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Choudhary ML, Chaudhary U, Salve M, Shinde P, Padbidri V, Sangle SA, Salvi S, Bavdekar AR, D'costa P, Alagarasu K. Functional Single-Nucleotide Polymorphisms in the MBL2 and TLR3 Genes Influence Disease Severity in Influenza A (H1N1)pdm09 Virus-Infected Patients from Maharashtra, India. Viral Immunol 2022; 35:303-309. [PMID: 35196173 DOI: 10.1089/vim.2021.0179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The clinical outcome in influenza A (H1N1)pdm09 virus-infected subjects is determined by several factors, including host genetics. In the present study, single-nucleotide polymorphisms (SNPs) in the IFITM, MBL2, TLR3, TLR8, DDX58, IFIH1, CD55, and FCGR2, genes were investigated in influenza A (H1N1)pdm09 virus-infected subjects to find out their association with disease severity. Influenza A (H1N1)pdm09 virus-infected subjects with severe disease (n = 86) and mild disease (n = 293) from western India were included in the study. The SNPs were investigated by PCR-based methods. The results revealed a higher frequency of TLR3 rs5743313 T/T genotype [odds ratio (OR) with 95% confidence interval (CI) 2.55 (1.08-6.04) p = 0.039] and TLR3 two-locus haplotype rs3775291-rs3775290 T-A [OR with 95% CI 7.94 (2.05-30.68)] in severe cases. Lower frequency of the mutant allele of MBL2 rs1800450 [OR with 95% CI 0.51 (0.27-0.87), p = 0.01] and TLR3 two-locus haplotype rs3775291-rs3775290 T-G [OR with 95% CI 0.48 (0.27-0.85)] was observed in severe cases compared with cases with mild disease. Higher frequency of TLR3 two-locus haplotype rs3775291-rs3775290 T-A was observed in severe cases [OR with 95% CI 7.9 (2.0-30.7)]. The allele and genotype frequencies of other SNPs were not different between the study categories. The results suggest that the functional SNPs in MBL2 and TLR3 are associated with severe disease in influenza A (H1N1)pdm09 virus-infected subjects.
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Affiliation(s)
| | | | | | - Pooja Shinde
- ICMR-National Institute of Virology, Pune, India
| | | | | | - Sonali Salvi
- Department of Medicine, BJ Medical College, Pune, India
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Mohandas S, Jain R, Yadav PD, Shete-Aich A, Sarkale P, Kadam M, Kumar A, Deshpande G, Baradkar S, Patil S, Sapkal G, Mali D, Salve M, Patil D, Majumdar T, Suryawanshi A, Kaushal H, Lakra R, Dighe H, Gupta N, Abraham P, Gangakhedkar RR. Evaluation of the susceptibility of mice & hamsters to SARS-CoV-2 infection. Indian J Med Res 2020; 151:479-482. [PMID: 32611917 PMCID: PMC7530454 DOI: 10.4103/ijmr.ijmr_2235_20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Rajlaxmi Jain
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Manoj Kadam
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Abhimanyu Kumar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Gururaj Deshpande
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Shreekant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Gajanan Sapkal
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Deepak Mali
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Malvika Salve
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Dilip Patil
- Animal House, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Annasaheb Suryawanshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Himanshu Kaushal
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Rajen Lakra
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Hitesh Dighe
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Raman R Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi 110 029, India
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Yadav PD, Shete-Aich A, Nyayanit DA, Pardeshi P, Majumdar T, Balasubramanian R, Ullas PT, Mohandas S, Dighe H, Sawant P, Patil S, Patil D, Gokhale MD, Mathapati B, Sudeep AB, Baradkar S, Kumar A, Kharde R, Salve M, Joshi Y, Gupta N, Mourya DT. Detection of coronaviruses in Pteropus & Rousettus species of bats from different States of India. Indian J Med Res 2020; 151:226-235. [PMID: 32317409 PMCID: PMC7366549 DOI: 10.4103/ijmr.ijmr_795_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background & objectives: Bats are considered to be the natural reservoir for many viruses, of which some are potential human pathogens. In India, an association of Pteropus medius bats with the Nipah virus was reported in the past. It is suspected that the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also has its association with bats. To assess the presence of CoVs in bats, we performed identification and characterization of bat CoV (BtCoV) in P. medius and Rousettus species from representative States in India, collected during 2018 and 2019. Methods: Representative rectal swab (RS) and throat swab specimens of Pteropus and Rousettus spp. bats were screened for CoVs using a pan-CoV reverse transcription-polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase (RdRp) gene. A single-step RT-PCR was performed on the RNA extracted from the bat specimens. Next-generation sequencing (NGS) was performed on a few representative bat specimens that were tested positive. Phylogenetic analysis was carried out on