The 2019 Wuhan outbreak is caused by the bacteria Prevotella, which is aided by the coronavirus, possibly to adhere to epithelial cells - Prevotella is present in huge amounts in patients from both China and Hong Kong

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A hitherto unknown cause of the Wuhan coronavirus outbreak [1–3] is reported here - a bacteria from the Prevotella genus. The number of Wuhan coronavirus deaths in mainland China has overtaken the SARS epidemic in the country. The high mortality is being caused by targeting only the virus (which is also present). This is a two pronged attack, as previously noted in ‘infection with human coronavirus NL63 enhances streptococcal adherence to epithelial cells‘ [6]. Prevotella is a well known pathogen, and can induce ‘Severe Bacteremic Pneumococcal Pneumonia in Mice with Upregulated Platelet-Activating Factor Receptor Expression’ [7].The RNA-seq data from Wuhan, China (PRJNA603194) has millions of reads of Prevotella proteins, and a few thousands from 2019-nCoV (Table 1). Similarly, the DNA sequences (PRJNA601630) of 6 patients from the same family in Hong Kong [3] shows significant presence of this bacteria. These sequences can be found at SI:China.RNA-seq/SampleSequences.fa(n=480K) and SI:HongKong/ALLsequences.fa(n=50k).Finally, the expression levels (Table 2) shows that the elongation factor Tu is the most expressed. ‘Elon- gation factor Tu (Tuf) is a new virulence factor of Streptococcus pneumoniae that binds human complement factors, aids in immune evasion and host tissue invasion’ [8].These are the only two studies I could find. Detection of the Prevotella in other samples will add more credence to this theory. Detection of the nCoV can be made very specific by looking for a 500bp in the spike protein [4], which would be a good candidate for vaccine development, protein-inhibition and diagnosis (which was non-specific for SARS in many cases, including the CDC test [5]). Anti-virals neeed to be supplemented with anti-bacterial agents to treat this disease.

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... The modulation of microflora under the influence of pathogens is a major factor deciding fate of infections. During a recent metagenomic study carried out on COVID-2019 patients (NCBI Bioproject Accession ID: PRJNA603194), it was found that some bacteria are overrepresented in the lungs of infected patients (Chakraborty, 2020). The over expressed proteins in the most abundant Prevotella species were also found. ...
... We elucidated a mechanistic insight of these hostpathogen interactions in the severity of COVID-2019. IDs from lung metagenomic study (Chakraborty, 2020). ...
... Different species of Prevotella represented highest 23% share of lung metagenome after 61% unidentified spots (dark matter). Moreover, the overexpressed proteins in Prevotella strains associated with COVID-2019 patients identified in above study is presented in Table 1 in order to give overview about key proteins (Chakraborty, 2020). Table S1 and S2 respectively. ...
Motivation: The outbreak of COVID-2019 initiated at Wuhan, China has become a global threat by rapid transmission and severe fatalities. Recent studies have uncovered whole genome sequence of SARS-CoV-2 (causing COVID-2019). In addition, lung metagenomic studies on infected patients revealed overrepresented Prevotella spp. producing certain proteins in abundance. We performed host-pathogen protein-protein interaction analysis between SARS-CoV-2 and overrepresented Prevotella proteins with human proteome. We also performed functional overrepresentation analysis of interacting proteins to understand their role in COVID-2019 severity. Results: It was found that over-expressed Prevotella proteins can promote viral infection. As per the results, Prevotella proteins, but not viral proteins are involved in multiple interactions with NF-kB, which is involved in increasing clinical severity of COVID-2019. Prevotella may have role in COVID-2019 outbreak and should be given importance for understanding disease mechanisms and improving treatment outcomes. Supplementary information: Supplementary data are available at Bioinformatics online.
... [29] Metagenomic analyses of patients with SARS-CoV-2 frequently detected high bacterial loads of Prevotella intermedia, a major causative agent for several acute periodontal lesions, along with Fusobacterium and Treponema species. [40] Recently mucormycosis otherwise called black fungus, a rare fungal infection, has been reported across many states in India and has affected at least 7250 people in India and 9 new cases are under treatment in the state of Kerala. [41] The disease is considered to be associated with immunosuppressive treatment of COVID-19 which frequently infects the sinus and later progresses into the orbit and cranium. ...
Introduction: The emergence of coronavirus disease 2019 (COVID-19) crisis has evoked an exigent need to explicate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and oral mucosal lesions. The present systematic review aims to elucidate the recent literature on oral manifestations related to COVID-19 so as to help the dental professionals for better screening and early diagnosis of the disease. Materials and Methods: A comprehensive literature search on PubMed, Science direct, Scopus, and Embase databases was carried out from December 2019 to March 2021 using keywords “Coronavirus,” “COVID-19,” “SARSCoV-2,” “Oral mucosal lesions,” and “Oral manifestation.” Additional information was obtained from Cochrane, World Health Organization, and Medscape. The full text articles of case reports and cross-sectional studies were analyzed and included. The review included 25 articles. Results: Four most common oral manifestations were found: gustatory and olfactory dysfunction, xerostomia, oral mucosal lesions, and salivary gland diseases. Vasculitis, opportunistic infections, drug eruption secondary to administration of Non-Steroidal Anti-inflammatory Drugs (NSAIDs), stress, immunosuppression, and hyperinflammatory immune response secondary to COVID-19 might be some of the relevant predisposing factors responsible for the onset of oral manifestations in patients with COVID-19. Conclusion: The early detection of oral symptoms of SARS-CoV-2 infection could help the clinicians to perform a better screening, and in recognizing early manifestations of the disease. However, the oral manifestations might be misdiagnosed due to subsequent challenge of undergoing oral examinations, hence diverse studies should be undertaken by the researchers to gain a better insight into the topic.
