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Article: Isolation and Characterization of Human Intestinal Bacteria

Yadav, Monika / Kumar, Tarun / Kanakan, Akshay / Maurya, Ranjeet / Pandey, Rajesh / Chauhan, Nar Singh

2022 Volume 13, Page(s) 932795

Abstract: Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based ... ...

Abstract	Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based therapeutics. The present study is aimed to isolate and evaluate the probiotic potential of a human gut isolate. Physiochemical, morphological, and phylogenetic characterization of a human gut isolate identifies it as a rod-shaped gram-negative microbe taxonomically affiliated with the
Language	English
Publishing date	2022-07-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.932795
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Infection outcome needs two to tango: human host and the pathogen.

Maurya, Ranjeet / Kanakan, Akshay / Vasudevan, Janani Srinivasa / Chattopadhyay, Partha / Pandey, Rajesh

Briefings in functional genomics

2021 Volume 21, Issue 2, Page(s) 90–102

Abstract: Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. ...

Abstract	Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response (including noncoding RNA) and the pathogen's genome architecture. Modern genomic tools and techniques have been crucial for the detection and genomic characterization of pathogens with respect to the emerging infectious diseases. Aided by next-generation sequencing (NGS), risk stratification of host population/s allows for the identification of susceptible subgroups and better disease management. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain. In this review, we elucidate how a better understanding of the human host-pathogen interplay can substantially enhance, and in turn benefit from, current and future applications of multi-omics based approaches in infectious and rare diseases. This includes the RNA-level response, which modulates the disease severity and outcome. The need to understand the role of human genetic variants in disease severity and clinical outcome has been further highlighted during the Coronavirus disease 2019 (COVID-19) pandemic. This would enhance and contribute toward our future pandemic preparedness.
MeSH term(s)	COVID-19/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Humans ; Pandemics
Language	English
Publishing date	2021-07-07
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elab037
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Article: Geographical Landscape and Transmission Dynamics of SARS-CoV-2 Variants Across India: A Longitudinal Perspective.

Jha, Neha / Hall, Dwight / Kanakan, Akshay / Mehta, Priyanka / Maurya, Ranjeet / Mir, Quoseena / Gill, Hunter Mathias / Janga, Sarath Chandra / Pandey, Rajesh

Frontiers in genetics

2021 Volume 12, Page(s) 753648

Abstract: Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from ... ...

Abstract	Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcare officials for advance planning. An integrative analysis of the publicly available datasets in GISAID from India reveals the differential distribution of clades, lineages, gender, and age over a year (Apr 2020-Mar 2021). The significant insights include the early evidence towards B.1.617 and B.1.1.7 lineages in the specific states of India. Pan-India longitudinal data highlighted that B.1.36* was the predominant clade in India until January-February 2021 after which it has gradually been replaced by the B.1.617.1 lineage, from December 2020 onward. Regional analysis of the spread of SARS-CoV-2 indicated that B.1.617.3 was first seen in India in the month of October in the state of Maharashtra, while the now most prevalent strain B.1.617.2 was first seen in Bihar and subsequently spread to the states of Maharashtra, Gujarat, and West Bengal. To enable a real time understanding of the transmission and evolution of the SARS-CoV-2 genomes, we built a transmission map available on https://covid19-indiana.soic.iupui.edu/India/EmergingLineages/April2020/to/March2021. Based on our analysis, the rate estimate for divergence in our dataset was 9.48 e-4 substitutions per site/year for SARS-CoV-2. This would enable pandemic preparedness with the addition of future sequencing data from India available in the public repositories for tracking and monitoring the VOCs and variants of interest (VOI). This would help aid decision making from the public health perspective.
Language	English
Publishing date	2021-12-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.753648
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Article ; Online: SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key.

