Pratip Shil

@niv.co.in

Scientist D, Bioinformatics & Data Management
ICMR National Institute of Virology

EDUCATION

M.Sc (Physics) with Biophysics Specialization (2001)
Ph.D (Physics) with Biophysics Specialization (2007)

RESEARCH INTERESTS

Mathematical modelling applications in Virology including disease modelling, climate effects on viral diseases, vectors and vector-borne diseases. Bioinformatics: in silico antigen-antibody interaction studies.

Scopus Publications

642

Scholar Citations

Scholar h-index

Scholar i10-index

Scopus Publications

Identification of B-cell epitopes of Indian Zika virus strains using immunoinformatics
Rohan Raj Roy, Nitali Tadkalkar, Gururaj Rao Deshpande, Nitin M. Atre, Pratip Shil, and Gajanan Sapkal
Frontiers Media SA
IntroductionThe Zika virus is an emerging Flavivirus known to cause Zika infection in humans. It is associated with severe health problems such as microcephaly and Guillain-Barré syndrome post the Brazilian epidemic in 2015-16. The spread of the Zika virus to the Asian subcontinent, especially to India is a matter of great concern. Two recent co-circulating Indian Zika virus strains such as Rajasthan and Maharashtra detected in 2018 and 2021 were studied to identify B-cell epitopes in the envelope and non-structural 1 protein as these epitopes are major indicators of robust humoral immune response. The study aimed at identifying novel epitopes, followed by molecular docking with potent Zika virus-specific monoclonal antibodies. The novel epitopes identified in this study shall be essential in designing multi-epitope vaccines capable of inducing antibody response against Zika virus infection.MethodsABCpred, BepiPred 2.0 and Kolaskar-Tongaonkar methods were used for predicting the linear B-cell epitopes, and Discotope 2.0 and ElliPro were used for the prediction of conformational epitopes. Linear epitopes were further checked for protective antigenicity, allergenicity and toxicity. Based on the stringent study design criteria, only the novel epitopes were considered for molecular docking with complementary determining regions of potent Zika virus-specific monoclonal antibodies.ResultsNineteen linear and five conformational epitopes were shortlisted based on protective potential, non-allergic and non-toxic properties for Zika virus E protein, from which nine linear and three conformational epitopes were identified as novel. Molecular docking studies revealed that the novel linear epitopes, one each from EDIII, EDII, EDI and EDI/DIII hinge were involved in epitope-CDR interactions with potent neutralizing Zika virus E-specific mouse monoclonal antibody ZV-67. Moreover, the novel EDII epitope was exclusively engaged in epitope-CDR interactions of potent neutralizing Zika virus E-specific human monoclonal antibody Z3L1. None of the linear epitopes of Zika virus NS1 were ascertained as novel based on our study criteria. Conformational epitopes were identified as novel for NS1 protein.ConclusionThis study identified Zika virus-specific novel epitopes of envelope and non-structural -1 proteins in the currently co-circulating Indian strains. Furthermore, in-silico validation through molecular docking added insight into antigen-antibody interactions, paving way for future in vitro and in vivo studies.

Structural and functional characterization of avian influenza H9N2 virus neuraminidase with a combination of five novel mutations
Deeksha S. Tare, Shailesh D. Pawar, Pratip Shil, and Nitin M. Atre
Elsevier BV

Genomic Characterization of Mosquito Isolates of Chikungunya Virus (Outbreak Strains 2022) Using Next-Generation Sequencing
Amol Nath, Surendra Kumar, Yogesh K. Gurav, Abhranil Gangopadhayya, Onkar Ghuge, Pallipurathu R. Sreelakshmi, Abhijeet Jadhav, Lekshmi S. Rajan, Kishore Yadav, Krishna Shinde,et al.
Mary Ann Liebert Inc
Background: A massive outbreak of dengue-like illness was reported from Pune district of Maharashtra, India during May-June 2022. Isolation and characterization of the etiological agent at genomic level for possible mutations that led to higher transmissibility is the topic of the study. Methods: Entomological investigations were carried out by ICMR-National Institute of Virology (Pune, India); Aedes aegypti mosquitoes were collected and processed for virus detection by molecular techniques. Positive mosquito pools were processed for virus isolation in cell culture. Sanger sequencing and whole-genome sequencing (WGS) using Oxford Nanopore Technology platform were used for genomic characterization. Results: Reverse transcriptase RT-PCR and qRT-PCR analysis detected chikungunya virus (CHIKV) in mosquito samples. Six CHIKV isolates were obtained. WGS revealed four nonsynonymous mutations in the structural polyprotein region, and five in the nonstructural polyprotein encoding region when compared with Yawat-2000 and Shivane-2016 strains. Sixty-four nucleotide changes in the nonstructural polyprotein region and 35 in the structural polyprotein region were detected. One isolate had an exclusive amino acid change, T1123I, in the nsP2 (protease) region. Conclusion: Abundant Ae. aegypti breeding and detection of CHIKV RNA in mosquitoes confirmed it as a chikungunya outbreak. Novel mutations detected in the epidemic strain warrants investigations to address their role in disease severity, transmission, and fitness.