This article reviews the most common oral health problems, which could be associated with coronavirus disease 2019 (COVID-19). Several reports were published, which described various oral manifestations of COVID, including dysgeusia, petechiae, candidiasis, traumatic ulcers, herpesvirus infection, geographic tongue, thrush like ulcers, among others. Alterations of smell and taste seem to be the most common manifestations of COVID in the orofacial area, which could be directly related to the effect of the virus. Other oral conditions seem to be secondary to the decrease of host defense, or else caused by the drugs and intensive care used in the treatment of COVID-19.
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The implications of the microbiome on Coronavirus disease 2019 (COVID-19) prognosis has not been thoroughly studied. In this study we aimed to characterize the lung and blood microbiome and their implication on COVID-19 prognosis through analysis of peripheral blood mononuclear cell (PBMC) samples, lung biopsy samples, and bronchoalveolar lavage fluid (BALF) samples. In all three tissue types, we found panels of microbes differentially abundant between COVID-19 and normal samples correlated to immune dysregulation and upregulation of inflammatory pathways, including key cytokine pathways such as interleukin (IL)-2, 3, 5-10 and 23 signaling pathways and downregulation of anti-inflammatory pathways including IL-4 signaling. In the PBMC samples, six microbes were correlated with worse COVID-19 severity, and one microbe was correlated with improved COVID-19 severity. Collectively, our findings contribute to the understanding of the human microbiome and suggest interplay between our identified microbes and key inflammatory pathways which may be leveraged in the development of immune therapies for treating COVID-19 patients.
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Co-infection with ancillary pathogens is a significant modulator of morbidity and mortality in infectious diseases. There have been limited reports of co-infections accompanying SARS-CoV-2 infections, albeit lacking India specific study. The present study has made an effort toward elucidating the prevalence, diversity and characterization of co-infecting respiratory pathogens in the nasopharyngeal tract of SARS-CoV-2 positive patients. Two complementary metagenomics based sequencing approaches, Respiratory Virus Oligo Panel (RVOP) and Holo-seq, were utilized for unbiased detection of co-infecting viruses and bacteria. The limited SARS-CoV-2 clade diversity along with differential clinical phenotype seems to be partially explained by the observed spectrum of co-infections. We found a total of 43 bacteria and 29 viruses amongst the patients, with 18 viruses commonly captured by both the approaches. In addition to SARS-CoV-2, Human Mastadenovirus, known to cause respiratory distress, was present in a majority of the samples. We also found significant differences of bacterial reads based on clinical phenotype. Of all the bacterial species identified, ∼60% have been known to be involved in respiratory distress. Among the co-pathogens present in our sample cohort, anaerobic bacteria accounted for a preponderance of bacterial diversity with possible role in respiratory distress. Clostridium botulinum , Bacillus cereus and Halomonas sp. are anaerobes found abundantly across the samples. Our findings highlight the significance of metagenomics based diagnosis and detection of SARS-CoV-2 and other respiratory co-infections in the current pandemic to enable efficient treatment administration and better clinical management. To our knowledge this is the first study from India with a focus on the role of co-infections in SARS-CoV-2 clinical sub-phenotype.
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The oral cavity, as the entry point to the body, may play a critical role in the pathogenesis of SARS-CoV-2 infection that has caused a global outbreak of the coronavirus disease 2019 (COVID-19). Available data indicate that the oral cavity may be an active site of infection and an important reservoir of SARS-CoV-2. Considering that the oral surfaces are colonized by a diverse microbial community, it is likely that viruses have interactions with the host microbiota. Patients infected by SARS-CoV-2 may have alterations in the oral and gut microbiota, while oral species have been found in the lung of COVID-19 patients. Furthermore, interactions between the oral, lung, and gut microbiomes appear to occur dynamically whereby a dysbiotic oral microbial community could influence respiratory and gastrointestinal diseases. However, it is unclear whether SARS-CoV-2 infection can alter the local homeostasis of the resident microbiota, actively cause dysbiosis, or influence cross-body sites interactions. Here, we provide a conceptual framework on the potential impact of SARS-CoV-2 oral infection on the local and distant microbiomes across the respiratory and gastrointestinal tracts (‘oral-tract axes’), which remains largely unexplored. Studies in this area could further elucidate the pathogenic mechanism of SARS-CoV-2 and the course of infection as well as the clinical symptoms of COVID-19 across different sites in the human host.
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