kolkata, West Bengal, India
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44
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Ulahannan JP, Narayanan N, Thalhath N, Prabhakaran P, Chaliyeduth S, Suresh SP, Mohammed M, Rajeevan E, Joseph S, Balakrishnan A, Uthaman J, Karingamadathil M, Thomas ST, Sureshkumar U, Balan S, Vellichirammal NN. A citizen science initiative for open data and visualization of COVID-19 outbreak in Kerala, India. J Am Med Inform Assoc 2020; 27:1913-1920. [PMID: 32761211 PMCID: PMC7454688 DOI: 10.1093/jamia/ocaa203] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/05/2020] [Indexed: 01/10/2023] Open
Abstract
Objective India reported its first coronavirus disease 2019 (COVID-19) case in the state of Kerala and an outbreak initiated subsequently. The Department of Health Services, Government of Kerala, initially released daily updates through daily textual bulletins for public awareness to control the spread of the disease. However, these unstructured data limit upstream applications, such as visualization, and analysis, thus demanding refinement to generate open and reusable datasets. Materials and Methods Through a citizen science initiative, we leveraged publicly available and crowd-verified data on COVID-19 outbreak in Kerala from the government bulletins and media outlets to generate reusable datasets. This was further visualized as a dashboard through a front-end Web application and a JSON (JavaScript Object Notation) repository, which serves as an application programming interface for the front end. Results From the sourced data, we provided real-time analysis, and daily updates of COVID-19 cases in Kerala, through a user-friendly bilingual dashboard (https://covid19kerala.info/) for nonspecialists. To ensure longevity and reusability, the dataset was deposited in an open-access public repository for future analysis. Finally, we provide outbreak trends and demographic characteristics of the individuals affected with COVID-19 in Kerala during the first 138 days of the outbreak. Discussion We anticipate that our dataset can form the basis for future studies, supplemented with clinical and epidemiological data from the individuals affected with COVID-19 in Kerala. Conclusions We reported a citizen science initiative on the COVID-19 outbreak in Kerala to collect and deposit data in a structured format, which was utilized for visualizing the outbreak trend and describing demographic characteristics of affected individuals.
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Affiliation(s)
| | | | - Nishad Thalhath
- School of Library, Information and Media Studies, University of Tsukuba, Tsukuba, Japan
| | - Prem Prabhakaran
- Department of Advanced Materials and Chemical Engineering, Hannam University, Daejeon, South Korea
| | - Sreekanth Chaliyeduth
- Centre for Cognitive and Brain Sciences, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sooraj P Suresh
- Department of Humanities and Social Sciences, National Institute of Technology Tiruchirappalli, Tiruchirappalli, India
| | - Musfir Mohammed
- Embedded Analytics, ML and Data Sciences, Experion Technologies, Thiruvananthapuram, India
| | - E Rajeevan
- Department of Philosophy, Government Brennen College, Kannur University, Kannur, India
| | - Sindhu Joseph
- Department of Travel and Tourism Management, Govinda Pai Memorial Government College, Kannur University, Kannur, India
| | | | - Jeevan Uthaman
- Department of Marine Geophysics, Cochin University of Science and Technology, Kochi, India
| | | | - Sunil Thonikkuzhiyil Thomas
- Department of Electronics, College of Engineering Attingal, APJ Abdul Kalam Technical University, Thiruvananthapuram, India
| | - Unnikrishnan Sureshkumar
- Astronomical Observatory of the Jagiellonian University, Faculty of Physics, Astronomy and Applied Science, Jagiellonian University, Kraków, Poland
| | - Shabeesh Balan
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Japan
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45
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Hamer SA, Pauvolid-Corrêa A, Zecca IB, Davila E, Auckland LD, Roundy CM, Tang W, Torchetti M, Killian ML, Jenkins-Moore M, Mozingo K, Akpalu Y, Ghai RR, Spengler JR, Behravesh CB, Fischer RSB, Hamer GL. Natural SARS-CoV-2 infections, including virus isolation, among serially tested cats and dogs in households with confirmed human COVID-19 cases in Texas, USA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.08.416339. [PMID: 33330861 PMCID: PMC7743065 DOI: 10.1101/2020.12.08.416339] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The natural infections and epidemiological roles of household pets in SARS-CoV-2 transmission are not understood. We conducted a longitudinal study of dogs and cats living with at least one SARS-CoV-2 infected human in Texas and found 47.1% of 17 cats and 15.3% of 59 dogs from 25.6% of 39 households were positive for SARS-CoV-2 via RT-PCR and genome sequencing or neutralizing antibodies. Virus was isolated from one cat. The majority (82.4%) of infected pets were asymptomatic. Re-sampling of one infected cat showed persistence of viral RNA at least 32 d-post human diagnosis (25 d-post initial test). Across 15 antibody-positive animals, titers increased (33.3%), decreased (33.3%) or were stable (33.3%) over time. A One Health approach is informative for prevention and control of SARS-CoV-2 transmission.
