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Article ; Online: Genomic characterization, transcriptome analysis, and pathogenicity of the Nipah virus (Indian isolate).

Mohandas, Sreelekshmy / Shete, Anita / Sarkale, Prasad / Kumar, Abhinendra / Mote, Chandrasekhar / Yadav, Pragya

2023 Volume 14, Issue 1, Page(s) 2224642

Abstract: Nipah virus (NiV) is a high-risk pathogen which can cause fatal infections in humans. The Indian isolate from the 2018 outbreak in the Kerala state of India showed ~ 4% nucleotide and amino acid difference in comparison to the Bangladesh strains of NiV ... ...

Abstract	Nipah virus (NiV) is a high-risk pathogen which can cause fatal infections in humans. The Indian isolate from the 2018 outbreak in the Kerala state of India showed ~ 4% nucleotide and amino acid difference in comparison to the Bangladesh strains of NiV and the substitutions observed were mostly not present in the region of any functional significance except for the phosphoprotein gene. The differential expression of viral genes was observed following infection in Vero (ATCC® CCL-81™) and BHK-21 cells. Intraperitoneal infection in the 10-12-week-old, Syrian hamster model induced dose dependant multisystemic disease characterized by prominent vascular lesions in lungs, brain, kidney and extra vascular lesions in brain and lungs. Congestion, haemorrhages, inflammatory cell infiltration, thrombosis and rarely endothelial syncitial cell formation were seen in the blood vessels. Intranasal infection resulted in respiratory tract infection characterised by pneumonia. The model showed disease characteristics resembling the human NiV infection except that of myocarditis similar to that reported by NiV-Malaysia and NiV-Bangladesh isolates in hamster model. The variation observed in the genome of the Indian isolate at the amino acid levels should be explored further for any functional significance.
MeSH term(s)	Cricetinae ; Animals ; Humans ; Nipah Virus/genetics ; Virulence ; Henipavirus Infections/epidemiology ; Henipavirus Infections/pathology ; Mesocricetus ; Genomics ; Gene Expression Profiling
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2657572-3
ISSN	2150-5608 ; 2150-5594
ISSN (online)	2150-5608
ISSN	2150-5594
DOI	10.1080/21505594.2023.2224642
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Electron microscopy imaging of SARS-CoV-2 at different temperatures.

Prasad, Sharda / Meena, Virendra Kumar / Yadav, Pragya D / Sarkale, Prasad / Baradkar, Shreekant / Cherian, Sarah / Abraham, Priya / Basu, Atanu

The Indian journal of medical research

2021 Volume 153, Issue 5&6, Page(s) 692–695

MeSH term(s)	COVID-19 ; Humans ; Microscopy, Electron ; Microscopy, Electron, Transmission ; SARS-CoV-2 ; Temperature
Language	English
Publishing date	2021-06-18
Publishing country	India
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
DOI	10.4103/ijmr.IJMR_4264_20
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Article: Development of single step RT-PCR for detection of Kyasanur forest disease virus from clinical samples.

Chaubal, Gouri / Sarkale, Prasad / Kore, Pravin / Yadav, Pragya

Heliyon

2018 Volume 4, Issue 2, Page(s) e00549

Abstract: Background: Kyasanur Forest Disease (KFD), a tick borne flavivirus, which was earlier endemic to Karnataka state, India, has been confirmed and detected from neighboring states of Tamil Nadu, Maharashtra, Goa and Kerala states in India. Increased human ... ...

