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Article ; Online: Langmuir monolayer of lysozyme at variable subphase pH conditions: a comprehensive study on structure, morphology and hysteresis behaviour.

Nath, Himadri / Sarmah, Raktim J / Kundu, Sarathi

RSC advances

2023 Volume 13, Issue 33, Page(s) 22789–22799

Abstract: Formation of a pure Langmuir monolayer of lysozyme at the air-water interface and its investigation by means of a surface pressure ( ...

Abstract	Formation of a pure Langmuir monolayer of lysozyme at the air-water interface and its investigation by means of a surface pressure (
Language	English
Publishing date	2023-07-27
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d3ra03710j
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Article ; Online: Regarding: Masyeni S, Santoso MS, Widyaningsih PD, Wedha Asmara DG, Nainu F, Harapan H, et al. Serological cross-reaction and co-infection of dengue and COVID-19 in Asia: Experience from Indonesia. Int J Infect Dis 2020;102:152-4. https://doi.org/10.1016/j.ijid.2020.10.043.

Biswas, Subhajit / Sukla, Soumi / Roy, Subrata / Nath, Himadri / Mallick, Abinash

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 104, Page(s) 737–738

MeSH term(s)	Asia ; COVID-19 ; Coinfection ; Dengue/epidemiology ; Humans ; Indonesia/epidemiology ; SARS-CoV-2
Language	English
Publishing date	2021-02-05
Publishing country	Canada
Document type	Letter ; Comment
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.01.063
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Article ; Online: Non-structural protein 1 (NS1) variants from dengue virus clinical samples revealed mutations that influence NS1 production and secretion.

Ghosh, Anisa / Sukla, Soumi / Nath, Himadri / Saha, Rajdeep / De, Abhishek / Biswas, Subhajit

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2022 Volume 41, Issue 5, Page(s) 803–814

Abstract: Dengue diagnosis primarily relies on NS1 ELISA and serological (IgG/IgM) tests. There are reports of low and variable sensitivity of the widely used NS1 ELISA tests. Poor sensitivity has been attributed to patient's infection status, prevalent serotypes, ...

Abstract	Dengue diagnosis primarily relies on NS1 ELISA and serological (IgG/IgM) tests. There are reports of low and variable sensitivity of the widely used NS1 ELISA tests. Poor sensitivity has been attributed to patient's infection status, prevalent serotypes, and the geographical origin of the samples. We investigated whether NS1 mutations directly have any impact on NS1 ELISA-based dengue virus (DENV) detection in clinical samples. Fifty-eight serum samples were collected from dengue-endemic area during 2015-2017 and tested with three commonly used NS1 ELISA kits. The samples were subjected to diagnostic RT-PCR and sequencing of structural gene(s). Sequencing of NS1 gene revealed amino acid changes which were transferred to respective wild type NS1 backbone to determine their effects on NS1 production and secretion in Huh-7, Vero, and A549 cells. Eighty-seven percent samples were virus RNA-positive but 65% of these were NS1 ELISA-positive. NS1-gene mutations like Val236➔Ala (DENV2) or Trp68➔stop codon in DENV3 were associated with decreased NS1 production and secretion. These mutations were originally identified in NS1 ELISA-negative clinical isolates. All DENV1 and > 80% DENV2 were NS1 ELISA-positive. The three NS1 ELISA could not detect recently circulating DENV3 single infections despite being RNA-positive. Among serotypes 1-3, wild-type NS1 production was highest for DENV1 and lowest for DENV3 in all cell lines tested. Mutations in circulating DENV directly correlated with NS1 production and secretion and, hence, ELISA-based NS1 detection. Further studies to define more NS1 mutations in clinical samples are needed to optimize ELISA kits for more sensitive dengue diagnosis.
MeSH term(s)	Antibodies, Viral ; Dengue ; Dengue Virus ; Enzyme-Linked Immunosorbent Assay ; Humans ; Mutation ; RNA, Viral ; Sensitivity and Specificity ; Viral Nonstructural Proteins
Chemical Substances	Antibodies, Viral ; RNA, Viral ; Viral Nonstructural Proteins
Language	English
Publishing date	2022-04-09
Publishing country	Germany
Document type	Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-022-04441-4
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Article: Computational modelling supports that dengue virus envelope antibodies can bind to SARS-CoV-2 receptor binding sites: Is pre-exposure to dengue virus protective against COVID-19 severity?

