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Sagar R, Raghavendhar S, Jain V, Khan N, Chandele A, Patel AK, Kaja M, Ray P, Kapoor N. Viremia and clinical manifestations in acute febrile patients of Chikungunya infection during the 2016 CHIKV outbreak in Delhi, India. Infect Med (Beijing) 2024; 3:100088. [PMID: 38444748 PMCID: PMC10914418 DOI: 10.1016/j.imj.2024.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/16/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Background Chikungunya virus (CHIKV) is an infectious agent that caused several outbreaks among different countries and affected approximately 1.3 million Indian populations. It is transmitted by Aedes mosquito-either A. albopictus or A. aegypti. Generally, the clinical manifestations of CHIKV infection involve high-grade fever, joint pain, skin rashes, headache, and myalgia. The present study aims to investigate the relationship between the CHIKV virus load and clinical symptoms of the CHIKV infection so that better patient management can be done in the background of the CHIKV outbreak as there is no licensed anti-viral drug and approved vaccines available against CHIKV. Methods CHIKV RTPCR positive samples (n = 18) (Acute febrile patients having D.O.F ≤ 7 days) were taken for the quantification of CHIKV viremia by Real-Time PCR. Clinical features of the febrile patients were recorded during the collection of blood samples. Results The log mean virus load of 18 RT-PCR-positive samples was 1.3 × 106 copies/mL (1.21 × 103-2.33 × 108 copies/mL). Among the observed clinical features, the log mean virus load (CHIKV) of the patients without skin rash is higher than in the patients with skin rash (6.61 vs 5.5, P = 0.0435). Conclusion The conclusion of the study was that the patients with skin rashes had lower viral load and those without skin rashes had higher viral load.
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Affiliation(s)
- Rohit Sagar
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
- Department of Life Sciences, School of Sciences, IGNOU, New Delhi 110068, India
| | - Siva Raghavendhar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Vineet Jain
- HAH Centenary Hospital, Jamia Hamdard, New Delhi 110062, India
| | - Naushad Khan
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, ICGEB, New Delhi 110067, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Murali Kaja
- ICGEB-Emory Vaccine Center, ICGEB, New Delhi 110067, India
- Department of Pediatrics, Emory University School of Medicine, 30322 Atlanta, GA, USA
| | - Pratima Ray
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Neera Kapoor
- Department of Life Sciences, School of Sciences, IGNOU, New Delhi 110068, India
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Gaurav N, Kumar S, Raghavendhar S, Tripathi PK, Gupta S, Arya R, Patel AK. Transcriptome analysis of Huh7 cells upon Chikungunya virus infection and capsid transfection reveals regulation of distinct cellular and metabolic pathways. Virology 2024; 589:109953. [PMID: 38043141 DOI: 10.1016/j.virol.2023.109953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Chikungunya virus (CHIKV) causes persistent arthritis and neurological problems imposing a huge burden globally. The present study aims to understand the interaction mechanism of Chikungunya virus and CHIKV-capsid in Huh7 cells. The RNA-sequencing and qRT-PCR method was used for the transcript and gene profiles of CHIKV virus and CHIKV capsid alone. Transcriptional analysis showed capsid induced 1114 and 956 differentially expressed genes (DEGs) to be upregulated and downregulated respectively, while in virus, 933 genes were upregulated and 956 were downregulated. Total 202 DEGs were common in both capsid and virus; and nine were validated using qRT-PCR. Identified DEGs were found to be associated with metabolic pathways such as Diabetes, cardiac disease, and visual impairment. Further, knock-down study on one of the DEGs (MafA) responsible for insulin regulation showed low viral proteins expression suggesting a reduction in virus-infection. Thus, the study provides insight into the interplay of the virus-host factors assisting virus replication.
