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Article ; Online: IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution.

Limaye, Sanket / Shelke, Anant / Kale, Mohan M / Kulkarni-Kale, Urmila / Kuchipudi, Suresh V

2024 Volume 16, Issue 3

Abstract: Influenza D virus (IDV) is the most recent addition to ... ...

Abstract	Influenza D virus (IDV) is the most recent addition to the
MeSH term(s)	Humans ; Animals ; Cattle ; Deltainfluenzavirus ; Thogotovirus/genetics ; Orthomyxoviridae ; Orthomyxoviridae Infections
Language	English
Publishing date	2024-02-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16030373
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis.

Mane, Arati / Limaye, Sanket / Patil, Linata / Kulkarni-Kale, Urmila

Journal of medical microbiology

2022 Volume 71, Issue 1

Abstract: Introduction. ...

Abstract	Introduction.
MeSH term(s)	Carcinogenesis ; DNA, Viral/genetics ; Female ; Genetic Variation ; Human papillomavirus 16/genetics ; Humans ; Mutation ; Oncogene Proteins, Viral/genetics ; Papillomavirus Infections/virology ; Phylogeny ; Uterine Cervical Neoplasms/virology
Chemical Substances	DNA, Viral ; Oncogene Proteins, Viral
Language	English
Publishing date	2022-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001475
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Article ; Online: Genetic variability in minor capsid protein (L2 gene) of human papillomavirus type 16 among Indian women.

Mane, Arati / Limaye, Sanket / Patil, Linata / Kulkarni-Kale, Urmila

Medical microbiology and immunology

2022 Volume 211, Issue 2-3, Page(s) 153–160

Abstract: Human papillomavirus type 16 (HPV-16) is the predominant genotype worldwide associated with invasive cervical cancer and hence remains as the focus for diagnostic development and vaccine research. L2, the minor capsid protein forms the packaging unit for ...

Abstract	Human papillomavirus type 16 (HPV-16) is the predominant genotype worldwide associated with invasive cervical cancer and hence remains as the focus for diagnostic development and vaccine research. L2, the minor capsid protein forms the packaging unit for the HPV genome along with the L1 protein and is primarily associated with transport of genomic DNA to the nucleus. Unlike L1, L2 is known to elicit cross-neutralizing antibodies and thus becomes a suitable candidate for pan-HPV prophylactic vaccine development. In the present study, a total of 148 cervical HPV-16 isolates from Indian women were analyzed by PCR-directed sequencing, phylogenetic analysis and in silico immunoinformatics tools to determine the L2 variations that may impact the immune response and oncogenesis. Ninety-one SNPs translating to 35 non-synonymous amino acid substitutions were observed, of these 16 substitutions are reported in the Indian isolates for the first time. T245A, L266F, S378V and S384A substitutions were significantly associated with high-grade cervical neoplastic status. Multiple substitutions were observed in samples from high-grade cervical neoplastic status as compared to those from normal cervical status (p = 0.027), specifically from the D3 sub-lineage. It was observed that substitution T85A was part of both, B and T cell epitopes recognized by MHC-I molecules; T245A was common to B and T cell epitopes recognized by MHC-II molecules and S122P/A was common to the region recognized by both MHC-I and MHC-II molecules. These findings reporting L2 protein substitutions have implications on cervical oncogenesis and design of next-generation L2-based HPV vaccines.
MeSH term(s)	Antibodies, Viral ; Capsid Proteins/genetics ; Carcinogenesis ; Epitopes, T-Lymphocyte ; Female ; Histocompatibility Antigens Class II/genetics ; Human papillomavirus 16/genetics ; Humans ; Oncogene Proteins, Viral/genetics ; Papillomaviridae/genetics ; Papillomavirus Infections ; Papillomavirus Vaccines/genetics ; Phylogeny
Chemical Substances	Antibodies, Viral ; Capsid Proteins ; Epitopes, T-Lymphocyte ; Histocompatibility Antigens Class II ; Oncogene Proteins, Viral ; Papillomavirus Vaccines
Language	English
Publishing date	2022-05-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	120933-4
ISSN	1432-1831 ; 0300-8584
ISSN (online)	1432-1831
ISSN	0300-8584
DOI	10.1007/s00430-022-00739-4
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Article ; Online: Neutralizing Antibody Response to Genotypically Diverse Measles Viruses in Clinically Suspected Measles Cases.

