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Article ; Online: COVID-19: a boon or a bane for the microbiologists.

Ravi, Vasanthapuram / Chakrabarti, Arunaloke / Wattal, Chand / Raveendran, Reena

2022 Volume 40, Issue 1, Page(s) 7–11

Abstract: Background: In the situation where COVID-19 pandemic has placed unprecedented demands and pressure on the health care system, we wanted to analyze how the medical microbiologists of our country were affected. Was it actually an opportunity to showcase ... ...

Abstract	Background: In the situation where COVID-19 pandemic has placed unprecedented demands and pressure on the health care system, we wanted to analyze how the medical microbiologists of our country were affected. Was it actually an opportunity to showcase the specialty or was it a doom? A debate was organized as a key session in the national e-conference of the Indian Association of Medical Microbiologists, held on 10 December 2020. Objectives: The objective of the debate was to examine and analyze the various positive as well as negative impacts of COVID-19 on the discipline of the medical microbiology of our country. Content: Before the debate a voting session was conducted to assess the opinion of the audience followed by a very interesting debate where both the speakers presented their view points. The points in favor of the discipline were, mainly up-gradation of the specialty of microbiology in terms of learning, skill development, infrastructure, networking & research opportunities related to COVID-19. While the main points against were, nerve wracking work load without much acknowledgement, performance pressure from hospital administration to maintain rapid turnaround time, and a forceful neglect of all other infectious diseases like tuberculosis and antimicrobial resistance which were the key battle fields of the medical microbiologists. Postgraduate & even undergraduate training programs got completely derailed to their disadvantage. By the end of the debate, it was concluded that COVID-19 was neither a boon nor a bane to the microbiologists. A balanced approach to the problem in hand is required without ignoring the pre-existing infectious diseases in our country. The post debate voting swayed the audience considerably for it to be a bane & the faculty debating for boon had a huge margin to begin with but finally won with a whisker indicating the intensity of the debate.
MeSH term(s)	COVID-19 ; Delivery of Health Care ; Humans ; Medicine ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2022-01-19
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1038798-5
ISSN	1998-3646 ; 0255-0857
ISSN (online)	1998-3646
ISSN	0255-0857
DOI	10.1016/j.ijmmb.2021.12.020
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Article ; Online: Prohibitin 1/2 mediates Dengue-3 entry into human neuroblastoma (SH-SY5Y) and microglia (CHME-3) cells

Amita Sharma / Ravi Vasanthapuram / Manjunatha M Venkataswamy / Anita Desai

Journal of Biomedical Science, Vol 27, Iss 1, Pp 1-

2020 Volume 17

Abstract: Abstract Background Very few studies have identified receptor molecules for dengue virus (DENV) on neural cells. This study was designed to identify putative receptor/(s) involved in entry of DENV-3 in human neural cells of various lineages; neuronal-SH- ... ...

Abstract	Abstract Background Very few studies have identified receptor molecules for dengue virus (DENV) on neural cells. This study was designed to identify putative receptor/(s) involved in entry of DENV-3 in human neural cells of various lineages; neuronal-SH-SY5Y, astroglial-U-87 MG and microglial-CHME-3 cells. Result Virus overlay protein binding assay, LC-MS/MS and SEQUEST identified prohibitin1/2 (PHB1/2) as interacting proteins on SH-SY5Y, CHME-3, and U-87 MG cells. Infection inhibition and siRNA assays confirmed the role of PHB1/2 in the entry of DENV-3 into SH-SY5Y and CHME-3 cells but not in U-87 MG cells. Indirect immunofluorescence and flow-cytometry demonstrated the presence of PHB1/2 on the surface of SH-SY5Y and CHME-3 cells. Co-immunoprecipitation and Western blot, as well as double labelling, reconfirmed the interaction between PHB1/2 and DENV-3 EDIII protein. Conclusion These observations together for the first time indicate that PHB1/2 may serve as a putative receptor for DENV-3 in SH-SY5Y and CHME-3 cells. The study provided insights into DENV-3 and neural cell interactions.
Keywords	Dengue virus serotype-3 ; Neural cells ; SH-SY5Y ; CHME-3 cells ; Receptor/ interacting proteins ; Prohibitin ; Medicine ; R
Subject code	570
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2.