Diversity of sandflies in Vidarbha region of Maharashtra, India, a region endemic to Chandipura virus encephalitis
A. Sudeep, P. Shil, K. Selarka, Y. S. Godke, P. Sonawane and M. Gokhale

Background & objectives Sandflies are implicated as vectors of Chandipura virus (CHPV) (Vesiculovirus: Rhabdoviridae). The virus is prevalent in central India including Vidarbha region of Maharashtra. CHPV causes encephalitis in children below 15 yr of age with case fatality rates ranging from 56 to 78 per cent. The present study was undertaken to determine the sandfly fauna in the CHPV endemic Vidharba region. Methods A year round survey of sandflies was conducted at 25 sites in three districts of Vidarbha region. Sandflies were collected from their resting sites using handheld aspirators and identified using taxonomical keys. Results A total of 6568 sandflies were collected during the study. Approximately 99 per cent of the collection belonged to genus Sergentomyia, which was represented by Ser. babu, Ser. bailyi and Ser. punjabensis. Genus Phlebotomus was represented by Ph. argentipes and Ph. papatasi. Ser. babu was the predominant species (70.7%) collected during the study. Ph. argentipes was detected in four villages with 0.89 per cent, whereas Ph. papatasi was detected in only one village with 0.32 per cent of the total collection. CHPV could not be isolated despite processing all the sandflies for virus isolation in cell culture. Interpretation & conclusions The present study showed influence of higher temperature and relative humidity on sandfly population dynamics. An important observation during the study was the absence or decline in the population of Ph. papatasi and Ph. argentipes in the study area. Surge in Sergentomyia population and their breeding/resting in close vicinity to humans pose a concern as they are known to harbour CHPV and other viruses of public health importance.

ArVirInd-a database of arboviral antigenic proteins from the Indian subcontinent
Nitin Motilal Atre, Kalichamy Alagarasu, and Pratip Shil
PeerJ
Background Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighboring countries have a huge burden of arboviral diseases. Data mining for country-specific sequences from existing bioinformatics databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arboviruses isolated from the countries of the Indian subcontinent. Methods Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data was incorporated into the database. The front end was designed and developed using HTML, CSS, and PHP. For the backend of the database, we have used MySQL. Results A database, named ArVirInd, is created as a repository of information on curated antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry, antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country, and year of collection (or in combination) as well as peptide search for epitopes. It is available publicly via the Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immune informatics, diagnostics, and vaccinology for arboviruses.

Epidemiological findings for the first and second waves of COVID-19 pandemic in Maharashtra, India
Pratip Shil, Nitin M Atre, and Babasaheb V Tandale
Elsevier BV

District-wise estimation of Basic reproduction number (R<inf>0</inf>) for COVID-19 in India in the initial phase
Pratip Shil, Nitin M. Atre, Avinash A. Patil, Babasaheb V. Tandale, and Priya Abraham
Springer Science and Business Media LLC
SARS-CoV-2 or COVID-19 was introduced into India by multiple sources generating local clusters and leading to the nationwide spread. A retrospective study has been conducted on the epidemiological features and spatial spread of COVID-19 in India during February 2020–March 2021. For each district, the cumulative number of confirmed COVID-19 cases were fitted to exponential growth model for the initial phase of the outbreak (the first 7–15 days). From the estimated growth rate, epidemiological parameters like the Basic reproduction number (R0) and epidemic doubling time (τ) were determined. Using Q-GIS software, we have generated the all India distribution maps for R0 and τ. COVID-19 spread rapidly covering majority of the districts of India between March and June 2020. As on 1st March 2021, a total of 715 out of 717 districts have been affected. The R0 range is at par with the global average. A few districts, where outbreaks were caused by migrant workers coming home, intense transmission was recorded R0 > 7. We also found that the spread of COVID-19 was not uniform across the different districts of India. The methodology developed in the study can be used by researchers and public health professionals to analyze and study epidemics in future.

Design of a multi-epitope peptide vaccine candidate against chandipura virus: an immuno-informatics study
Daya V. Pavitrakar, Nitin M. Atre, Anuradha S. Tripathy, and Pratip Shil
Informa UK Limited
Chandipura virus (CHPV) is an emerging pathogen responsible for acute encephalitic syndrome (AES) in pediatric population in India. Several outbreaks of CHPV have been reported from different states of India since the year 2003. At present there is no vaccine or therapeutic measures available to curtail the disease. In this study, we have identified both T-cell and B-cell epitopes of different antigenic proteins of CHPV like Nucleoprotein (N), Phosphoprotein (P) and Matrix protein (M) along with the immuno-dominant glycoprotein (G) and conducted in silico characterization for the same. The idea is to design a multi-epitope peptide construct using the epitopes, which were found to be non-toxic, non-allergenic and possessing high immunogenicity. The final multi-epitope construct named as: MEC-CHPV, comprised of β-defensin adjuvant at N-terminal for enhancement of immunogenicity followed by fourteen B-cell epitopes, four Helper T-cell epitopes and six Cytotoxic T-cell epitopes. The characterization of designed construct was carried out in terms of physicochemical parameters, antigenicity and allergenicity. The 3D structure prediction was performed. Molecular docking and molecular-dynamics simulation of MEC-CHPV with Toll like receptors (TLR-3 and TLR-8) showed stable interactions. In silico cloning of MEC-CHPV in pET30a(+) expression vector was also conducted using codon optimization. The in silico immune-simulation indicated a typical immune response against MEC-CHPV when used as a potential vaccine. This study provides a cost-effective and time-saving way to design a peptide vaccine candidate against CHPV using immuno-informatics approach. Development of the MEC-CHPV construct may pave the way for future laboratory experiments. Communicated by Ramaswamy H. Sarma.