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Affiliation(s)
- Sarah A. Hamer
- Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA
- Laboratory of Respiratory Viruses and Measles, SARS-CoV-2 National Reference Laboratory and Regional Reference Laboratory in Americas (PAHO/WHO), Fiocruz, Rio de Janeiro, Brazil
| | - Italo B. Zecca
- Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA
| | - Edward Davila
- Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA
| | - Lisa D. Auckland
- Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA
| | | | - Wendy Tang
- Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA
| | - Mia Torchetti
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA
| | | | - Katie Mozingo
- National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA
| | - Yao Akpalu
- Brazos County Health Department, Bryan, Texas, USA
| | - Ria R. Ghai
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | - Gabriel L. Hamer
- Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA
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46
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Malenovská H. Coronavirus Persistence on a Plastic Carrier Under Refrigeration Conditions and Its Reduction Using Wet Wiping Technique, with Respect to Food Safety. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:361-366. [PMID: 33057921 PMCID: PMC7557311 DOI: 10.1007/s12560-020-09447-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/07/2020] [Indexed: 05/17/2023]
Abstract
The global SARS-CoV-2 pandemic dictates that anti-contagion strategies should become matters of essential routine in everyday life. Fomite transference is one of the routes of transmission that has been considered for this virus. However, the risks associated with contaminated surfaces of food packaging kept in refrigerators have not yet been adequately assessed. In this study, a surrogate virus, Alphacoronavirus 1, was used to investigate the persistence of coronavirus dried on a plastic carrier at 4 °C. Techniques of wet wiping, with or without disinfectant saturation, were employed to evaluate their effectiveness in the elimination of the virus. If not wiped, the loss of infectivity of the virus on plastic surfaces was, on average, 0.93 log10 (i.e. 83%) per day of storage at 4 °C. Wiping with water-saturated material reduced the initial virus titre on the plastic carrier by 2.4 log10 (99.6%); the same results were achieved through wiping with bactericidal wipes containing ethanol. Wipes saturated with a combination of disinfectant agents (didecyl-dimethyl-ammonium chloride, hydrogen peroxide) decreased the virus titre still more efficiently, by 3.8 log10 (99.98%) and also significantly prevented further transfer of the virus to a secondary surface through wiping. Thus SARS-CoV-2 transmission potential via contaminated plastic packaging and food may be efficiently eliminated by wet-wiping, especially when wipes saturated with specific disinfectants are used.
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Affiliation(s)
- Hana Malenovská
- Collection of Animal Pathogenic Microorganisms, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.