Vaidya, Sunil R / Kumbhar, Neelakshi S / Andhare, Gargi K / Pawar, Nilesh / Walimbe, Atul M / Kinikar, Meenal / Kasibhatla, Sunitha M / Kulkarni-Kale, Urmila

Viruses

2023 Volume 15, Issue 11

Abstract: The neutralizing antibody (Nt-Ab) response to vaccine and wild-type measles viruses (MeV) was studied in suspected measles cases reported during the years 2012-2016. The neutralization activity against MeV A, D4 and D8 genotypes was studied on sera ( ... ...

Abstract	The neutralizing antibody (Nt-Ab) response to vaccine and wild-type measles viruses (MeV) was studied in suspected measles cases reported during the years 2012-2016. The neutralization activity against MeV A, D4 and D8 genotypes was studied on sera (Panel A; n = 68 (measles-immunized) and Panel B; n = 50 (unvaccinated)) that were either laboratory confirmed or not confirmed by the presence of IgM antibodies. Additionally, the Nt-Ab response in Panel A was measured against the MeV vaccine and four wild-type viruses. Neutralization results were compared using homology modeling and molecular dynamics simulation (MDS) of MeV-hemagglutinin (H) and fusion (F) proteins. Overall, the Nt-Ab titres for MeV-A were found to be significantly lower than MeV-D4 and MeV-D8 viruses for Panel A. No major difference was noted in Nt-Ab titres between MeV-D8 viruses (Jamnagar and New Delhi), whereas MeV-D4 (Sindhudurg and Bagalkot (BGK) viruses) showed significant differences between Nt-Ab titres for Panel B. Interestingly, the substitutions observed in epitopes of H-protein, L249P and G316A are observed to be unique to MeV-BGK. MDS of H-protein revealed significant fluctuations in neutralizing epitopes due to L249P substitution. The majority of the clinically suspected cases showed Nt-Abs to MeV wild-types. Higher IgG antibody avidity and Nt-Ab titres were noted in IgM-negatives than in IgM-positives cases, indicating reinfection or breakthrough. MDS revealed reduced neutralization due to decreased conformational flexibility in the H-epitope.
MeSH term(s)	Humans ; Antibodies, Neutralizing ; Antibodies, Viral ; Neutralization Tests ; Measles virus/genetics ; Measles ; Measles Vaccine ; Epitopes ; Immunoglobulin M
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Measles Vaccine ; Epitopes ; Immunoglobulin M
Language	English
Publishing date	2023-11-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15112243
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Article: Inhibition of miR-155 Promotes TGF-β Mediated Suppression of HIV Release in the Cervical Epithelial Cells

Gokavi, Jyotsna / Sadawarte, Sharwari / Shelke, Anant / Kulkarni-Kale, Urmila / Thakar, Madhuri / Saxena, Vandana

Viruses. 2021 Nov. 12, v. 13, no. 11

2021

Abstract: TGF-β has been shown to play a differential role in either restricting or aiding HIV infection in different cell types, however its role in the cervical cells is hitherto undefined. Among females, more than 80% of infections occur through heterosexual ... ...