Cyclophilin A: a possible host modulator in Chandipura virus infection
Daya V. Pavitrakar, Nitin M. Atre, Anuradha S. Tripathy, and Pratip Shil
Springer Science and Business Media LLC
Chandipura virus (CHPV), belonging to the genus Vesiculovirus of the family Rhabdoviridae, has been identified as one of the causes of pediatric encephalitis in India. Currently, neither vaccines nor therapeutic drugs are available against this agent. Considering that the disease progresses very fast with a high mortality rate, working towards the development of potential therapeutics against it will have a public health impact. Although the use of viral inhibitors as antiviral agents is the most common way to curb virus replication, the mutation-prone nature of viruses results in the development of resistance to antiviral agents. The recent development of proteomic platforms for analysis of purified viral agents has allowed certain upregulated host proteins that are involved in the morphogenesis and replication of viruses to be identified. Thus, the alternative approach of inhibition of host proteins involved in the regulation of virus replication could be explored for their therapeutic effectiveness. In the current study, we have evaluated the effect of inhibition of cyclophilin A (CypA), an immunophilin with peptidyl-prolyl cis/trans-isomerase activity, on the replication of CHPV. Treatment with cyclosporin A, used in vitro for the inhibition of CypA, resulted in a 3-log reduction in CHPV titer and an undetectable level of CypA in comparison to an untreated control. An in silico analysis of the interaction of the CHPV nucleoprotein with the human CypA protein showed stable interaction in molecular docking and molecular dynamics simulations. Overall, the results of this study suggest a possible role of CypA in facilitating CHPV replication, thus making it one of the potential host factors to be explored in future antiviral studies. Supplementary information The online version contains supplementary material available at 10.1007/s00705-021-05237-1.

Predictions of Disease Spikes Induced by Climate Variability: A Pilot Real Time Forecasting Model Project from Maharashtra, India
Sujata Saunik, Pratip Shil, Subrata N. Das, Sangita P. Rajankar, Omkar Khare, Krishna A. Hosalikar, and Yusuf Kabir
Springer International Publishing
Climate change is manifest globally through extreme weather events, altered rainfall patterns and spread of viral diseases. The emergence and re-emergence of arthropod-borne viral diseases viz. dengue, chikungunya, West Nile, Japanese encephalitis and Zika are of global public health concern. Over the last decade India has faced a huge burden of Dengue and chikungunya with more than ten million individuals affected. This not only necessitates studies on the role of environmental effects on disease, but also requires policy-framing towards effective prevention or control of epidemics. In this chapter we are presenting the initiative taken by the Government of Maharashtra state, Republic of India to establish a pilot project to record and document disease outbreaks in the different districts of the state and to develop a predictive model that can analyse the effect of meteorological parameters on disease occurrences. A web portal has been developed for recording of data and online display and efforts are on to develop mathematical models for analyses and estimation disease occurrences. As a first, we have successfully developed a Poisson regression model to describe the effects of meteorological parameters on dengue occurrences in the Nagpur region of the Maharashtra state.

Involvement of dual serotypes during a severe dengue outbreak in Wadi area, Nagpur district, Maharashtra 2017
AB Sudeep, P Shil, MM Charmode, S Mohandas, S Bansod, MD Gokhale, M Jagtap, and PS Shah
Medknow
BACKGROUND & OBJECTIVES An outbreak of dengue-like illness was reported from Wadi area within the Nagpur Municipal Corporation during September-October 2017 with five deaths. Major symptoms reported were high fever (103-106 oF), acute joint pains, myalgia, drowsiness, breathlessness, etc. An investigation was conducted to confirm the etiological agent, its characterization and the vectors involved in the outbreak. METHODS Serological analysis was conducted to detect dengue (DEN)/chikungunya IgM antibodies in 158 sera samples. Nested-PCR was carried out to serotype eight ELISA positive samples. Adult and larval mosquito collections were conducted in the affected areas to determine species composition and mosquito density. RESULTS Dengue IgM antibodies were detected in 44 sera samples. Molecular typing revealed involvement of DEN-2 and DEN-3 serotypes. Dengue hemorrhagic fever symptoms were observed in two patients. Aedes aegypti breeding was found rampant with Breteu index and house index ranging from 23 to 70 and 17 to 56, respectively. Major breeding habitats encountered were, used tyres, cement tanks and refrigerator trays. INTERPRETATION & CONCLUSION Clinical symptoms, detection of anti-DEN IgM antibodies in high number of samples and heavy breeding of Ae. aegypti confirmed it was a dengue outbreak.

Assessment of NS1 protein as an early diagnostic marker for Kyasanur forest disease virus
Devendra Mourya, Pragya Yadav, Gouri Chaubal, Sarita Jena, and Pratip Shil
Medknow
Background & objectives: Due to the emergence of Kyasanur forest disease (KFD) virus to new regions in India, there is an urgent need to develop an early diagnostic system, which is cost-effective and can be efficiently used with minimum paraphernalia. The non-structural-1 (NS1) protein is known to be an early diagnostic marker for flaviviruses. Furthermore, NS1 antigen capture ELISA kits developed using bacterially expressed dengue NS1 protein are commercially available. Methods: Based on the data available on dengue virus, West Nile virus and other flaviviruses, bacterially expressed Kyasanur forest disease virus (KFDV) NS1 protein and polyclonal serum raised against the NS1 protein in mice and rabbit were used to develop an antigen capture ELISA for early diagnosis of the virus. The feasibility of this ELISA was further tested using in silico predictions. Results: KFDV NS1 gene was cloned, expressed and confirmed by SDS-PAGE and western blotting. An antigen detection ELISA was standardized and sensitivity and specificity was tested with other flaviviruses. KFDV acute phase 43 samples were tested and only two were found to be positive for KFDV NS1 antigen. Superimposition of KFDV NS1 and TBEV NS1 revealed a root mean square distance (RMSD) of ~0.79 Å covering 1220 backbone atoms. This implies that the structures are very similar in terms of 3D fold. The identity of amino acid composition between these proteins was 73.4% and similarity was 92.9%, as revealed from the pairwise comparison. Interpretation & conclusion: The study points out that the half-life, expression and secretion levels of KFDV NS1 protein are not sufficient enough for its use as early diagnostic marker. The protein may have to be expressed in eukaryotic host to counter the lack of glycosylation in bacterial plasmid based expression of proteins. Hence, bacterially expressed KFDV NS1 protein may not be an ideal early diagnostic marker for the virus.