Maurya, Ranjeet / Mishra, Pallavi / Swaminathan, Aparna / Ravi, Varsha / Saifi, Sheeba / Kanakan, Akshay / Mehta, Priyanka / Devi, Priti / Praveen, Shaista / Budhiraja, Sandeep / Tarai, Bansidhar / Sharma, Shimpa / Khyalappa, Rajesh J / Joshi, Meghnad G / Pandey, Rajesh

Frontiers in cellular and infection microbiology

2022 Volume 12, Page(s) 868414

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an enormous burden on the healthcare system worldwide as a consequence of its new emerging variants of concern (VOCs) since late 2019. Elucidating viral genome characteristics and its ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an enormous burden on the healthcare system worldwide as a consequence of its new emerging variants of concern (VOCs) since late 2019. Elucidating viral genome characteristics and its influence on disease severity and clinical outcome has been one of the crucial aspects toward pandemic management. Genomic surveillance holds the key to identify the spectrum of mutations
MeSH term(s)	COVID-19/genetics ; Genome, Viral ; Humans ; Mutation ; Pandemics ; Phylogeny ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-03-21
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.868414
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Article: Threading the Pieces Together: Integrative Perspective on SARS-CoV-2

Kanakan, Akshay / Mishra, Neha / Srinivasa Vasudevan, Janani / Sahni, Shweta / Khan, Azka / Sharma, Sachin / Pandey, Rajesh

Pathogens. 2020 Nov. 04, v. 9, no. 11

2020

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has challenged the research community globally to innovate, interact, and integrate findings across hierarchies. Research on SARS-CoV-2 has produced an abundance of data spanning ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has challenged the research community globally to innovate, interact, and integrate findings across hierarchies. Research on SARS-CoV-2 has produced an abundance of data spanning multiple parallels, including clinical data, SARS-CoV-2 genome architecture, host response captured through transcriptome and genetic variants, microbial co-infections (metagenome), and comorbidities. Disease phenotypes in the case of COVID-19 present an intriguing complexity that includes a broad range of symptomatic to asymptomatic individuals, further compounded by a vast heterogeneity within the spectrum of clinical symptoms displayed by the symptomatic individuals. The clinical outcome is further modulated by the presence of comorbid conditions at the point of infection. The COVID-19 pandemic has produced an expansive wealth of literature touching many aspects of SARS-CoV-2 ranging from causal to outcome, predisposition to protective (possible), co-infection to comorbidity, and differential mortality globally. As challenges provide opportunities, the current pandemic’s challenge has underscored the need and opportunity to work for an integrative approach that may be able to thread together the multiple variables. Through this review, we have made an effort towards bringing together information spanning across different domains to facilitate researchers globally in pursuit of their response to SARS-CoV-2.
Keywords	Coronavirus infections ; Severe acute respiratory syndrome coronavirus ; architecture ; comorbidity ; genetic variation ; genome ; information ; literature ; metagenomics ; mixed infection ; mortality ; pandemic ; pathogens ; phenotype ; research ; researchers ; signs and symptoms (animals and humans) ; transcriptome
Language	English
Dates of publication	2020-1104
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens9110912
Database	NAL-Catalogue (AGRICOLA)

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Article: Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations?

Kanakan, Akshay / Mehta, Priyanka / Devi, Priti / Saifi, Sheeba / Swaminathan, Aparna / Maurya, Ranjeet / Chattopadhyay, Partha / Tarai, Bansidhar / Das, Poonam / Jha, Vinita / Budhiraja, Sandeep / Pandey, Rajesh

Frontiers in microbiology

2022 Volume 13, Page(s) 763169

Abstract: Vaccine development against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been of primary importance to contain the ongoing global pandemic. However, studies have demonstrated that vaccine effectiveness is reduced and the immune ... ...

Abstract	Vaccine development against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been of primary importance to contain the ongoing global pandemic. However, studies have demonstrated that vaccine effectiveness is reduced and the immune response is evaded by variants of concern (VOCs), which include Alpha, Beta, Delta, and, the most recent, Omicron. Subsequently, several vaccine breakthrough (VBT) infections have been reported among healthcare workers (HCWs) due to their prolonged exposure to viruses at healthcare facilities. We conducted a clinico-genomic study of ChAdOx1 (Covishield) VBT cases in HCWs after complete vaccination. Based on the clinical data analysis, most of the cases were categorized as mild, with minimal healthcare support requirements. These patients were divided into two sub-phenotypes based on symptoms: mild and mild plus. Statistical analysis showed a significant correlation of specific clinical parameters with VBT sub-phenotypes. Viral genomic sequence analysis of VBT cases revealed a spectrum of high- and low-frequency mutations. More in-depth analysis revealed the presence of low-frequency mutations within the functionally important regions of SARS-CoV-2 genomes. Emphasizing the potential benefits of surveillance, low-frequency mutations, D144H in the
Language	English
Publishing date	2022-03-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.763169
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Threading the Pieces Together: Integrative Perspective on SARS-CoV-2.