Abstract	Background: Kyasanur Forest Disease (KFD), a tick borne flavivirus, which was earlier endemic to Karnataka state, India, has been confirmed and detected from neighboring states of Tamil Nadu, Maharashtra, Goa and Kerala states in India. Increased human and vector surveillance therefore becomes essential for the identification of KFD affected regions and control of further spread of the disease. Currently, available KFD detection assays include realtime RT-PCR and nested RT-PCR assays. Here we describe the development of a sensitive single step RT-PCR assay for the detection of KFD viral RNA. This can be easily used in any BSL-2 laboratory for screening of KFD suspected cases or for differential diagnosis of viral hemorrhagic fever panel. Method: Three primer sets were designed and checked for sensitivity using known dilutions of KFD viral RNA (Ranging from 10 Result: No false positive or false negative results were seen for human, monkey or tick samples. The assay was specific for KFD and could detect upto 100 copies of KFD viral RNA. Discussion and conclusion: The previously published sensitive real time RT-PCR assay requires higher cost in terms of reagents and machine setup and technical expertise has been the primary reason for development of this assay. A single step RT-PCR is relatively easy to perform and more cost effective than real time RT-PCR in smaller setups in the absence of Biosafety Level-3 facility. This study reports the development and optimization of single step RT-PCR assay which is more sensitive and less time-consuming than nested RT-PCR and cost effective for rapid diagnosis of KFD viral RNA.
Language	English
Publishing date	2018-03-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2018.e00549
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Article: Comparative pathogenicity of BA.2.12, BA.5.2 and XBB.1 with the Delta variant in Syrian hamsters.

Mohandas, Sreelekshmy / Shete, Anita / Kumar, Abhimanyu / Wakchaure, Kundan / Rai, Vishal / Mote, Chandrasekhar / Dighe, Hitesh / Sarkale, Prasad / Gawande, Pranita / Yemul, Jyoti / Suryawanshi, Annasaheb / Joshi, Yash / Yadav, Pragya D

Frontiers in microbiology

2023 Volume 14, Page(s) 1183763

Abstract: Omicron variant is evolving into numerous sub variants with time and the information on the characteristics of these newly evolving variants are scant. Here we performed a pathogenicity evaluation of Omicron sub variants BA.2.12, BA.5.2 and XBB.1 against ...

Abstract	Omicron variant is evolving into numerous sub variants with time and the information on the characteristics of these newly evolving variants are scant. Here we performed a pathogenicity evaluation of Omicron sub variants BA.2.12, BA.5.2 and XBB.1 against the Delta variant in 6-8-week-old Syrian hamster model. Body weight change, viral load in respiratory organs by real time RT-PCR/titration, cytokine mRNA quantification and histopathological evaluation of the lungs were performed. The intranasal infection of the BA.2.12, BA.5.2 and XBB.1 variants in hamster model resulted in body weight loss/reduced weight gain, inflammatory cytokine response and interstitial pneumonia with lesser severity compared to the Delta variant infection. Among the variants studied, BA.2.12 and XBB.1 showed lesser viral shedding through the upper respiratory tract, whereas the BA.5.2 showed comparable viral RNA shedding as that of the Delta variant. The study shows that the Omicron BA.2 sub variants may show difference in disease severity and transmissibility amongst each other whereas the overall disease severity of the Omicron sub variants studied were less compared to the Delta variant. The evolving Omicron sub variants and recombinants should be monitored for their properties.
Language	English
Publishing date	2023-06-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1183763
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Article ; Online: Isolation and characterization of the new SARS-CoV-2 variant in travellers from the United Kingdom to India: VUI-202012/01 of the B.1.1.7 lineage.

Yadav, Pragya D / Nyayanit, Dimpal A / Sahay, Rima R / Sarkale, Prasad / Pethani, Jayshri / Patil, Savita / Baradkar, Shreekant / Potdar, Varsha / Patil, Deepak Y

Journal of travel medicine

2021 Volume 28, Issue 2

MeSH term(s)	Adult ; COVID-19/genetics ; COVID-19 Testing/methods ; Humans ; India ; Middle Aged ; SARS-CoV-2/isolation & purification ; Travel ; United Kingdom
Language	English
Publishing date	2021-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1212504-0
ISSN	1708-8305 ; 1195-1982
ISSN (online)	1708-8305
ISSN	1195-1982
DOI	10.1093/jtm/taab009
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Article ; Online: Comparison of SARS-CoV-2 Variants of Concern 202012/01 (U.K. Variant) and D614G Variant Transmission by Different Routes in Syrian Hamsters.

Mohandas, Sreelekshmy / Yadav, Pragya D / Nyayanit, Dimpal / Shete, Anita / Sarkale, Prasad / Hundekar, Supriya / Kumar, Sanjay / Lole, Kavita

Vector borne and zoonotic diseases (Larchmont, N.Y.)