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47
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Agarwal A, Mukherjee A, Kumar G, Chatterjee P, Bhatnagar T, Malhotra P. Convalescent plasma in the management of moderate covid-19 in adults in India: open label phase II multicentre randomised controlled trial (PLACID Trial). BMJ 2020; 371:m3939. [PMID: 33093056 PMCID: PMC7578662 DOI: 10.1136/bmj.m3939] [Citation(s) in RCA: 443] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To investigate the effectiveness of using convalescent plasma to treat moderate coronavirus disease 2019 (covid-19) in adults in India. DESIGN Open label, parallel arm, phase II, multicentre, randomised controlled trial. SETTING 39 public and private hospitals across India. PARTICIPANTS 464 adults (≥18 years) admitted to hospital (screened 22 April to 14 July 2020) with confirmed moderate covid-19 (partial pressure of oxygen in arterial blood/fraction of inspired oxygen (PaO2/FiO2) ratio between 200 mm Hg and 300 mm Hg or a respiratory rate of more than 24/min with oxygen saturation 93% or less on room air): 235 were assigned to convalescent plasma with best standard of care (intervention arm) and 229 to best standard of care only (control arm). INTERVENTIONS Participants in the intervention arm received two doses of 200 mL convalescent plasma, transfused 24 hours apart. The presence and levels of neutralising antibodies were not measured a priori; stored samples were assayed at the end of the study. MAIN OUTCOME MEASURE Composite of progression to severe disease (PaO2/FiO2 <100 mm Hg) or all cause mortality at 28 days post-enrolment. RESULTS Progression to severe disease or all cause mortality at 28 days after enrolment occurred in 44 (19%) participants in the intervention arm and 41 (18%) in the control arm (risk difference 0.008 (95% confidence interval -0.062 to 0.078); risk ratio 1.04, 95% confidence interval 0.71 to 1.54). CONCLUSION Convalescent plasma was not associated with a reduction in progression to severe covid-19 or all cause mortality. This trial has high generalisability and approximates convalescent plasma use in real life settings with limited laboratory capacity. A priori measurement of neutralising antibody titres in donors and participants might further clarify the role of convalescent plasma in the management of covid-19. TRIAL REGISTRATION Clinical Trial Registry of India CTRI/2020/04/024775.
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Affiliation(s)
- Anup Agarwal
- Clinical Trial and Health Systems Research Unit, Indian Council of Medical Research, V Ramalingaswamy Bhawan, PO Box 4911, Ansari Nagar, New Delhi, 110029, India
| | - Aparna Mukherjee
- Clinical Trial and Health Systems Research Unit, Indian Council of Medical Research, V Ramalingaswamy Bhawan, PO Box 4911, Ansari Nagar, New Delhi, 110029, India
| | - Gunjan Kumar
- Clinical Trial and Health Systems Research Unit, Indian Council of Medical Research, V Ramalingaswamy Bhawan, PO Box 4911, Ansari Nagar, New Delhi, 110029, India
| | - Pranab Chatterjee
- Clinical Trial and Health Systems Research Unit, Indian Council of Medical Research, V Ramalingaswamy Bhawan, PO Box 4911, Ansari Nagar, New Delhi, 110029, India
| | - Tarun Bhatnagar
- ICMR School of Public Health, Indian Council of Medical Research - National Institute of Epidemiology, Chennai, Tamil, India
| | - Pankaj Malhotra
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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48
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Nyayanit DA, Yadav PD, Kharde R, Shete-Aich A. Quasispecies analysis of the SARS-CoV-2 from representative clinical samples: A preliminary analysis. Indian J Med Res 2020; 152:105-107. [PMID: 32773417 PMCID: PMC7853256 DOI: 10.4103/ijmr.ijmr_2251_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dimpal A. Nyayanit
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pashan, Pune 411 021, Maharashtra, India
| | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pashan, Pune 411 021, Maharashtra, India
| | - Rutuja Kharde
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pashan, Pune 411 021, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pashan, Pune 411 021, Maharashtra, India
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49
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Deshpande GR, Sapkal GN, Tilekar BN, Yadav PD, Gurav Y, Gaikwad S, Kaushal H, Deshpande KS, Kaduskar O, Sarkale P, Baradkar S, Suryawanshi A, Lakra R, Sugunan AP, Balakrishnan A, Abraham P, Salve P. Neutralizing antibody responses to SARS-CoV-2 in COVID-19 patients. Indian J Med Res 2020; 152:82-87. [PMID: 32859866 PMCID: PMC7853248 DOI: 10.4103/ijmr.ijmr_2382_20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background & objectives: The global pandemic caused by SARS-CoV-2 virus has challenged public health system worldwide due to the unavailability of approved preventive and therapeutic options. Identification of neutralizing antibodies (NAb) and understanding their role is important. However, the data on kinetics of NAb response among COVID-19 patients are unclear. To understand the NAb response in COVID-19 patients, we compared the findings of microneutralization test (MNT) and plaque reduction neutralization test (PRNT) for the SARS-CoV-2. Further, the kinetics of NAb response among COVID-19 patients was assessed. Methods: A total of 343 blood samples (89 positive, 58 negative for SARS-CoV-2 and 17 cross-reactive and 179 serum from healthy individuals) were collected and tested by MNT and PRNT. SARS-CoV-2 virus was prepared by propagating the virus in Vero CCL-81 cells. The intra-class correlation was calculated to assess the correlation between MNT and PRNT. The neutralizing endpoint as the reduction in the number of plaque count by 90 per cent (PRNT90) was also calculated. Results: The analysis of MNT and PRNT quantitative results indicated that the intra-class correlation was 0.520. Of the 89 confirmed COVID-19 patients, 64 (71.9%) showed NAb response. Interpretation & conclusions: The results of MNT and PRNT were specific with no cross-reactivity. In the early stages of infection, the NAb response was observed with variable antibody kinetics. The neutralization assays can be used for titration of NAb in recovered/vaccinated or infected COVID-19 patients.