the partial sequences of RdRp gene sequences retrieved from both the bat species and complete viral genomes recovered from Rousettus spp. Results: Bat samples from the seven States were screened, and the RS specimens of eight Rousettus spp. and 21 Pteropus spp. were found positive for CoV RdRp gene. Among these, by Sanger sequencing, partial RdRp sequences could be retrieved from three Rousettus and eight Pteropus bat specimens. Phylogenetic analysis of the partial RdRp region demonstrated distinct subclustering of the BtCoV sequences retrieved from these Rousettus and Pteropus spp. bats. NGS led to the recovery of four sequences covering approximately 94.3 per cent of the whole genome of the BtCoVs from Rousettus bats. Three BtCoV sequences had 93.69 per cent identity to CoV BtRt-BetaCoV/GX2018. The fourth BtCoV sequence was 96.8 per cent identical to BtCoV HKU9-1. Interpretation & conclusions: This study was a step towards understanding the CoV circulation in Indian bats. Detection of potentially pathogenic CoVs in Indian bats stresses the need for enhanced screening for novel viruses in them. One Health approach with collaborative activities by the animal health and human health sectors in these surveillance activities shall be of use to public health. This would help in the development of diagnostic assays for novel viruses with outbreak potential and be useful in disease interventions. Proactive surveillance remains crucial for identifying the emerging novel viruses with epidemic potential and measures for risk mitigation.
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Affiliation(s)
- 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
| | - Dimpal A Nyayanit
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prachi Pardeshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - R Balasubramanian
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra; ICMR-National Institute of Virology Kerala Unit, Alappuzha, Kerala, India
| | | | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Hitesh Dighe
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pradeep Sawant
- Enteric Virus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Dilip Patil
- Animal House, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - M D Gokhale
- Entomology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Basavaraj Mathapati
- Poliovirus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A B Sudeep
- Entomology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sreekant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Abhimanyu Kumar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rutuja Kharde
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Malvika Salve
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yash Joshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Sapkal G, Shete-Aich A, Jain R, Yadav PD, Sarkale P, Lakra R, Baradkar S, Deshpande GR, Mali D, Tilekar BN, Majumdar T, Kaushal H, Gurav Y, Gupta N, Mohandas S, Deshpande K, Kaduskar O, Salve M, Patil S, Gaikwad S, Sugunan A, Ashok M, Giri S, Shastri J, Abraham P, Gangakhedkar RR. Development of indigenous IgG ELISA for the detection of anti-SARS-CoV-2 IgG. Indian J Med Res 2020; 151:444-449. [PMID: 32611915 PMCID: PMC7530443 DOI: 10.4103/ijmr.ijmr_2232_20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND & OBJECTIVES Since the beginning of the year 2020, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted humankind adversely in almost all spheres of life. The virus belongs to the genus Betacoronavirus of the family Coronaviridae. SARS-CoV-2 causes the disease known as coronavirus disease 2019 (COVID-19) with mild-to-severe respiratory illness. The currently available diagnostic tools for the diagnosis of COVID-19 are mainly based on molecular assays. Real-time reverse transcription-polymerase chain reaction is the only diagnostic method currently recommended by the World Health Organization for COVID-19. With the rapid spread of SARS-CoV-2, it is necessary to utilize other tests, which would determine the burden of the disease as well as the spread of the outbreak. Considering the need for the development of such a screening test, an attempt was made to develop and evaluate an IgG-based ELISA for COVID-19. METHODS A total of 513 blood samples (131 positive, 382 negative for SARS-CoV-2) were collected and tested by microneutralization test (MNT). Antigen stock of SARS-CoV-2 was prepared by propagating the virus in Vero CCL-81 cells. An IgG capture ELISA was developed for serological detection of anti-SARS-CoV-2 IgG in serum samples. The end point cut-off values were determined by using receiver operating characteristic (ROC) curve. Inter-assay variability was determined. RESULTS The developed ELISA was found to be 92.37 per cent sensitive, 97.9 per cent specific, robust and reproducible. The positive and negative predictive values were 94.44 and 98.14 per cent, respectively. INTERPRETATION & CONCLUSIONS This indigenously developed IgG ELISA was found to be sensitive and specific for the detection of anti-SARS-CoV-2 IgG in human serum samples. This assay may be used for determining seroprevalence of SARS-CoV-2 in a population exposed to the virus.