Gupta, Swati / Kumar, Amit / Gupta, Nivedita / Bharti, Deepak R / Aggarwal, Neeraj / Ravi, Vasanthapuram

BMC genomics

2022 Volume 23, Issue 1, Page(s) 755

Abstract: Background: Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay ...

Abstract	Background: Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India. Results: We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC. Conclusion: Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Pandemics ; RNA, Viral/genetics ; RNA, Viral/analysis ; Sensitivity and Specificity ; COVID-19/diagnosis ; COVID-19/epidemiology
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-11-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-022-08999-3
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Article ; Online: Infection of human microglial cell line CHME-3 to study neuropathogenesis of chikungunya virus.

Qadri, Syed Wasifa / Kumar, Narendra / Santhoshkumar, Rashmi / Desai, Anita / Ravi, Vasanthapuram / Venkataswamy, Manjunatha M

Journal of neurovirology

2022 Volume 28, Issue 3, Page(s) 374–382

Abstract: Chikungunya virus (CHIKV) infection, generally characterised by fever, rash and debilitating polyarthralgia, and/or arthritis, also causes complications of the central nervous system, including encephalitis. However, the role of microglial cells in the ... ...

Abstract	Chikungunya virus (CHIKV) infection, generally characterised by fever, rash and debilitating polyarthralgia, and/or arthritis, also causes complications of the central nervous system, including encephalitis. However, the role of microglial cells in the neuropathogenesis of CHIKV is poorly understood. The current study characterised the progression of CHIKV infection in the human microglial cell line CHME-3. The susceptibility of these cells to CHIKV and the viral replication kinetics were assessed during the early and late phases of infection. The cell viability was determined using the cell viability assay. Ultrastructural changes in CHIKV infected CHME-3 cells were assessed using transmission electron microscopy. The results showed that CHME-3 cells are susceptible to CHIKV infection and support viral replication with no significant loss in cell viability until 72 h post infection. Ultrastructural studies revealed the formation of cytopathic vacuoles-I (CPV-I) in the early stages and CPV-II in later stages with several virions organized along the membrane of CPV-II. Profuse vacuolation was observed in the later stages of infection. Abnormal giant mitochondria with altered cristae were observed in infected cells with an electron-dense matrix. The study establishes CHME-3 cells as a potential model for investigating the role of human microglial cells in neuropathogenicity of CHIKV.
MeSH term(s)	Cell Line ; Chikungunya Fever ; Chikungunya virus/physiology ; Humans ; Microglia/pathology ; Virus Replication/physiology
Language	English
Publishing date	2022-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1283265-0
ISSN	1538-2443 ; 1355-0284
ISSN (online)	1538-2443
ISSN	1355-0284
DOI	10.1007/s13365-022-01070-7
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Article ; Online: Acid and Alkaline Phosphatases Specific activities and Expression as Biomarkers in Brain Tumor Grading and Correlation of Anaplastic Oligodendroglioma G-III to Meningiomas G-I among Brain Tumors and their primary culture.

Muddobalaiah, Prabha / Ravi, Vasanthapuram / Thammanna, Chethan Chandagalu / Sagar, Bhadravathi Kenchappa Chandrasekhar / Swamy, Narayana Swamy Ramachandra

Journal of chemical neuroanatomy

2022 Volume 125, Page(s) 102140

Abstract: Background: Acid Phosphatase (ACP) and Alkaline Phosphatases (ALP) are hydrolases that remove phosphate groups from protein and nucleic acid respectively for regulation of cell function from ACP as lysosomal defence function and ALP membrane-bound as a ... ...