Nath, Himadri / Mallick, Abinash / Roy, Subrata / Sukla, Soumi / Biswas, Subhajit

Computational and structural biotechnology journal

2020 Volume 19, Page(s) 459–466

Abstract: The world is going through the scourge of the COVID-19 pandemic since January 2020. However, the pandemic appears to be less severe in highly dengue endemic countries. In this connection, several studies reported that sero-diagnostic tests for dengue ... ...

Abstract	The world is going through the scourge of the COVID-19 pandemic since January 2020. However, the pandemic appears to be less severe in highly dengue endemic countries. In this connection, several studies reported that sero-diagnostic tests for dengue virus (DV) yielded considerable false-positive results for SARS-CoV-2 and
Language	English
Publishing date	2020-12-29
Publishing country	Netherlands
Document type	Journal Article
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.12.037
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Article ; Online: Archived dengue serum samples produced false-positive results in SARS-CoV-2 lateral flow-based rapid antibody tests.

Nath, Himadri / Mallick, Abinash / Roy, Subrata / Sukla, Soumi / Basu, Keya / De, Abhishek / Biswas, Subhajit

Journal of medical microbiology

2021 Volume 70, Issue 6

Abstract: Co-endemicity of SARS-CoV-2 and dengue virus (DV) infection is becoming a matter of serious concern as it has been already reported that antibodies (Ab) elicited by SARS-CoV-2 infection can produce false-positive results in dengue IgG and IgM rapid tests ...

Abstract	Co-endemicity of SARS-CoV-2 and dengue virus (DV) infection is becoming a matter of serious concern as it has been already reported that antibodies (Ab) elicited by SARS-CoV-2 infection can produce false-positive results in dengue IgG and IgM rapid tests and
MeSH term(s)	Adult ; Antibodies, Viral/blood ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Serological Testing/methods ; Cross Reactions ; Dengue/diagnosis ; Dengue/epidemiology ; False Positive Reactions ; Female ; Humans ; Immunoglobulin G/blood ; Immunoglobulin M/blood ; India/epidemiology ; Male ; Young Adult
Chemical Substances	Antibodies, Viral ; Immunoglobulin G ; Immunoglobulin M
Language	English
Publishing date	2021-06-10
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.0.001369
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Zs.A 634: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Detection of Leptomonas seymouri narna-like virus in serum samples of visceral leishmaniasis patients and its possible role in disease pathogenesis.

Sukla, Soumi / Nath, Himadri / Kamran, Mohd / Ejazi, Sarfaraz Ahmad / Ali, Nahid / Das, Pradeep / Ravichandiran, V / Roy, Syamal / Biswas, Subhajit

Scientific reports

2022 Volume 12, Issue 1, Page(s) 14436

Abstract: Kala-azar/Visceral Leishmaniasis (VL) caused by Leishmania donovani (LD) is often associated with Leptomonas seymouri (LS) co-infection in India. Leptomonas seymouri narna-like virus 1 (Lepsey NLV1) has been reported in multi-passaged laboratory isolates ...

Abstract	Kala-azar/Visceral Leishmaniasis (VL) caused by Leishmania donovani (LD) is often associated with Leptomonas seymouri (LS) co-infection in India. Leptomonas seymouri narna-like virus 1 (Lepsey NLV1) has been reported in multi-passaged laboratory isolates of VL samples which showed LD-LS co-infection. A pertinent question was whether this virus of LS is detectable in direct clinical samples. DNA from the serum of twenty-eight LD diagnosed patients was subjected to LD-specific and LS-specific PCR to reconfirm the presence of LD parasites and to detect LD-LS co-infections. RNA extracted from same samples was subjected to RT-PCR, qRT-PCR and sequencing using virus-specific primers to detect/identify and quantify the virus. The presence of the virus was confirmed in thirteen of eighteen (72%) recently collected VL and PKDL samples. Cytokine profiling showed significantly elevated IL-18 in only LD infected patients compared to the virus-positive LD and control samples. IL-18 is crucial for Th1 and macrophage activation which eventually clears the parasite. The Lepsey NLV1 interaction with the immune system results in reduced IL-18 which favors LD survival and increased parasitic burden. The study emphasizes the need to revisit LD pathogenesis in the light of the association and persistence of a protozoan virus in kala-azar and PKDL patients.
MeSH term(s)	Coinfection/diagnosis ; Humans ; India ; Interleukin-18 ; Leishmania donovani/genetics ; Leishmaniasis, Cutaneous ; Leishmaniasis, Visceral/parasitology ; Trypanosomatina/genetics
Chemical Substances	Interleukin-18
Language	English
Publishing date	2022-08-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-18526-9
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Article ; Online: COVID-19 serum can be cross-reactive and neutralizing against the dengue virus, as observed by the dengue virus neutralization test.