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Affiliation(s)
- Gajanan Sapkal
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajlaxmi Jain
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rajen Lakra
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Srikant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Gururaj Rao Deshpande
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Deepak Mali
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Bipin N. Tilekar
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Himanshu Kaushal
- Human Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yogesh Gurav
- Epidemiology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ketki Deshpande
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ojas Kaduskar
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Malvika Salve
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Shivshankar Gaikwad
- Diagnostic Virology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A.P. Sugunan
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - M. Ashok
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Jayanthi Shastri
- Department of Microbiology, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Raman R. Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Cubiella J, Salve M, Díaz-Ondina M, Vega P, Alves MT, Iglesias F, Sánchez E, Macía P, Blanco I, Bujanda L, Fernández-Seara J. Diagnostic accuracy of the faecal immunochemical test for colorectal cancer in symptomatic patients: comparison with NICE and SIGN referral criteria. Colorectal Dis 2014; 16:O273-82. [PMID: 24456168 DOI: 10.1111/codi.12569] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/06/2013] [Indexed: 12/15/2022]
Abstract
AIM The diagnostic accuracy of the faecal immunochemical test (FIT) at a 100 ng/ml threshold for colorectal cancer (CRC) was compared with National Institute for Health and Care Excellence (NICE) and the Scottish Intercollegiate Guidelines Network (SIGN) referral criteria. METHOD A multicentre, prospective, blind study of diagnostic tests was carried out in two Spanish health areas. In 787 symptomatic patients referred for a diagnostic colonoscopy, we determined whether patients met NICE and SIGN referral criteria. All patients performed one FIT determination (OCsensor(™) ). The sensitivity and specificity for CRC detection were determined with McNemar's test. The diagnostic odds ratio as well as the number needed to scope (NNS) to detect a CRC were calculated. RESULTS We detected CRC in 97 (12.3%) patients; 241 (30.6%) had an FIT ≥ 100 ng/ml and 300 (38.1%) and 473 (60.1%) met NICE and SIGN referral criteria. The FIT had a higher sensitivity for CRC detection than NICE criteria (87.6%, 61.9%; P < 0.001) and SIGN criteria (82.5%; P = 0.4). The specificity of FIT was also higher than NICE and SIGN criteria (77.4%, 65.2%, 42.7%; P < 0.001). The odds ratios of FIT, NICE and SIGN criteria for the diagnosis of CRC were 24.24 (95% CI 12.91-45.53), 3.04 (95% CI 1.96-4.71) and 3.51 (95% CI 2.03-6.06). The NNS to detect a CRC in individuals with an FIT ≥ 100 ng/ml was 2.83 (95% CI 2.4-3.41) and in individuals who met NICE and SIGN criteria it was 5 (95% CI 3.98-6.37) and 5.95 (95% CI 4.85-7.35). CONCLUSION Our study suggests that FIT is more accurate for the detection of CRC than the current NICE and SIGN referral criteria in symptomatic patients referred for colonoscopy.
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Affiliation(s)
- J Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Ourense, Spain
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Damaskin B, Polynovskaya N, Palm U, Salve M. On the theory of ionic adsorption from binary electrolyte solutions at electrodes. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0022-0728(88)80163-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Damaskin B, Pankratova I, Palm U, Anni K, Väärtnǒu M, Salve M. Comparison of the ionic adsorption theories for the electrode/solution interface by computer simulation. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0022-0728(87)80160-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Damaskin B, Kuznetsova L, Palm U, Väärtnu M, Salve M. Specific adsorption of ions and charge distribution in an electrical double layer. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/s0022-0728(79)80173-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Damaskin B, Palm U, Petyärv E, Salve M. Comparison of isotherms for specific adsorption of ions from constant ionic strength solutions. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s0022-0728(74)80304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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