Differential susceptibility & replication potential of Vero E6, BHK-21, RD, A-549, C6/36 cells & Aedes aegypti mosquitoes to three strains of chikungunya virus
AnakkathilBalan Sudeep, PratikB Vyas, Deepti Parashar, and Pratip Shil
Medknow
Background & objectives: Chikungunya virus (CHIKV), a mosquito-borne arthritogenic virus causes infections ranging from febrile illness to debilitating polyarthralgia in humans. Re-emergence of the virus has affected millions of people in Africa and Asia since 2004. During the outbreak, a new lineage of the virus has evolved as an adaptation for enhanced replication and transmission by Aedes albopictus mosquito. A study was designed to compare the susceptibility of four vertebrate cell lines, namely Vero E6 (African green monkey kidney), BHK-21 (Baby hamster kidney), RD (human rhabdomyosarcoma), A-549 (human alveolar basal epithelial cell) and C6/36 (Ae. albopictus) to Asian genotype and two lineages of East, Central and South African (E1:A226 and E1:A226V) of CHIKV. Methods: One-step growth kinetics of different CHIKV strains was carried out in the above five cell lines to determine the growth kinetics and virus yield. Virus titre was determined by 50 per cent tissue culture infectious dose assay and titres were calculated by the Reed and Muench formula. Growth and virus yield of the three strains in Ae. aegypti mosquitoes was studied by intrathoracic inoculation and virus titration in Vero E6 cell line. Results: Virus titration showed Vero E6, C6/36 and BHK-21 cell lines are high virus yielding with all the three lineages while RD and A-549 yielded low virus titres. C6/36 cell line was the most sensitive and yielded the maximum titre. Ae. aegypti mosquitoes, when inoculated with high titre virus, yielded an almost equal growth with the three strains while rapid growth of E1:A226V and Asian strain was observed with 1 log virus. Interpretation & conclusions: C6/36 cell line was found to be the most sensitive and high yielding for CHIKV irrespective of lineages while Vero E6 and BHK-21 cell lines yielded high titres and may find application for vaccine/diagnostic development. Infection of Ae. aegypti mosquitoes with the three CHIKV strains gave almost identical pattern of growth.

Complete genome sequencing of Kaisodi virus isolated from ticks in India belonging to Phlebovirus genus, family Phenuiviridae
P.D. Yadav, D.A. Nyayanit, A.M. Shete, S. Jain, T.P. Majumdar, G.Y. Chaubal, P. Shil, P.M. Kore, and D.T. Mourya
Elsevier BV
An unknown virus was repeatedly isolated from hard tick (Haemaphysalis spinigera) during a proactive arbovirus survey in ticks conducted in 1957, in India. The virus remained uncharacterized for a long time. The passages of this virus in different vertebrate and invertebrate cells along with human and monkey-derived cell culture showed no cytopathic effect. It was identified later to be a member of Kaisodi group among Phlebovirus genus in the family Phenuiviridae (Order: Bunyavirales) by serological methods. Due to its genomic diversity, sequencing of this virus was a challenge for a while. In this study, we were able to sequence the complete genome of this virus isolate using next-generation sequencing (NGS) platform. The unknown virus was identified to be Kaisodi virus (KASDV) using NGS analysis. De novo genome assembly derived three genomic segments for the KASDV which encode for RNA-dependent RNA polymerase, glycoprotein precursor, and nucleoprotein. Functional as well as conserved domains for Kaisodi serogroup viruses were predicted and compared to a known representative of the genus Phlebovirus. The phylogenetic tree revealed its closeness to Silverwater virus, of Kaisodi serogroup with nucleotide (69%, 62%, and 61%) and amino acid (52%, 51%, and 62%) identity for L, M, and S segment, respectively. The study demonstrates the presence of a conserved motif (72TRGNK76) around the RNA binding motif region in tick-borne phleboviruses. The intergenic region encompassing the S segment of Kaisodi serogroup was GC-rich whereas the other Phlebovirus had AT-rich genome. KASDV has the largest intergenic region and larger loops, suggesting stem-loops formed due to larger loops as a possible factor for instability and cause of transcription termination. This paper also describes the real-time RT-PCR and RT-PCR assays developed and used for the detection of KASDV RNA in ticks from Karnataka, Kerala and Maharashtra State, India. The KASDV positivity observed in the recently collected tick pools indicates that the KASDV, isolated from Karnataka state in 1957, is also circulating in the adjoining Kerala state. On the basis of the current study, it should be possible to develop diagnostic assays which would facilitate an in-depth field survey exploring the veterinary and medical significance of KASDV.