Nath, Himadri / Mallick, Abinash / Roy, Subrata / Kayal, Tathagata / Ranjan, Sumit / Sengupta, Susanta / Sukla, Soumi / Biswas, Subhajit

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2022 Volume 122, Page(s) 576–584

Abstract: Objectives: Observing the serological cross-reactivity between SARS-CoV-2 and dengue virus (DV), we aimed to elucidate its effect on dengue serodiagnosis and infectivity in a highly dengue-endemic city in India.: Methods: A total of 52 COVID-19 ( ... ...

Abstract	Objectives: Observing the serological cross-reactivity between SARS-CoV-2 and dengue virus (DV), we aimed to elucidate its effect on dengue serodiagnosis and infectivity in a highly dengue-endemic city in India. Methods: A total of 52 COVID-19 (reverse transcription-polymerase chain reaction [RT-PCR] positive) serum samples were tested in rapid lateral flow immunoassays and DV immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) to detect DV or SARS-CoV-2 IgG/immunoglobulin M. The COVID-19 antibody (Ab) positive samples were subjected to a virus neutralization test (Huh7 cells) using DV type 1 (DV1) clinical isolate. Results: Most (93%) of the SARS-CoV-2 Ab-positive serum samples cross-reacted with DV in rapid or ELISA tests. All were DV RNA and nonstructural protein 1 (NS1) antigen-negative. COVID-19 serum samples that were DV cross-reactive neutralized DV1. Of these, 57% had no evidence of DV pre-exposure (DV NS1 Ab-negative). The computational study also supported potential interactions between SARS-CoV-2 Ab and DV1. Conclusion: DV serodiagnosis will be inconclusive in areas co-endemic for both viruses. The COVID-19 pandemic appears to impart a protective response against DV in DV-endemic populations.
MeSH term(s)	Antibodies, Viral ; COVID-19/diagnosis ; Dengue ; Dengue Virus ; Enzyme-Linked Immunosorbent Assay ; Humans ; Immunoglobulin G ; Immunoglobulin M ; Neutralization Tests ; Pandemics ; SARS-CoV-2 ; Sensitivity and Specificity ; Serologic Tests
Chemical Substances	Antibodies, Viral ; Immunoglobulin G ; Immunoglobulin M
Language	English
Publishing date	2022-07-08
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2022.07.013
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Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: SARS-CoV-2 has observably higher propensity to accept uracil as nucleotide substitution: Prevalence of amino acid substitutions and their predicted functional implications in circulating SARS-CoV-2 in India up to July, 2020

Roy, Subrata / Nath, Himadri / Mallick, Abinash / Biswas, Subhajit

bioRxiv

Abstract: SARS-CoV-2 has emerged as pandemic all over the world since late 2019. In this study, we investigated the diversity of the virus in the context of SARS-CoV-2 spread in India. Full-length SARS-CoV-2 genome sequences of the circulating viruses from all ... ...

Abstract	SARS-CoV-2 has emerged as pandemic all over the world since late 2019. In this study, we investigated the diversity of the virus in the context of SARS-CoV-2 spread in India. Full-length SARS-CoV-2 genome sequences of the circulating viruses from all over India were collected from GISAID, an open data repository, until 25thJuly, 2020. We have focused on the non-synonymous changes across the genome that resulted in amino acid substitutions. Analysis of the genomic signatures of the non-synonymous mutations demonstrated a strong association between the time of sample collection and the accumulation of genetic diversity. Most of these isolates from India belonged to the A2a clade (63.4%) which has overcome the selective pressure and is spreading rapidly across several continents. Interestingly a new clade I/A3i has emerged as the second-highest prevalent type among the Indian isolates, comprising 25.5% of the Indian sequences. Emergence of new mutations in the S protein was observed. Major SARS-CoV-2 clades in India have defining mutations in the RdRp. Maximum accumulation of mutations was observed in ORF1a. Other than the clade-defining mutations, few representative non-synonymous mutations were checked against the available crystal structures of the SARS-CoV-2 proteins in the DynaMut server to assess their thermodynamic stability. We have observed that SARS-CoV-2 genomes contain more uracil than any other nucleotide. Furthermore, substitution of nucleotides to uracil was highest among the non-synonymous mutations observed. The A+U content in SARS-CoV-2 genome is much higher compared to other RNA viruses, suggesting that the virus RdRp has a propensity towards uracil incorporation in the genome. This implies that thymidine analogues may have a better chance to competitively inhibit SARS-CoV-2 RNA replication than other nucleotide analogues.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
Note	WHO #Covidence: #329771
DOI	10.1101/2020.10.07.329771
Database	COVID19