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Affiliation(s)
- Nitika Gaurav
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; University of Colorado, Anschutz Medical Campus, Colorado, USA
| | - Shivani Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Siva Raghavendhar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; Division of Infectious Diseases, University of Utah, Salt Lake City, UT, 84132, USA
| | - Praveen Kumar Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; Indian Council of Medical Research, National Institute of Malaria Research, Ranchi, Jharkhand, 834010, India
| | - Shipra Gupta
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ravi Arya
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Tripathi PK, Upadhyay S, Singh M, Raghavendhar S, Bhardwaj M, Sharma P, Patel AK. Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2. Int J Biol Macromol 2020; 164:2622-2631. [PMID: 32853604 PMCID: PMC7444494 DOI: 10.1016/j.ijbiomac.2020.08.166] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a global catastrophe. The virus requires main protease for processing the viral polyproteins PP1A and PP1AB translated from the viral RNA. In search of a quick, safe and successful therapeutic agent; we screened various clinically approved drugs for the in-vitro inhibitory effect on 3CLPro which may be able to halt virus replication. The methods used includes protease activity assay, fluorescence quenching, surface plasmon resonance (SPR), Thermofluor® Assay, Size exclusion chromatography and in-silico docking studies. We found that Teicoplanin as most effective drug with IC50 ~ 1.5 μM. Additionally, through fluorescence quenching Stern-Volmer quenching constant (KSV) for Teicoplanin was estimated as 2.5 × 105 L·mol-1, which suggests a relatively high affinity between Teicoplanin and 3CLPro protease. The SPR shows good interaction between Teicoplanin and 3CLPro with KD ~ 1.6 μM. Our results provide critical insights into the mechanism of action of Teicoplanin as a potential therapeutic against COVID-19. We found that Teicoplanin is about 10-20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CLPro of SARS-CoV-2.
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Affiliation(s)
- Praveen Kumar Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, 110016, India
| | - Saurabh Upadhyay
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, 110016, India
| | - Manju Singh
- Morarji Desai National Institute of Yoga, New Delhi 110 001, India
| | - Siva Raghavendhar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, 110016, India
| | - Mohit Bhardwaj
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, 110016, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, 110016, India.
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Upadhyay S, Tripathi PK, Singh M, Raghavendhar S, Bhardwaj M, Patel AK. Evaluation of medicinal herbs as a potential therapeutic option against SARS-CoV-2 targeting its main protease. Phytother Res 2020; 34:3411-3419. [PMID: 32748969 PMCID: PMC7436756 DOI: 10.1002/ptr.6802] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022]
Abstract
The COVID‐19 disease caused by the SARS‐CoV‐2 has emerged as a worldwide pandemic and caused huge damage to the lives and economy of more than hundred countries. As on May 10, 2020, more than 4,153,300 people stand infected from the virus due to an unprecedented rate of transmission and 282,700 have lost their lives because of the disease. In this context, medicinal plants may provide a way to treat the disease by targeting specific essential proteins of the virus. We screened about 51 medicinal plants and found that Tea (Camellia sinensis) and Haritaki (Terminalia chebula) has potential against SARS‐COV‐2 3CLpro, with an IC50 for Green Tea as 8.9 ± 0.5 μg/ml and Haritaki 8.8 ± 0.5 μg/ml. The in‐silico studies suggested that Tea component Thearubigins binds to the cysteine 145 of protease active site and could be a pharmacoactive molecule. We predict that the inhibition in protease activity may be able to halt the SARS‐CoV‐2 replication cycle and therefore, we propose Green Tea, Black Tea, and Haritaki plant extracts as potential therapeutic candidates for SARS‐CoV‐2 infection. Further investigation on role of bioactive constituents of extracts is needed to establish the molecular basis of inhibition and towards expedited drug discovery.
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Affiliation(s)
- Saurabh Upadhyay
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Praveen K Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Manju Singh
- Morarji Desai National Institute of Yoga, New Delhi, India
| | - Siva Raghavendhar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Mohit Bhardwaj
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Ashok K Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
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Tripathi PK, Soni A, Singh Yadav SP, Kumar A, Gaurav N, Raghavendhar S, Sharma P, Sunil S, Ashish, Jayaram B, Patel AK. Evaluation of novobiocin and telmisartan for anti-CHIKV activity. Virology 2020; 548:250-260. [PMID: 32791353 DOI: 10.1016/j.virol.2020.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/08/2020] [Accepted: 05/26/2020] [Indexed: 11/24/2022]
Abstract
Chikungunya has re-emerged as an epidemic with global distribution and high morbidity, necessitating the need for effective therapeutics. We utilized already approved drugs with a good safety profile used in other diseases for their new property of anti-chikungunya activity. It provides a base for a fast and efficient approach to bring a novel therapy from bench to bedside by the process of drug-repositioning. We utilized an in-silico drug screening with FDA approved molecule library to identify inhibitors of the chikungunya nsP2 protease, a multifunctional and essential non-structural protein required for virus replication. Telmisartan, an anti-hypertension drug, and the antibiotic novobiocin emerged among top hits on the screen. Further, SPR experiments revealed strong in-vitro binding of telmisartan and novobiocin to nsP2 protein. Additionally, small angle x-ray scattering suggested binding of molecules to nsP2 and post-binding compaction and retention of monomeric state in the protein-inhibitor complex. Protease activity measurement revealed that both compounds inhibited nsP2 protease activity with IC50 values in the low micromolar range. More importantly, plaque formation assays could show the effectiveness of these drugs in suppressing virus propagation in host cells. We propose novobiocin and telmisartan as potential inhibitors of chikungunya replication. Further research is required to establish the molecules as antivirals of clinical relevance against chikungunya.