Abstract	Background: Acid Phosphatase (ACP) and Alkaline Phosphatases (ALP) are hydrolases that remove phosphate groups from protein and nucleic acid respectively for regulation of cell function from ACP as lysosomal defence function and ALP membrane-bound as a barrier of the cell. The ACP and ALP-specific activities of Meningiomas (n = 75) and gliomas (n = 81) were compared among brain tumors, normal brain, and derived primary cell culture. Methods: Total Protein and Phosphatases assays estimated by Spectrophotometer and Native PAGE Gel Electrophoresis. Brain tumor and primary explant lysosome studies were performed with an electron microscope. Results: Average ACP specific activity exhibited 9.32617 ± 4.1144 for meningiomas (n = 55) and 5.91 ± 5.8305 for gliomas (n = 60) respectively as compared to normal brain 7.104 ± 1.33 (n = 120) nm/min/mg of protein. Average ALP exhibited 37.1862 ± 39.91 (n = 36) for meningiomas and 5.91 ± 5.83 (n = 60) for gliomas respectively as compared to normal brain (n = 117) 2.463 ± 1.01 nm/min/mg of protein. ACP and ALP exhibited higher activities for meningiomas but not for gliomas as compared to normal brain, in contrast, both expressed more activities in the majority of glioma cell lines and lower in meningioma cell lines. Interestingly gliomas exhibited similar average specific activities for ACP and ALP. While GBM IV exhibits lower ALP activities due to cell migration and higher ACP activity correlate too many storage lysosomes from Electron microscopic observation as compared to meningiomas. Conclusions: Higher ALP activities can be surrogate markers from meningiomas G-I, G-II to G-III respectively. However meningiomas G-III are similar to gliomas excluding Anaplastic Oligodendroglioma G- III which is similar to Meningiomas G-I even for cells growth patterns. Therefore, an ALP level in meningiomas indicates complementary diagnosis as antibody-ALP conjugates with anticancer drugs for efficiency in targeting brain tumor reduction.
MeSH term(s)	Humans ; Meningioma/metabolism ; Meningioma/pathology ; Oligodendroglioma/pathology ; Neoplasm Grading ; Brain Neoplasms/metabolism ; Glioma/metabolism ; Glioma/pathology ; Brain/metabolism ; Biomarkers, Tumor ; Meningeal Neoplasms/metabolism ; Meningeal Neoplasms/pathology ; Phosphoric Monoester Hydrolases/metabolism
Chemical Substances	Biomarkers, Tumor ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2022-07-30
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639443-7
ISSN	1873-6300 ; 0891-0618
ISSN (online)	1873-6300
ISSN	0891-0618
DOI	10.1016/j.jchemneu.2022.102140
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Article ; Online: Neurological manifestations of scrub typhus infection

Ali M Alam / Conor S Gillespie / Jack Goodall / Tina Damodar / Lance Turtle / Ravi Vasanthapuram / Tom Solomon / Benedict D Michael

PLoS Neglected Tropical Diseases, Vol 16, Iss 11, p e

A systematic review and meta-analysis of clinical features and case fatality.

2022 Volume 0010952

Abstract: Background Scrub typhus has become a leading cause of central nervous system (CNS) infection in endemic regions. As a treatable condition, prompt recognition is vital. However, few studies have focused on describing the symptomology and outcomes of ... ...