Identification of a conserved neutralizing epitope in the G-protein of Chandipura virus
Daya V. Pavitrakar, Rekha G. Damle, Anuradha S. Tripathy, and Pratip Shil
Springer Science and Business Media LLC
Chandipura virus (CHPV), associated with an encephalitic illness in humans, has caused multiple outbreaks with high mortality in central and western India in recent years. The present study compares surface glycoprotein (G-protein) from prototype and recent outbreak strains using in silico tools and in vitro experiments. In silico epitope predictions (B-cell and T-helper cell) for the sequences, 3D structure prediction and comparison of the G-proteins of the strains: I653514 (Year 1965), CIN0327 (Year 2003) and 148974 (Year 2014) revealed that the CHPV G-protein is stable and antigenic determinants are conserved. A monoclonal antibody developed against strain CIN0327 (named NAbC) was found to neutralize prototype I653514 as well as the currently circulating strain 148974. In silico antigen-antibody interaction studies using molecular docking of predicted structures of NAbC and G-proteins of various CHPV strains led to the identification of a conserved neutralizing epitope in the fusion domain of G-protein, which also contained a putative T-helper peptide. The identification of a conserved neutralizing epitope in domain IV (fusion domain amino acids 53 to 172) of CHPV G-protein is an important finding that may have the scope towards the development of protective targets against CHPV infection.

Differences in Type I interferon response in human lung epithelial cells infected by highly pathogenic H5N1 and low pathogenic H11N1 avian influenza viruses
Milind M. Thube, Pratip Shil, Rewati Kasbe, Avinash A. Patil, Shailesh D. Pawar, and Jayati Mullick
Springer Science and Business Media LLC
Influenza A virus infection induces type I interferons (IFNs α/β) which activate host antiviral responses through a cascade of IFN signaling events. Herein, we compared highly pathogenic H5N1 and low pathogenic H11N1 avian influenza viruses isolated from India, for their replication kinetics and ability to induce IFN-β and interferon-stimulating genes (ISGs). The H5N1 virus showed a higher replication rate and induced less IFN-β and ISGs compared to the H11N1 virus when grown in the human lung epithelial A549 cells, reflecting the generation of differential innate immune responses during infection by these viruses. The non-structural 1 (NS1) protein, a major IFN-antagonist, known to help the virus in evading host innate immune response was compared from both the strains using bioinformatics tools. Analyses revealed differences in the composition of the NS1 proteins from the two strains that may have an impact on the modulation of the innate immune response. Intriguingly, H5N1 virus attenuated IFN-β response in a non-NS1 manner, suggesting the possible involvement of other viral proteins (PB2, PA, PB1/PB1-F2) of H5N1 in synergy with NS1. Preliminary analyses of the above proteins of the two strains by sequence comparison show differences in charged residues. The insight gained will be useful in designing experimental studies to elucidate a probable role of the polymerase protein(s) in association with NS1 in inhibiting the IFN signaling and understanding the molecular mechanism governing the difference.

Rainfall and Chikungunya incidences in India during 2010–2014
Pratip Shil, Dilip R. Kothawale, and Anakkathil B. Sudeep
Springer Science and Business Media LLC
Changing climate scenario has resulted in recent emergence and re-emergence of various arboviral diseases including Chikungunya. This disease is caused by Chikungunya virus (CHIKV), which belongs to Togaviridae family of viruses and spread by Aedes mosquitoes. A resurgence of CHIKV and its rapid global spread has been observed since 2004. The disease reemerged in India in 2005, after a gap of 32 years, causing massive outbreaks in some states and circulating thereafter. In the present paper we analyze CHIKV incidence data from India (2010–2014) with a view to understand association with environmental parameters, if any. Data on country-wide occurrences of CHIKV cases were considered from the National Vector Borne Disease Control Board, India. Meteorological data for different climatic subdivisions of India were obtained and processed mathematically. State-wise association of number of cases with rainfall, if any, were studied by statistical analyses. We observe that prevailing temperature range was favorable for CHIKV propagation and the occurrences were modulated by average rainfall. Most affected states were West Bengal, Maharashtra and Karnataka. Overall for India, favorable climatic conditions have contributed to incidences of CHIKV during the study period. There is strong positive association between rainfall variations and occurrence of CHIKV cases.

Bioinformatics characterization of envelope glycoprotein from kyasanur forest disease virus
DevendraT Mourya, Pratip Shil, PragyaDhruv Yadav, AvinashA Patil, and R Balasubramanian
Medknow
Background & objectives: Kyasanur Forest disease (KFD) is a febrile illness characterized by haemorrhages and caused by KFD virus (KFDV), which belongs to the Flaviviridae family. It is reported to be an endemic disease in Shimoga district of Karnataka State, India, especially in forested and adjoining areas. Several outbreaks have been reported in newer areas, which raised queries regarding the changing nature of structural proteins if any. The objective of the study was to investigate amino acid composition and antigenic variability if any, among the envelope glycoprotein (E-proteins) from old and new strains of KFDV. Methods: Bioinformatic tools and techniques were used to predict B-cell epitopes and three-dimensional structures and to compare envelope glycoprotein (E-proteins) between the old strains of KFDV and those from emerging outbreaks till 2015. Results: The strain from recent outbreak in Thirthahalli, Karnataka State (2014), was similar to the older strain of KFDV (99.2%). Although mutations existed in strains from 2015 in Kerala KFD sequences, these did not alter the epitopes. Interpretation & conclusions: The study revealed that though mutations existed, there were no drastic changes in the structure or antigenicity of the E-proteins from recent outbreaks. Hence, no correlation could be established between the mutations and detection in new geographical areas. It seems that KFDV must be present earlier also in many States and due to availability of testing system and alertness coming into notice now.