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Article ; Online: SARS-CoV-2 has observably higher propensity to accept uracil as nucleotide substitution: Prevalence of amino acid substitutions and their predicted functional implications in circulating SARS-CoV-2 in India up to July, 2020

Roy, Subrata / Nath, Himadri / Mallick, Abinash / Biswas, Subhajit

bioRxiv

Abstract	SARS-CoV-2 has emerged as pandemic all over the world since late 2019. In this study, we investigated the diversity of the virus in the context of SARS-CoV-2 spread in India. Full-length SARS-CoV-2 genome sequences of the circulating viruses from all over India were collected from GISAID, an open data repository, until 25thJuly, 2020. We have focused on the non-synonymous changes across the genome that resulted in amino acid substitutions. Analysis of the genomic signatures of the non-synonymous mutations demonstrated a strong association between the time of sample collection and the accumulation of genetic diversity. Most of these isolates from India belonged to the A2a clade (63.4%) which has overcome the selective pressure and is spreading rapidly across several continents. Interestingly a new clade I/A3i has emerged as the second-highest prevalent type among the Indian isolates, comprising 25.5% of the Indian sequences. Emergence of new mutations in the S protein was observed. Major SARS-CoV-2 clades in India have defining mutations in the RdRp. Maximum accumulation of mutations was observed in ORF1a. Other than the clade-defining mutations, few representative non-synonymous mutations were checked against the available crystal structures of the SARS-CoV-2 proteins in the DynaMut server to assess their thermodynamic stability. We have observed that SARS-CoV-2 genomes contain more uracil than any other nucleotide. Furthermore, substitution of nucleotides to uracil was highest among the non-synonymous mutations observed. The A+U content in SARS-CoV-2 genome is much higher compared to other RNA viruses, suggesting that the virus RdRp has a propensity towards uracil incorporation in the genome. This implies that thymidine analogues may have a better chance to competitively inhibit SARS-CoV-2 RNA replication than other nucleotide analogues.
Keywords	covid19
Language	English
Publishing date	2020-10-07
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.10.07.329771
Database	COVID19

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Book ; Online: Computational modelling predicts that Dengue virus antibodies can bind to SARS-CoV-2 receptor binding sites

Nath, Himadri / Mallick, Abinash / Roy, Subrata / Sukla, Soumi / Biswas, Subhajit

Is pre-exposure to dengue virus protective against COVID-19 severity?

2020

Abstract: The world is going through the scourge of COVID-19 pandemic since last several months. The pandemic appears to be less severe in highly Dengue endemic countries. Furthermore, COVID-19 in two elderly patients (with no evidence of Dengue virus (DV) ... ...

Abstract	The world is going through the scourge of COVID-19 pandemic since last several months. The pandemic appears to be less severe in highly Dengue endemic countries. Furthermore, COVID-19 in two elderly patients (with no evidence of Dengue virus (DV) infection) elicited antibodies that gave false-positive results in DV serological tests. We anticipated that SARS-CoV-2 and DV share antigenic similarity and performed molecular docking studies. Our computational modelling studies predicted that human anti-DV antibodies can indeed, bind to RBD of SARS-CoV-2 Spike protein. Some of these interactions can also potentially intercept human ACE2 receptor binding to RBM. Our computational analysis showed that m396 Ab (against SARS-CoV-1) did not dock with RBM of SARS-CoV-2, a fact already proven experimentally. This confirmed reliability and robustness of our approach. So, immunological memory to DV in endemic countries is thwarting COVID-19. Available Dengue vaccines can be repurposed against SARS-CoV-2 in DV non-endemic countries until approved vaccines/ antivirals become available against COVID-19. Based on the observations that COVID-19 and Dengue severity maps do not tend to overlap and the fact that serological cross-reactivity has been reported for COVID-19 antibodies with Dengue antigen (s), together with results from our computational studies, it is imperative that serology-based diagnosis should be complemented with NAT/virus antigen detection-based tests for definitive diagnosis of either disease in regions where both of these viruses are now co-existent. Furthermore, we still do not know whether antibodies to SARS-CoV-2 will hinder/ameliorate DV infections by binding to DV particles and reduce dengue incidences in the future or, augment DV infection and severity by means of antibody-dependent enhancement (ADE).
Keywords	covid19
Publisher	Center for Open Science
Publishing country	us
Document type	Book ; Online
DOI	10.31219/osf.io/dutx4
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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