Abstract	TGF-β has been shown to play a differential role in either restricting or aiding HIV infection in different cell types, however its role in the cervical cells is hitherto undefined. Among females, more than 80% of infections occur through heterosexual contact where cervicovaginal mucosa plays a critical role, however the early events during the establishment of infection at female genital mucosa are poorly understood. We earlier showed that increased TGF-β level has been associated with cervical viral shedding in the HIV infected women, however a causal relationship could not be examined. Therefore, here we first established an in vitro cell-associated model of HIV infection in the cervical epithelial cells (ME-180) and demonstrated that TGF-β plays an important role as a negative regulator of HIV release in the infected cervical epithelial cells. Inhibition of miR-155 upregulated TGF-β signaling and mRNA expression of host restriction factors such as APOBEC-3G, IFI-16 and IFITM-3, while decreased the HIV release in ME-180 cells. To conclude, this is the first study to decipher the complex interplay between TGF-β, miR-155 and HIV release in the cervical epithelial cells. Collectively, our data suggest the plausible role of TGF-β in promoting HIV latency in cervical epithelial cells which needs further investigations.
Keywords	HIV infections ; female genitalia ; gene expression ; models ; mucosa
Language	English
Dates of publication	2021-1112
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112266
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Article ; Online: Inhibition of miR-155 Promotes TGF-β Mediated Suppression of HIV Release in the Cervical Epithelial Cells.

Gokavi, Jyotsna / Sadawarte, Sharwari / Shelke, Anant / Kulkarni-Kale, Urmila / Thakar, Madhuri / Saxena, Vandana

Viruses

2021 Volume 13, Issue 11

Abstract	TGF-β has been shown to play a differential role in either restricting or aiding HIV infection in different cell types, however its role in the cervical cells is hitherto undefined. Among females, more than 80% of infections occur through heterosexual contact where cervicovaginal mucosa plays a critical role, however the early events during the establishment of infection at female genital mucosa are poorly understood. We earlier showed that increased TGF-β level has been associated with cervical viral shedding in the HIV infected women, however a causal relationship could not be examined. Therefore, here we first established an in vitro cell-associated model of HIV infection in the cervical epithelial cells (ME-180) and demonstrated that TGF-β plays an important role as a negative regulator of HIV release in the infected cervical epithelial cells. Inhibition of miR-155 upregulated TGF-β signaling and mRNA expression of host restriction factors such as
MeSH term(s)	Antiviral Restriction Factors/genetics ; Cell Line ; Cervix Uteri/cytology ; Cervix Uteri/metabolism ; Cervix Uteri/virology ; Epithelial Cells/metabolism ; Epithelial Cells/virology ; Female ; HIV-1/physiology ; Humans ; MicroRNAs/antagonists & inhibitors ; MicroRNAs/genetics ; Signal Transduction/genetics ; Transforming Growth Factor beta/antagonists & inhibitors ; Transforming Growth Factor beta/metabolism ; Virus Shedding
Chemical Substances	Antiviral Restriction Factors ; MIRN155 microRNA, human ; MicroRNAs ; Transforming Growth Factor beta
Language	English
Publishing date	2021-11-12
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112266
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Article ; Online: Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak.

Limaye, Sanket / Kasibhatla, Sunitha M / Ramtirthkar, Mukund / Kinikar, Meenal / Kale, Mohan M / Kulkarni-Kale, Urmila

Viruses

2021 Volume 13, Issue 11

Abstract: The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. ...

Abstract	The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as 'Others' in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus-host interactions, differential glycosylation, immune evasion, and escape from neutralization.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Evolution, Molecular ; Genome, Viral ; Humans ; India/epidemiology ; Models, Molecular ; Mutation ; Phylogeny ; Protein Conformation ; Protein Domains ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Selection, Genetic ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Whole Genome Sequencing
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-11-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112238
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Article ; Online: Antibody Class(es) Predictor for Epitopes (AbCPE): A Multi-Label Classification Algorithm.

Kadam, Kiran / Peerzada, Noor / Karbhal, Rajiv / Sawant, Sangeeta / Valadi, Jayaraman / Kulkarni-Kale, Urmila

Frontiers in bioinformatics

2021 Volume 1, Page(s) 709951

Abstract: Development of vaccines and therapeutic antibodies to deal with infectious and other diseases are the most perceptible scientific interventions that have had huge impact on public health including that in the current Covid-19 pandemic. From inactivation ... ...