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Affiliation(s)
- Praveen Kumar Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Anjali Soni
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India; Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | | | - Ankit Kumar
- Vector-Borne Disease Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Nitika Gaurav
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Siva Raghavendhar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sujatha Sunil
- Vector-Borne Disease Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Bhyravabhotla Jayaram
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India; Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Raghavendhar S, Tripati PK, Ray P, Patel AK. Evaluation of medicinal herbs for Anti-CHIKV activity. Virology 2019; 533:45-49. [PMID: 31082733 DOI: 10.1016/j.virol.2019.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 01/01/2023]
Abstract
Chikungunya, a mosquito-borne viral disease is now a global public health problem. In tropical countries such as India, periodic chikungunya outbreaks can occur due the high prevalence of the mosquito vector, circulation of virus and the high population density. To curtail the virus in outbreak situation, a ready to use drug for chikungunya is necessary. Using the literature mentioned plant extracts, we used four assays to screen and identify indigenous plants with CHIKV inhibitory activity. Our results showed that the aqueous extract of five plant extracts exhibited anti-CHIKV activity by inhibiting viral attachment, four plant extracts exhibited replication inhibition through inhibition of helicase activity, two plants showed inhibition of protease activity. Two plant extracts showed both viral attachment inhibition and replication inhibition and also exhibited dose dependent response in virus replication inhibition assay. These findings warrant further investigation to standardize these plant extracts as antiviral formulation for chikungunya infection.
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Affiliation(s)
| | | | - Pratima Ray
- Dept. of Biotechnology, Jamia Hamdard University, New Delhi, 110062, India
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Tiku VR, Sharma S, Verma A, Kumar P, Raghavendhar S, Aneja S, Paul VK, Bhan MK, Ray P. Rotavirus diversity among diarrheal children in Delhi, India during 2007-2012. Vaccine 2015; 32 Suppl 1:A62-7. [PMID: 25091683 DOI: 10.1016/j.vaccine.2014.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rotavirus is the leading cause of severe gastroenteritis in young children worldwide and is responsible for around 100,000 deaths in India annually. Vaccination against rotavirus (RV) is a high priority: 'ROTAVAC' an indigenous vaccine will soon be licensed in India. Surveillance to determine the impact of vaccines on emerging RV strains is required. In this study we compared the pattern of RV strains circulating in Delhi over a 5 year period with the strains over the past 12 years. The most commonly detected G genotypes were G1 (22.4%), G2 (17.2%), and G9 (25.2%) with P[4] (25.5%), P[6] (20%) and P[8] (16.9%) specificity. G12 genotype was found to be the fourth common G-type with 14.8% prevalence. Among the G-P combinations; G1P[8], G2P[4], G9P[8] and G12P[6] were detected at 7.2%, 7.2%, 5.2% and 10%, respectively. Of note, G9P[4] and G2P[6] that were rarely detected during 2000-2007 in Delhi, were observed quite frequently with prevalence of 6.5% and 3.4%, respectively. In total, 16 different G-P combinations were detected in the present study demonstrating the rich diversity of rotavirus strains in Delhi. Our data from the 12 year period indicate wide circulation of G1 and G9 genotypes in combination with P[8], G2 with P[4] and G12 with P[6] with high frequency of RV strains having rare G-P combinations in Delhi. Since the indigenous vaccine 'ROTAVAC' has a monovalent formulation, the impact of vaccines on strains and the effect of strain diversity on the efficacy of the vaccine should be monitored.
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Affiliation(s)
- Vasundhara Razdan Tiku
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sumit Sharma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Anil Verma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Praveen Kumar
- Kalawati Saran Children's Hospital, Lady Hardinge Medical College, New Delhi 110001, India
| | - Siva Raghavendhar
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Satinder Aneja
- Kalawati Saran Children's Hospital, Lady Hardinge Medical College, New Delhi 110001, India
| | - Vinod Kumar Paul
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Maharaj Kishan Bhan
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima Ray
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, Hamdard Nagar New Delhi 110062, India.
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