Numerical analyses of electroporation-mediated doxorubicin uptake in eukaryotic cells: Role of membrane cholesterol content

Aedes vittatus (Bigot) mosquito: An emerging threat to public health
AB Sudeep and P Shil
Medknow
Aedes vittatus (Bigot) mosquito is a voracious biter of humans and has a geographical distribution throughout tropical Asia, Africa and the Mediterranean region of Europe. It is predominantly a rock-hole breeder, though it can breed in diverse macro- and micro-habitats. The mosquito plays an important role in the maintenance and transmission of yellow fever (YFV), dengue (DENV), chikungunya (CHIKV) and Zika (ZIKV) viruses. It has been implicated as an important vector of YFV in several African countries as evidenced by repeated virus isolations from the mosquito and its potential to transmit the virus experimentally. Similarly, DENV-2 has been isolated from wild caught Ae. vittatus mosquitoes in Senegal, Africa which has been shown to circulate the virus in sylvatic populations without causing human infection. Experimental studies have shown replication of the virus at a low scale in naturally infected mosquitoes while high rate of infection and dissemination have been reported in parenterally infected mosquitoes. Natural isolation of ZIKV has been reported from Senegal and Cote d’Ivoire from these mosquitoes. They were found highly competent to transmit the virus experimentally and the transmission rate is at par with Ae. leuteocephalus, the primary vector of ZIKV. A few CHIKV isolations have also been reported from the mosquitoes in Senegal and other countries in Africa. Experimental studies have demonstrated high susceptibility, early dissemination and efficient transmission of CHIKV by Ae. vittatus mosquitoes. The mosquitoes with their high susceptibility and competence to transmit important viruses, viz. YFV, DENV, CHIKV and ZIKV pose a major threat to public health due to their abundance and anthropophilic behaviour.

Influenza A(H1N1)pdm09 outbreak detected in inter-seasonal months during the surveillance of influenza-like illness in Pune, India, 2012-2015
Y. K. GURAV, M. S. CHADHA, B. V. TANDALE, V. A. POTDAR, S. D. PAWAR, P. SHIL, A. R. DEOSHATWAR, R. AARTHY, and A. BHUSHAN
Cambridge University Press (CUP)
SUMMARYAn outbreak of influenza A(H1N1)pdm09 was detected during the ongoing community-based surveillance of influenza-like illness (ILI). Among reported 119 influenza A(H1N1)pdm09 cases (59 cases in the year 2012 and 60 cases in 2015) in summer months, common clinical features were fever (100%), cough (90·7%), sore throat (85·7%), nasal discharge (48·7%), headache (55·5%), fatigue (18·5%), breathlessness (3·4%), and ear discharge (1·7%). Rise in ILI cases were negatively correlated with the seasonal factors such as relative humidity (Karl Pearson's correlation coefficient, i.e. r = −0·71 in the year 2012 and r = −0·44 in the year 2015), while rise in ILI cases were positively correlated with the temperature difference (r = 0·44 in the year 2012 and r = 0·77 in the year 2015). The effective reproduction number R, was estimated to be 1·30 in 2012 and 1·64 in 2015. The study highlights the rise in unusual influenza activity in summer month with high attack rate of ILI among children aged ⩽9 years. Children in this age group may need special attention for influenza vaccination. Influenza A(H1N1)pdm09 outbreak was confirmed in inter-seasonal months during the surveillance of ILI in Pune, India, 2012–2015.

In-vitro effect of human cathelicidin antimicrobial peptide LL-37 on dengue virus type 2
K. Alagarasu, P.S. Patil, P. Shil, M. Seervi, M.B. Kakade, H. Tillu, and A. Salunke
Elsevier BV
HIGHLIGHTSTreatment of dengue virus 2 with LL‐37 inhibited viral infection of Vero E6 cells.Treatment: of the virus with LL‐37 inhibited the production of virus particles.LL‐37 had no effect on viral load 24 h post infection.Treatment of Vero E6 cells with LL‐37 before infection had no effect on viral load.In‐silico analysis revealed the possible binding of LL‐37 to virus envelope. ABSTRACT Human Cathelicidin antimicrobial peptide LL‐37 is known to have antiviral activity against many viruses. In the present study, we investigated the in‐vitro effect of LL‐37 on dengue virus type 2 (DENV‐2) infection and replication in Vero E6 cells. To study the effect of pretreatment of virus or cells with LL‐37, the virus was pretreated with different concentrations of LL‐37 (2.5 &mgr;M–15 &mgr;M) or scrambled (Scr) LL‐37(5 &mgr;M–15 &mgr;M) and used for infection or the cells were first treated with LL‐37 and infected. To study the effect of LL‐37 post infection (PI), the cells were infected first followed by addition of LL‐37 to the culture medium 24 h after infection. In all conditions, after the incubation, the culture supernatant was assessed for viral RNA copy number by real time RT‐PCR, infectious virus particles by focus forming unit assay (FFU) and non structural protein 1 (NS1) antigen levels by ELISA. Percentage of infection was assessed using immunoflourescence assay (IFA). The results revealed that pretreatment of virus with 10–15 &mgr;M LL‐37 significantly reduced its infectivity as compared to virus control (P < 0.0001). Moreover, pretreatment of virus with 10–15 &mgr;M LL‐37 significantly reduced the levels of viral genomic RNA and NS1 antigen (P < 0.0001). Treatment of virus with 10–15 &mgr;M LL‐37 resulted in two to three log reduction of mean log10 FFU/ml as compared to virus control (P < 0.0001). Treatment of the virus with scrambled LL‐37 had no effect on percentage of infection and viral load as compared to virus control cultures (P > 0.05). Pretreatment of cells before infection or addition of LL‐37 to the culture 24 h PI had no effect on viral load. Molecular docking studies revealed possible binding of LL‐37 to both the units of DENV envelope (E) protein dimer. Together, the in‐vitro experiments and in‐silico analyses suggest that LL‐37 inhibits DENV‐2 at the stage of entry into the cells by binding to the E protein. The results might have implications for prophylaxis against DENV infections and need further in‐vivo studies.