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Affiliation(s)
- Gururaj Rao Deshpande
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Gajanan N Sapkal
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Bipin N Tilekar
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Pragya D Yadav
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yogesh Gurav
- Epidemiology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Shivshankar Gaikwad
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Himanshu Kaushal
- Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ketki S Deshpande
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Ojas Kaduskar
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Srikant Baradkar
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Annasaheb Suryawanshi
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajen Lakra
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A P Sugunan
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | | | - Priya Abraham
- Diagnostic Virology Group, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
| | - Pavan Salve
- Medical Department, Pimpri Chinchwad Municipal Corporation, Pune, Maharashtra, India
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50
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Nyayanit DA, Sarkale P, Baradkar S, Patil S, Yadav PD, Shete-Aich A, Kalele K, Gawande P, Majumdar T, Jain R, Sapkal G. Transcriptome & viral growth analysis of SARS-CoV-2-infected Vero CCL-81 cells. Indian J Med Res 2020; 152:70-76. [PMID: 32773420 PMCID: PMC7853258 DOI: 10.4103/ijmr.ijmr_2257_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Background & objectives: The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belonging to the family Coronaviridae, encodes for structural, non-structural, and accessory proteins, which are required for replication of the virus. These proteins are encoded by different genes present on the SARS-CoV-2 genome. The expression pattern of these genes in the host cells needs to be assessed. This study was undertaken to understand the transcription pattern of the SARS-CoV-2 genes in the Vero CCL-81 cells during the course of infection. Methods: Vero CCL-81 cells were infected with the SARS-CoV-2 virus inoculum having a 0.1 multiplicity of infection. The supernatants and cell pellets were harvested after centrifugation at different time points, post-infection. The 50% tissue culture infective dose (TCID50) and cycle threshold (Ct) values of the E and the RdRp-2 genes were calculated. Next-generation sequencing of the harvested sample was carried out to observe the expression pattern of the virus by mapping to the SARS-CoV-2 Wuhan HU-1 reference sequence. The expressions were in terms of the reads per kilobase million (RPKM) values. Results: In the inital six hours post-infection, the copy numbers of E and RdRp-2 genes were approximately constant, which raised 10 log-fold and continued to increase till the 12 h post-infection (hpi). The TCID50 was observed in the supernatant after 7 hpi, indicating the release of the viral progeny. ORF8 and ORF7a, along with the nucleocapsid transcript, were found to express at higher levels. Interpretation & conclusions: This study was a step towards understanding the growth kinetics of the SARS-CoV-2 replication cycle. The findings indicated that ORF8 and ORF7b gene transcripts were expressed in higher amounts indicating their essential role in viral replication. Future studies need to be conducted to explore their role in the SARS-CoV-2 replication.
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Affiliation(s)
- Dimpal A Nyayanit
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Shreekant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Savita Patil
- 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
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Kaumudi Kalele
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pranita Gawande
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajlaxmi Jain
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Gajanan Sapkal
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
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