Abstract	Background Scrub typhus has become a leading cause of central nervous system (CNS) infection in endemic regions. As a treatable condition, prompt recognition is vital. However, few studies have focused on describing the symptomology and outcomes of neurological scrub typhus infection. We conducted a systematic review and meta-analysis to report the clinical features and case fatality ratio (CFR) in patients with CNS scrub typhus infection. Methods A search and analysis plan was published in PROSPERO [ID 328732]. A systematic search of PubMed and Scopus was performed and studies describing patients with CNS manifestations of proven scrub typhus infection were included. The outcomes studied were weighted pooled prevalence (WPP) of clinical features during illness and weighted CFR. Results Nineteen studies with 1,221 (656 adults and 565 paediatric) patients were included. The most common clinical features in CNS scrub typhus were those consistent with non-specific acute encephalitis syndromes (AES), such as fever (WPP 100.0% [99.5%-100.0%, I2 = 47.8%]), altered sensorium (67.4% [54.9-78.8%, I2 = 93.3%]), headache (65.0% [51.5-77.6%, I2 = 95.1%]) and neck stiffness 56.6% (29.4-80.4%, I2 = 96.3%). Classical features of scrub typhus were infrequently identified; an eschar was found in only 20.8% (9.8%-34.3%, I2 = 95.4%) and lymphadenopathy in 24.1% (95% CI 11.8% - 38.9%, I2 = 87.8%). The pooled CFR (95% CI) was 3.6% (1.5%- 6.4%, I2 = 67.3%). Paediatric cohorts had a CFR of 6.1% (1.9-12.1%, I2 = 77%) whilst adult cohorts reported 2.6% (0.7-5.3%, I2 = 43%). Conclusion Our meta-analyses illustrate that 3.6% of patients with CNS manifestations of scrub typhus die. Clinicians should have a high index of suspicion for scrub typhus in patients presenting with AES in endemic regions and consider starting empiric treatment whilst awaiting results of investigations, even in the absence of classical signs such as an eschar or lymphadenopathy.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Subject code	610
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka [version 2; peer review

Chitra Pattabiraman / Darshan Sreenivas / Anson K. George / Nakka Vijay Kiran Reddy / Pramada Prasad / Risha Rasheed / Anita Desai / Ravi Vasanthapuram

Wellcome Open Research, Vol

2 approved]

2022 Volume 6

Abstract: Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and ... ...

Abstract	Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.1.36: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%,. B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences, 37 of these were in the B.1.36 lineage (37/65, 56.92%) Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.
Keywords	SARS-CoV-2 ; variants ; Variants of Concern ; VOC ; COVID-19 ; COVID-19 India ; eng ; Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Wellcome
Document type	Article ; Online
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Article ; Online: Correction: Contact tracing of COVID-19 in Karnataka, India: Superspreading and determinants of infectiousness and symptomatic infection.

Gupta, Mohak / Parameswaran, Giridara G / Sra, Manraj S / Mohanta, Rishika / Patel, Devarsh / Gupta, Amulya / Bansal, Bhavik / Jain, Vardhmaan / Mazumder, Archisman / Arora, Mehak / Aggarwal, Nishant / Bhatnagar, Tarun / Akhtar, Jawaid / Pandey, Pankaj / Ravi, Vasanthapuram / Babu, Giridhara R

PloS one

2024 Volume 19, Issue 1, Page(s) e0298090

Abstract: This corrects the article DOI: 10.1371/journal.pone.0270789.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pone.0270789.].
Language	English
Publishing date	2024-01-26
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0298090
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Article ; Online: Molecular Mimicry between Chikungunya Virus and Host Components

Vijayalakshmi Reddy / Anita Desai / Shankar Susarla Krishna / Ravi Vasanthapuram

PLoS Neglected Tropical Diseases, Vol 11, Iss 1, p e

A Possible Mechanism for the Arthritic Manifestations.

2017 Volume 0005238

Abstract: BACKGROUND:Chikungunya virus (CHIKV), a reemerging pathogen causes a self limited illness characterized by fever, headache, myalgia and arthralgia. However, 10-20% affected individuals develop persistent arthralgia which contributes to considerable ... ...