Radio-electro-chemotherapy of cancer: New perspectives for cancer treatment
P. Vidyasagar, S. Jagtap and O. Yemul
Jenny Stanford Publishing

Zika virus: Indian perspectives
DevendraT Mourya, Pratip Shil, GajananN Sapkal, and PragyaD Yadav
Medknow
The emergence of Zika virus (ZiV), a mosquito borne Flavivirus like dengue (DEN) and chikungunya (CHIK), in Brazil in 2014 and its spread to various countries have led to a global health emergency. Aedes aegypti is the major vector for ZiV. Fast dissemination of this virus in different geographical areas posses a major threat especially to regions where the population lacks herd immunity against the ZiV and there is abundance of Aedes mosquitoes. In this review, we focus on current global scenario, epidemiology, biology, diagnostic challenges and remedial measures for ZiVconsidering the Indian perspective.

Design and characterization of polytope construct with multiple B and T <inf>H</inf> epitopes of Japanese encephalitis virus
Reshma Kulkarni, Gajanan Sapkal, Lata Mahishi, Pratip Shil, and Milind M. Gore
Elsevier BV
Japanese encephalitis (JE) remains a major public health threat with vaccination as the only measure for its prevention. Epitope-based vaccination is a promising approach for achieving protective immunity and avoid immunopathology in Japanese encephalitis virus (JEV) infection due to flavivirus cross-reactivity. We have mapped B-cell epitopes from JEV envelope protein, responsible for elicitation of neutralizing antibodies. Incorporation of T helper (T(H)) epitopes, along with these, imparted protective immunity to the host. In the present study, based on in silico epitope selection we optimized and proposed a polytope DNA construct (P-JEV) consisting B-cell and T(H) epitopes from the JEV envelope (E) protein as well as non-structural protein-1 (NS1). The immunogenicity and protective efficacy of P-JEV was assessed by in vitro and in vivo experiments. The expressed P-JEV showed reactivity in in vitro assays with JEV monoclonal antibodies. Protective efficacy of P-JEV was assessed in BALB/c mice. Our findings indicate that P-JEV may be a candidate vaccine for the prevention of JEV infection.

RECENT SCHOLAR PUBLICATIONS

Identification of B-cell epitopes of Indian Zika virus strains using immunoinformatics
RR Roy, N Tadkalkar, GR Deshpande, NM Atre, P Shil, G Sapkal
Frontiers in Immunology 16, 1534737 2025

Structural and functional characterization of avian influenza H9N2 virus neuraminidase with a combination of five novel mutations
DS Tare, SD Pawar, P Shil, NM Atre
Archives of Biochemistry and Biophysics 757, 110041 2024

Genomic characterization of mosquito isolates of chikungunya virus (outbreak strains 2022) using next-generation sequencing
A Nath, S Kumar, YK Gurav, A Gangopadhayya, O Ghuge, ...
Vector-Borne and Zoonotic Diseases 23 (6), 341-349 2023

Diversity of sandflies in Vidarbha region of Maharashtra, India, a region endemic to Chandipura virus encephalitis
AB Sudeep, P Shil, K Selarka, YS Godke, PA Sonawane, MD Gokhale
Indian Journal of Medical Research 157 (4), 259-267 2023

ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent
NM Atre, K Alagarasu, P Shil
PeerJ 10, e13851 2022

Epidemiological findings for the first and second waves of COVID-19 pandemic in Maharashtra, India
P Shil, NM Atre, BV Tandale
Spatial and Spatio-temporal Epidemiology 41, 100507 2022

Design of a multi-epitope peptide vaccine candidate against chandipura virus: An immuno-informatics study
DV Pavitrakar, NM Atre, AS Tripathy, P Shil
Journal of Biomolecular Structure and Dynamics 40 (2), 648-659 2022

Cyclophilin A: a possible host modulator in Chandipura virus infection
DV Pavitrakar, NM Atre, AS Tripathy, P Shil
Archives of Virology 166, 3143-3150 2021

Forecasting Model Project from Maharashtra, India
S Saunik, P Shil, SN Das, SP Rajankar, O Khare, KA Hosalikar, Y Kabir
Management of Irrigation and Water Supply Under Climatic Extremes: Empirical 2021

Climate influence on Dengue occurrence in Pune Urban Zone: development of a SARIMA based forecasting model
P Shil, M Jagtap, P Awate
Dengue Bulletin 42, 108-125 2021

District-wise estimation of Basic reproduction number (R0) for COVID-19 in India in the initial phase
P Shil, N Atre, A Patil, B Tandale, P Abraham
Spatial Information Research, doi.org/10.1007/s41324-021-00412-7 2021

Predictions of disease spikes induced by climate variability: a pilot real time forecasting model project from Maharashtra, India
S Saunik, P Shil, SN Das, SP Rajankar, O Khare, KA Hosalikar, Y Kabir
Management of Irrigation and Water Supply Under Climatic Extremes: Empirical 2021

Meteorological Parameters and Mosquito Species Diversity and Abundance along the Arabian Sea Coastline of Alappuzha District, India: A Year-round Study (2017-18)
P Shil, R Balasubramanian
Journal of Mosquito Research 10 2020