Abstract	Development of vaccines and therapeutic antibodies to deal with infectious and other diseases are the most perceptible scientific interventions that have had huge impact on public health including that in the current Covid-19 pandemic. From inactivation methodologies to reverse vaccinology, vaccine development strategies of 21st century have undergone several transformations and are moving towards rational design approaches. These developments are driven by data as the combinatorials involved in antigenic diversity of pathogens and immune repertoire of hosts are enormous. The computational prediction of epitopes is central to these developments and numerous B-cell epitope prediction methods developed over the years in the field of immunoinformatics have contributed enormously. Most of these methods predict epitopes that could potentially bind to an antibody regardless of its type and only a few account for antibody class specific epitope prediction. Recent studies have provided evidence of more than one class of antibodies being associated with a particular disease. Therefore, it is desirable to predict and prioritize 'peptidome' representing B-cell epitopes that can potentially bind to multiple classes of antibodies, as an open problem in immunoinformatics. To address this, AbCPE, a novel algorithm based on multi-label classification approach has been developed for prediction of antibody class(es) to which an epitope can potentially bind. The epitopes binding to one or more antibody classes (IgG, IgE, IgA and IgM) have been used as a knowledgebase to derive features for prediction. Multi-label algorithms, Binary Relevance and Label Powerset were applied along with Random Forest and AdaBoost. Classifier performance was assessed using evaluation measures like Hamming Loss, Precision, Recall and F1 score. The Binary Relevance model based on dipeptide composition, Random Forest and AdaBoost achieved the best results with Hamming Loss of 0.1121 and 0.1074 on training and test sets respectively. The results obtained by AbCPE are promising. To the best of our knowledge, this is the first multi-label method developed for prediction of antibody class(es) for sequential B-cell epitopes and is expected to bring a paradigm shift in the field of immunoinformatics and immunotherapeutic developments in synthetic biology. The AbCPE web server is available at http://bioinfo.unipune.ac.in/AbCPE/Home.html.
Language	English
Publishing date	2021-09-07
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-7647
ISSN (online)	2673-7647
DOI	10.3389/fbinf.2021.709951
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Article ; Online: Phylogenetic Analysis of Spread of Hepatitis C Virus Identified during HIV Outbreak Investigation, Unnao, India.

Mane, Arati / Kasibhatla, Sunitha Manjari / Vidhate, Pallavi / Saxena, Vandana / Patil, Sandip / Rao, Amrita / Nirmalkar, Amit / Kulkarni-Kale, Urmila / Panda, Samiran

Emerging infectious diseases

2022 Volume 28, Issue 4, Page(s) 725–733

Abstract: An HIV outbreak investigation during 2017-2018 in Unnao District, Uttar Pradesh, India, unearthed high prevalence of hepatitis C virus (HCV) antibodies among the study participants. We investigated these HCV infections by analyzing NS5B and core regions. ...

Abstract	An HIV outbreak investigation during 2017-2018 in Unnao District, Uttar Pradesh, India, unearthed high prevalence of hepatitis C virus (HCV) antibodies among the study participants. We investigated these HCV infections by analyzing NS5B and core regions. We observed no correlation between HIV-HCV viral loads and clustering of HCV sequences, regardless of HIV serostatus. All HCV isolates belonged to genotype 3a. Monophyletic clustering of isolates in NS5B phylogeny indicates emergence of the outbreak from a single isolate or its closely related descendants. The nucleotide substitution rate for NS5B was 6 × 10
MeSH term(s)	Disease Outbreaks ; HIV Infections/epidemiology ; Hepacivirus ; Hepatitis C/epidemiology ; Humans ; India/epidemiology ; Phylogeny
Language	English
Publishing date	2022-03-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2804.211845
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Zs.A 4778: Show issues

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Article: Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

Limaye, Sanket / Kasibhatla, Sunitha M. / Ramtirthkar, Mukund / Kinikar, Meenal / Kale, Mohan M. / Kulkarni-Kale, Urmila

Viruses. 2021 Nov. 08, v. 13, no. 11

2021

Abstract	The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as ‘Others’ in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus–host interactions, differential glycosylation, immune evasion, and escape from neutralization.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; genome ; genomics ; glycosylation ; immune evasion ; monitoring ; monophyly ; neutralization ; pandemic ; population genetics ; trees ; India
Language	English
Dates of publication	2021-1108
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112238
Database	NAL-Catalogue (AGRICOLA)

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