2021 Volume 21, Issue 8, Page(s) 638–641

Abstract: Introduction: ...

Abstract	Introduction:
MeSH term(s)	Aerosols ; Animals ; COVID-19/transmission ; COVID-19/virology ; Cricetinae ; Disease Models, Animal ; Fomites/virology ; HIV Antibodies/analysis ; Immunoglobulin G/analysis ; Lung ; Male ; Mesocricetus ; Nasal Cavity/virology ; Pharynx/virology ; RNA, Viral/analysis ; Rectum/virology ; SARS-CoV-2/classification ; SARS-CoV-2/immunology ; SARS-CoV-2/physiology ; United Kingdom ; Viral Load ; Weight Loss
Chemical Substances	Aerosols ; HIV Antibodies ; Immunoglobulin G ; RNA, Viral
Language	English
Publishing date	2021-07-01
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2047199-3
ISSN	1557-7759 ; 1530-3667
ISSN (online)	1557-7759
ISSN	1530-3667
DOI	10.1089/vbz.2021.0032
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Article ; Online: Development of single step RT-PCR for detection of Kyasanur forest disease virus from clinical samples

Gouri Chaubal / Prasad Sarkale / Pravin Kore / Pragya Yadav

Heliyon, Vol 4, Iss

2018 Volume 2

Abstract	Background: Kyasanur Forest Disease (KFD), a tick borne flavivirus, which was earlier endemic to Karnataka state, India, has been confirmed and detected from neighboring states of Tamil Nadu, Maharashtra, Goa and Kerala states in India. Increased human and vector surveillance therefore becomes essential for the identification of KFD affected regions and control of further spread of the disease. Currently, available KFD detection assays include realtime RT-PCR and nested RT-PCR assays. Here we describe the development of a sensitive single step RT-PCR assay for the detection of KFD viral RNA. This can be easily used in any BSL-2 laboratory for screening of KFD suspected cases or for differential diagnosis of viral hemorrhagic fever panel. Method: Three primer sets were designed and checked for sensitivity using known dilutions of KFD viral RNA (Ranging from 106 copies to 10 copies). The primer set (2) was found to be most sensitive was selected and tested for specificity for Kyasanur forest disease virus (KFDV) by testing against zika, dengue, chikungunya, crimean congo hemorrhagic fever (CCHF), yellow fever, japanese encephalitis (JE) and west nile viruses. A total of 104 samples (human, monkey and tick positive and negative samples) were tested using this assay. Result: No false positive or false negative results were seen for human, monkey or tick samples. The assay was specific for KFD and could detect upto 100 copies of KFD viral RNA. Discussion and conclusion: The previously published sensitive real time RT-PCR assay requires higher cost in terms of reagents and machine setup and technical expertise has been the primary reason for development of this assay. A single step RT-PCR is relatively easy to perform and more cost effective than real time RT-PCR in smaller setups in the absence of Biosafety Level-3 facility. This study reports the development and optimization of single step RT-PCR assay which is more sensitive and less time-consuming than nested RT-PCR and cost effective for rapid diagnosis of KFD ...
Keywords	Infectious disease ; Molecular biology ; Virology ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	630
Language	English
Publishing date	2018-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Prolonged Shedding of SARS-CoV-2 in Feces of COVID-19 Positive Patients: Trends in Genomic Variation in First and Second Wave.

Lavania, Mallika / Joshi, Madhuri S / Ranshing, Sujata S / Potdar, Varsha A / Shinde, Manohar / Chavan, Nutan / Jadhav, Santosh M / Sarkale, Prasad / Mohandas, Sreelekshmy / Sawant, Pradeep M / Tikute, Sanjaykumar / Padbidri, Vikram / Patwardhan, Sampada / Kate, Rohan

Frontiers in medicine

2022 Volume 9, Page(s) 835168

Abstract: The main route of the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are through respiratory pathways and close contact of human-to-human. While information about other modes of transmission is comparatively less, some ... ...