Abstract	BACKGROUND:Chikungunya virus (CHIKV), a reemerging pathogen causes a self limited illness characterized by fever, headache, myalgia and arthralgia. However, 10-20% affected individuals develop persistent arthralgia which contributes to considerable morbidity. The exact molecular mechanisms underlying these manifestations are not well understood. The present study investigated the possible occurrence of molecular mimicry between CHIKV E1 glycoprotein and host human components. METHODOLOGY:Bioinformatic tools were used to identify peptides of CHIKV E1 exhibiting similarity to host components. Two peptides (A&B) were identified using several bioinformatic tools, synthesised and used to validate the results obtained in silico. An ELISA was designed to assess the immunoreactivity of serum samples from CHIKV patients to these peptides. Further, experiments were conducted in a C57BL/6J experimental mouse model to investigate if peptide A and peptide B were indeed capable of inducing pathology. FINDINGS:The serum samples showed reactivity of varying degrees, indicating that these peptides are indeed being recognized by the host immune system during CHIKV infection. Further, these peptides when injected into C57BL/6J mice were able to induce significant inflammation in the muscles of C57BL/6J mice, similar to that observed in animals that were injected with CHIKV alone. Additionally, animals that were primed initially with CHIKV followed by a subsequent injection of the CHIKV peptides exhibited enhanced inflammatory pathology in the skeletal muscles as compared to animals that were injected with peptides or virus alone. Collectively these observations validate the hypothesis that molecular mimicry between CHIKV E1 protein and host proteins does contribute to pathology in CHIKV infection.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Subject code	630
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: An ultrastructural and genomic study on the SARS-CoV-2 variant B.1.210 circulating during the first wave of COVID-19 pandemic in India.

Kumar, Narendra / Santhoshkumar, Rashmi / Prasad, Pramada / George, Anson K / Aiyar, Jayashree / Joshi, Saurabh / Narayanappa, Gayathri / Desai, Anita S / Ravi, Vasanthapuram / Venkataswamy, Manjunatha M

Indian journal of medical microbiology

2023 Volume 41, Page(s) 45–52

Abstract: Purpose: The study aims to isolate and understand cytopathogenesis, ultrastructure, genomic characteristics and phylogenetic analysis of SARS-CoV-2 virus of B.1.210 lineage, that circulated in India during first wave of the pandemic.: Methods: ... ...

Abstract	Purpose: The study aims to isolate and understand cytopathogenesis, ultrastructure, genomic characteristics and phylogenetic analysis of SARS-CoV-2 virus of B.1.210 lineage, that circulated in India during first wave of the pandemic. Methods: Clinical specimen from an interstate traveller from Maharashtra to Karnataka, in May 2020, who was positive by RT PCR for SARS-CoV-2 infection was subjected to virus isolation and Whole Genome Sequencing. Vero cells were used to study cytopathogenesis and ultrastructural features by Transmission Electron Microscopy (TEM). Phylogenetic analysis of the whole genome sequences of several SARS-CoV-2 variants downloaded from GISAID was performed in comparison with the B.1.210 variant identified in this study. Results: The virus was isolated in Vero cells and identified by immunofluorescence assay and RT PCR. The growth kinetics in infected Vero cells revealed a peak viral titre at 24 h post-infection. Ultrastructural studies revealed distinct morphological changes with accumulation of membrane-bound vesicles containing pleomorphic virions in the cytoplasm, with single or multiple intranuclear filamentous inclusions and dilated rough endoplasmic reticulum with viral particles. Whole genome sequence of the clinical specimen as well as the isolated virus revealed the virus to be of lineage B.1.210 with the D614G mutation in the spike protein. Phylogenetic analysis of the whole genome sequence in comparison with other variants reported globally revealed that the isolated SARS-CoV-2 virus of lineage B.1.210 is closely related to the original Wuhan virus reference sequence. Conclusions: The SARS-CoV-2 variant B.1.210 virus isolated here showed ultrastructural features and cytopathogenesis similar to that of the virus reported during early phase of pandemic. Phylogenetic analysis showed that the isolated virus is closely related to the original Wuhan virus, thereby suggesting that the SARS-CoV-2 lineage B.1.210 that was circulating in India during the early phase of pandemic is likely to have evolved from the original Wuhan strain.
MeSH term(s)	Humans ; Chlorocebus aethiops ; Animals ; SARS-CoV-2 ; COVID-19 ; Pandemics ; Phylogeny ; Vero Cells ; India ; Genomics
Language	English
Publishing date	2023-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	1038798-5
ISSN	1998-3646 ; 0255-0857
ISSN (online)	1998-3646
ISSN	0255-0857
DOI	10.1016/j.ijmmb.2022.12.009
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