Kanakan, Akshay / Mishra, Neha / Srinivasa Vasudevan, Janani / Sahni, Shweta / Khan, Azka / Sharma, Sachin / Pandey, Rajesh

Pathogens (Basel, Switzerland)

2020 Volume 9, Issue 11

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has challenged the research community globally to innovate, interact, and integrate findings across hierarchies. Research on SARS-CoV-2 has produced an abundance of data spanning multiple parallels, including clinical data, SARS-CoV-2 genome architecture, host response captured through transcriptome and genetic variants, microbial co-infections (metagenome), and comorbidities. Disease phenotypes in the case of COVID-19 present an intriguing complexity that includes a broad range of symptomatic to asymptomatic individuals, further compounded by a vast heterogeneity within the spectrum of clinical symptoms displayed by the symptomatic individuals. The clinical outcome is further modulated by the presence of comorbid conditions at the point of infection. The COVID-19 pandemic has produced an expansive wealth of literature touching many aspects of SARS-CoV-2 ranging from causal to outcome, predisposition to protective (possible), co-infection to comorbidity, and differential mortality globally. As challenges provide opportunities, the current pandemic's challenge has underscored the need and opportunity to work for an integrative approach that may be able to thread together the multiple variables. Through this review, we have made an effort towards bringing together information spanning across different domains to facilitate researchers globally in pursuit of their response to SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-11-04
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens9110912
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Article ; Online: FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip.

Kumar, Manoj / Gulati, Sneha / Ansari, Asgar H / Phutela, Rhythm / Acharya, Sundaram / Azhar, Mohd / Murthy, Jayaram / Kathpalia, Poorti / Kanakan, Akshay / Maurya, Ranjeet / Vasudevan, Janani Srinivasa / S, Aparna / Pandey, Rajesh / Maiti, Souvik / Chakraborty, Debojyoti

eLife

2021 Volume 10

Abstract: The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected ... ...

Abstract	The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations, some of which have recently been linked with increased viral load and prognostic complexities. Several of these variants are point mutations that are difficult to diagnose using the gold standard quantitative real-time PCR (qRT-PCR) method and necessitates widespread sequencing which is expensive, has long turn-around times, and requires high viral load for calling mutations accurately. Here, we repurpose the high specificity of
MeSH term(s)	COVID-19/genetics ; COVID-19 Nucleic Acid Testing ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; SARS-CoV-2/genetics
Language	English
Publishing date	2021-06-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.67130
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Article ; Online: Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.

Devi, Priti / Maurya, Ranjeet / Mehta, Priyanka / Shamim, Uzma / Yadav, Aanchal / Chattopadhyay, Partha / Kanakan, Akshay / Khare, Kriti / Vasudevan, Janani Srinivasa / Sahni, Shweta / Mishra, Pallavi / Tyagi, Akansha / Jha, Sujeet / Budhiraja, Sandeep / Tarai, Bansidhar / Pandey, Rajesh

Microbiology spectrum

2022 Volume 10, Issue 3, Page(s) e0231121

Abstract: The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial ... ...

Abstract	The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and
MeSH term(s)	Achromobacter denitrificans/genetics ; Bacillus cereus ; COVID-19 ; Coinfection ; Humans ; Microbiota/genetics ; Phylogeny ; Prospective Studies ; SARS-CoV-2/genetics ; Severity of Illness Index
Language	English
Publishing date	2022-05-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02311-21
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Article: Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India.

Shastri, Jayanthi / Parikh, Swapneil / Agrawal, Sachee / Chatterjee, Nirjhar / Pathak, Manish / Chaudhary, Sakshi / Sharma, Chetan / Kanakan, Akshay / A, Vivekanand / Srinivasa Vasudevan, Janani / Maurya, Ranjeet / Fatihi, Saman / Thukral, Lipi / Agrawal, Anurag / Pinto, Lancelot / Pandey, Rajesh / Sunil, Sujatha

Frontiers in medicine

2021 Volume 8, Page(s) 631769

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2021-03-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2021.631769
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