COVID-2019-associated overexpressed <i>Prevotella</i> proteins mediated host–pathogen interactions and their role in coronavirus outbreak

Khan, Abdul Arif; Khan, Zakir

doi:10.1093/bioinformatics/btaa285

Cited by 65 publications

(61 citation statements)

References 20 publications

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“…It was found that over-expressed Prevotella proteins can promote viral infection. As per the results, Prevotella proteins, rather than viral proteins, are involved in increasing clinical severity of COVID-2019, i.e., Prevotella plays role in COVID- 2019 outbreak and attention should be paid to understanding disease mechanisms and improving treatment outcomes ( Khan and Khan, 2020 ).…”

Section: Interaction Between Oral Microbiome and Virus Infectionmentioning

confidence: 97%

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

et al. 2020

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The new coronavirus SARS-CoV-2, the cause of COVID-19, has become a public health emergency of global concern. Like the SARS and influenza pandemics, there have been a large number of cases coinfected with other viruses, fungi, and bacteria, some of which originate from the oral cavity. Capnocytophaga , Veillonella , and other oral opportunistic pathogens were found in the BALF of the COVID-19 patients by mNGS. Risk factors such as poor oral hygiene, cough, increased inhalation under normal or abnormal conditions, and mechanical ventilation provide a pathway for oral microorganisms to enter the lower respiratory tract and thus cause respiratory disease. Lung hypoxia, typical symptoms of COVID-19, would favor the growth of anaerobes and facultative anaerobes originating from the oral microbiota. SARS-CoV-2 may aggravate lung disease by interacting with the lung or oral microbiota via mechanisms involving changes in cytokines, T cell responses, and the effects of host conditions such as aging and the oral microbiome changes due to systemic diseases. Because the oral microbiome is closely associated with SARS-CoV-2 co-infections in the lungs, effective oral health care measures are necessary to reduce these infections, especially in severe COVID-19 patients. We hope this review will draw attention from both the scientific and clinical communities on the role of the oral microbiome in the current global pandemic.

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Section: Interaction Between Oral Microbiome and Virus Infectionmentioning

confidence: 97%

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

et al. 2020

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“…Two of the main purposes of the authors who used proteomics were to elucidate the mechanism of host–pathogen interactions, its association with the severity of COVID-19, and to find possible therapeutic targets. Khan and Khan ( 26 ), predicted the interaction of the receptor ACE2, which is mainly expressed on the surface of airway epithelium and parenchyma of lung, with the glycoprotein found on the surface of SARS-CoV-2. Also, these authors suggest a possible role of Prevotella in the severity of COVID-19 by increasing severity of pneumonia.…”

Section: Discussionmentioning

confidence: 99%

Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review

Murillo

Villegas

Ulloa-Murillo

et al. 2021

Computers in Biology and Medicine

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Background The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic. Methods We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19 th , 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose. Results From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic. Conclusion We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.

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“…The HPI plays an important role in the pathogenesis of any infectious organisms, but their role is more prominent in viral pathogenesis due to their reliance on effective utilization of host machinery for establishing the infection. The role of HPIs in coronavirus infections is also discussed earlier [ 12 ], but computational study of host–pathogen protein–protein interactions is adding more value for understanding the pathogenesis of coronavirus [ 13 ]. BioGrid is a well-known database of protein, genetic and chemical interactions between various organisms and host.…”

Section: Discussionmentioning

confidence: 99%

Comparative host–pathogen protein–protein interaction analysis of recent coronavirus outbreaks and important host targets identification

Khan

Khan²

2020

Briefings in Bioinformatics

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Last two decades have witnessed several global infectious outbreaks. Among these, coronavirus is identified as a prime culprit ranging from its involvement in severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) to COVID-19. These infections involved in huge healthcare and economic cost incurred globally. Every time, coronavirus improved its infection ability and surprised the medical practitioners and researchers. Currently, COVID-19 is also causing numerous infections and stalled global activities. Global efforts are underway to identify potential viral targets for management of these outbreaks, but significant progress in prevention of these outbreaks is not yet achieved. We explored host–pathogen protein–protein interactions of MERS, SARS and COVID-19, and identified host targets common among all recent coronavirus outbreaks. Further, we tried to understand their potential for management of coronavirus. The common proteins involved in coronavirus host–pathogen interactions indicate their indispensable role in the pathogenesis and therefore targeting these proteins can give strategies to prevent current and future coronavirus outbreaks. Viral variability necessitates development of new therapeutic modalities for every outbreak, in contrast targeting necessary human proteins required by all coronaviruses can provide us a clue to prevent current and future coronavirus outbreaks. We found that targeting FURIN and TMPRSS2 can provide good results due to their common involvement in current and previous outbreaks. We also listed some known molecules against these two targets for their potential drug repurposing evaluation. Although, several recent studies undergoing with targeting these proteins for management of coronavirus, but safety evaluation and risk assessment must be given prime importance while targeting human proteins.

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COVID-2019-associated overexpressed Prevotella proteins mediated host–pathogen interactions and their role in coronavirus outbreak

Cited by 65 publications

References 20 publications

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review

Comparative host–pathogen protein–protein interaction analysis of recent coronavirus outbreaks and important host targets identification

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