Abstract	The main route of the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are through respiratory pathways and close contact of human-to-human. While information about other modes of transmission is comparatively less, some published literature supporting the likelihood of a fecal-oral mode of transmission has been accumulating. The diagnosis of SARS-COV-2 infected cases is based on the real-time reverse transcription-PCR (RT-PCR). The fecal excretion of SARS-COV-2 has been reported frequently, however, the role of fecal viral load with the severity of disease is not yet clear. Our study focused on the investigation of SARS-CoV-2 shedding in the fecal samples of patients with coronavirus disease 2019 (COVID-19). A total of 280 RT-PCR-positive patients were enrolled, among them 15.4% had gastrointestinal (GI) symptoms. It was shown that 62% of the patients were positive for SARS-CoV-2 RNA in fecal specimens. This positivity was not related to the presence of GI symptoms and the severity of disease. The next generation sequencing [NGS] of SARS-CoV-2 from fecal samples of patients was performed to analyze mutational variations. Findings from this study not only emphasized the potential presence of SARS-CoV-2 in feces, but also its continuing mutational changes and its possible role in fecal-oral transmission.
Language	English
Publishing date	2022-03-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2022.835168
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Article: Differential Cell Line Susceptibility to the SARS-CoV-2 Omicron BA.1.1 Variant of Concern.

Dighe, Hitesh / Sarkale, Prasad / Patil, Deepak Y / Mohandas, Sreelekshmy / Shete, Anita M / Sahay, Rima R / Lakra, Rajen / Patil, Savita / Majumdar, Triparna / Gawande, Pranita / Yemul, Jyoti / Vedpathak, Pratiksha / Yadav, Pragya D

Vaccines

2022 Volume 10, Issue 11

Abstract: The unique mutations of the SARS-CoV-2 Omicron variant are associated with increased transmissibility, immune escape, increased binding affinity to ACE-2, and increased viral load. Omicron exhibited a shift in tropism infecting the upper respiratory ... ...

Abstract	The unique mutations of the SARS-CoV-2 Omicron variant are associated with increased transmissibility, immune escape, increased binding affinity to ACE-2, and increased viral load. Omicron exhibited a shift in tropism infecting the upper respiratory tract compared to other variants of concern which have tropism for the lower respiratory tract. The tropism of omicron variants in cell lines of different hosts and tissue origins still remains unclear. Considering this, we assessed the susceptibility of different cell lines to the SARS-CoV-2 omicron BA.1.1 variant and permissiveness among different cell lines for omicron replication. Susceptibility and permissiveness of a total of eleven cell lines, including six animal cell lines and five human cell lines for omicron BA.1.1 infection, were evaluated by infecting individual cell lines with omicron BA.1.1 isolate at a 0.1 multiplicity of infection. Virus replication was assessed by observation of cytopathic effects followed by viral load determination by real-time PCR assay and virus infectivity determination by TCID50 assay. The characteristic cytopathic effect, increased viral load, and productive omicron replication was detected in Vero CCL-81, Vero E6, Vero/hSLAM, MA-104, and Calu-3 cells. Although LLC MK-2 cells showed an increased TCID50 titer at the second infection, the viral load did not show much difference in both infections. Caco-2 cells did not show evident CPE, but they supported omicron replication at a low level. A549, RD, MRC-5, and BHK-21 cells supported omicron BA.1.1 replication without the CPE. This is the first study on the comparison of susceptibility of different cell lines to Omicron variant BA.1.1, which might be useful for future studies on emerging SARS-CoV-2 variants.
Language	English
Publishing date	2022-11-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10111962
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Article: Inactivation of SARS-CoV-2 by gamma irradiation.

Jain, Rajlaxmi / Sarkale, Prasad / Mali, Deepak / Shete, Anita M / Patil, Deepak Y / Majumdar, Triparna / Suryawanshi, Annasaheb / Patil, Savita / Mohandas, Sreelekshmy / Yadav, Pragya D

The Indian journal of medical research

2021 Volume 153, Issue 1 & 2, Page(s) 196–198

MeSH term(s)	COVID-19 ; Coronavirus ; Coronavirus Infections ; Hot Temperature ; Humans ; SARS-CoV-2
Language	English
Publishing date	2021-04-09
Publishing country	India
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
DOI	10.4103/ijmr.IJMR_2789_20
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