Climate and dengue in the Pune region: prospects for an early warning system
P Shil, M Jagtap, CRH deSouza, AB Sudeep, P Awate
Dengue Bulletin 41, 49-76 2020

Involvement of dual serotypes during a severe dengue outbreak in Wadi area, Nagpur district, Maharashtra 2017
AB Sudeep, P Shil, MM Charmode, S Mohandas, S Bansod, MD Gokhale, ...
Journal of Vector Borne Diseases 56 (4), 295-302 2019

Assessment of NS1 protein as an early diagnostic marker for Kyasanur forest disease virus
P Yadav, G Chaubal, S Jena, S Pratip, D Mourya
Journal of Vector Borne Diseases 56 (3), 212-220 2019

Rainfall and dengue occurrences in India during 2010–2016
P Shil
Biomedical Research Journal 6 (2), 56-61 2019

Differential susceptibility & replication potential of Vero E6, BHK-21, RD, A-549, C6/36 cells & Aedes aegypti mosquitoes to three strains of chikungunya virus
AB Sudeep, PB Vyas, D Parashar, P Shil
Indian Journal of Medical Research 149 (6), 771-777 2019

Complete genome sequencing of Kaisodi virus isolated from ticks in India belonging to Phlebovirus genus, family Phenuiviridae
PD Yadav, DA Nyayanit, AM Shete, S Jain, TP Majumdar, GY Chaubal, ...
Ticks and tick-borne diseases 10 (1), 23-33 2019

Identification of a conserved neutralizing epitope in the G-protein of Chandipura virus
DV Pavitrakar, RG Damle, AS Tripathy, P Shil
Archives of Virology 163, 3215-3223 2018

MOST CITED SCHOLAR PUBLICATIONS

In-vitro effect of human cathelicidin antimicrobial peptide LL-37 on dengue virus type 2.
K Alagarasu, PS Patil, P Shil, et. al..
Peptides 92, 23-30 2017
Citations: 86

Aedes vittatus (Bigot) mosquito: An emerging threat to public health
AB Sudeep, P Shil
Journal of Vector Borne Diseases 54 (4), 295-300 2017
Citations: 61

Zika virus: Indian perspectives
DT Mourya, P Shil, GN Sapkal, PD Yadav
Indian Journal of Medical Research 143 (5), 553-564 2016
Citations: 50

Analysing the effects of surface distribution of pores in cell electroporation for a cell membrane containing cholesterol
P Shil, S Bidaye, PB Vidyasagar
Journal of Physics D: Applied Physics 41 (5), 055502 2008
Citations: 38

Electroporation enhances radiation and doxorubicin-induced toxicity in solid tumor in vivo
P Shil, A Kumar, PB Vidyasagar, KP Mishra
Journal of environmental pathology, toxicology and oncology 25 (4) 2006
Citations: 22

Molecular basis of antigenic drift in Influenza A/H3N2 strains (1968-2007) in the light of antigen antibody interactions
P Shil, S Chavan, S Cherian
Bioinformation 6 (7), 266 2011
Citations: 20

Enhancement of radiation cytotoxicity in murine cancer cells by electroporation: in vitro and in vivo studies
P Shil, SH Sanghvi, PB Vidyasagar, KP Mishra
Journal of environmental pathology, toxicology and oncology 24 (4) 2005
Citations: 19

Influenza A (H1N1) pdm09 outbreak detected in inter-seasonal months during the surveillance of influenza-like illness in Pune, India, 2012–2015
YK Gurav, MS Chadha, BV Tandale, VA Potdar, SD Pawar, P Shil, ...
Epidemiology & Infection 145 (9), 1898-1909 2017
Citations: 18

Mathematical Modeling of Viral Epidemics: A Review
P Shil
Biomed Res J 3 (2), 195–215 2016
Citations: 18

Delineation of an epitope on domain I of Japanese encephalitis virus Envelope glycoprotein using monoclonal antibodies
RS Gangwar, P Shil, SS Cherian, MM Gore
Virus Research 158 (1-2), 179-187 2011
Citations: 18

Transmission dynamics of novel influenza A/H1N1 2009 outbreak in a residential school in India
P Shil, YK Gurav, MS Chadha, AC Mishra
Current Science, 1177-1183 2011
Citations: 18

Rainfall and dengue occurrences in India during 2010–2016
P Shil
Biomedical Research Journal 6 (2), 56-61 2019
Citations: 17

Antigenic variability in Neuraminidase protein of Influenza A/H3N2 vaccine strains (1968–2009)
P Shil, SS Chavan, SS Cherian
Bioinformation 7 (2), 76 2011
Citations: 17

Rainfall and Chikungunya incidences in India during 2010–2014
P Shil, DR Kothawale, AB Sudeep
Virusdisease 29, 46-53 2018
Citations: 16

Induction of virus-specific neutralizing immune response against West Nile and Japanese encephalitis viruses by chimeric peptides representing T-helper and B-cell epitopes
RS Gangwar, P Shil, GN Sapkal, SA Khan, MM Gore
Virus Research 163 (1), 40-50 2012
Citations: 16

Design and characterization of polytope construct with multiple B and TH epitopes of Japanese encephalitis virus
R Kulkarni, G Sapkal, L Mahishi, P Shil, MM Gore
Virus Research 166 (1-2), 77-86 2012
Citations: 12

ISHAN: sequence homology analysis package
P Shil, N Dudani, PB Vidyasagar
In silico biology 6 (5), 373-377 2006
Citations: 12