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TMV RNA quantification in mouse lungs by real-time RT-PCR. A: TMV coat protein gene system; B: TMV replicase gene system. Control, non-inoculated mice.
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Plant viruses are generally considered incapable of infecting vertebrates. Accordingly, they are not considered harmful for humans. However, a few studies questioned the certainty of this paradigm. Tobacco mosaic virus (TMV) RNA has been detected in human samples and TMV RNA translation has been described in animal cells. We sought to determine if...
Citations
... In an exciting study, Li et al. [25] reported that the transfection of TMV RNA in HeLa cells leads to the production of TMV-CP and, thus, induction of autophagy activated by Toll-like receptors initiating antiviral responses. Additionally, a study of antibody production revealed that both mice and humans produced anti-TMV antibodies after exposure to TMV [26,27]. In the human case, the authors identified the increase in levels of IgG (subclasses IgG1, IgG2, IgG3, and IgG4), IgM, and IgA [27]. ...
Here, one hundred patients (50 smokers and 50 non-smokers) clinically diagnosed with COVID-19 were studied. Yet, bioinformatics was used to predict epitopes on Tobacco mosaic virus coat protein (TMV-CP) to produce antibodies towards SARS-CoV-2. Death was three times higher in non-smokers than in smokers. However, biochemical parameters did not separate the groups. Bioinformatics analysis predicted the presence of B-cell epitopes in TMV-CP, suggesting the production of antibodies anti-TMV-CP in smoker patients. Smokers may develop severe forms of COVID-19, but survival was superior in the evaluated group than in non-smokers. Anti-TMV-CP antibodies, potentially present in smokers, might act as a pro-immune agent against SARS-CoV-2 at earlier stages of infection. These data are helpful for future studies assessing COVID-19 in smokers.
... A N501Y mutation-specific qPCR assay that targets nucleotide at spike receptor binding domain (adenine replaced by uracil at position 23,063 with reference to NC_045512.2) was also tested to detect N501Y mutation (Bedotto et al., 2021). In addition, MNV was tested as a molecular process control (Kitajima et al., 2010), while crAssphage (Stachler et al., 2017), PMMoV (Haramoto et al., 2013;Zhang et al., 2006), and TMV (Balique et al., 2013) were tested as indicator viruses to compare their reductions with SARS-CoV-2. RT-qPCR assays for SARS-CoV-2 were performed in a 25-μL qPCR mixture containing 12.5 μL of Probe qPCR Mix with UNG (Takara Bio, Kusatsu, Japan), 0.1 μL each of 100-μM forward and reverse primers, 0.05 μL of 100-μM TaqMan probe, and 2.5 μL of template cDNA. ...
The applicability of wastewater-based epidemiology (WBE) has been extensively studied throughout the world with remarkable findings. This study reports the presence and reduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at two wastewater treatment plants (WWTPs) of Nepal, along with river water, hospital wastewater (HWW), and wastewater from sewer lines collected between July 2020 and February 2021. SARS-CoV-2 RNA was detected in 50%, 54%, 100%, and 100% of water samples from WWTPs, river hospitals, and sewer lines, respectively, by at least one of four quantitative PCR assays tested (CDC-N1, CDC-N2, NIID_2019-nCOV_N, and N_Sarbeco). The CDC-N2 assay detected SARS-CoV-2 RNA in the highest number of raw influent samples of both WWTPs. The highest concentration was observed for an influent sample of WWTP A (5.5 ± 1.0 log10 genome copies/L) by the N_Sarbeco assay. SARS-CoV-2 was detected in 47% (16/34) of the total treated effluents of WWTPs, indicating that biological treatments installed at the tested WWTPs are not enough to eliminate SARS-CoV-2 RNA. One influent sample was positive for N501Y mutation using the mutation-specific qPCR, highlighting a need for further typing of water samples to detect Variants of Concern. Furthermore, crAssphage-normalized SARS-CoV-2 RNA concentrations in raw wastewater did not show any significant association with the number of new coronavirus disease 2019 (COVID-19) cases in the whole district where the WWTPs were located, suggesting a need for further studies focusing on suitability of viral as well as biochemical markers as a population normalizing factor. Detection of SARS-CoV-2 RNA before, after, and during the peaking in number of COVID-19 cases suggests that WBE is a useful tool for COVID-19 case estimation in developing countries.
... Therefore, the reason for the virus' existence needed to be studied. However, a hypothesis was that this virus was caught by the patient when eating citrus fruits, since plant viruses are detected in human samples [29]. We found two SNVs in sample 2 and one SNV in sample 3 using our default (FastViromeExplorer + BWA) assembly method. ...
... Tobacco mosaic virus was a plant virus but had been detected in human samples. Previous studies showed tobacco mosaic virus could stay in mice cells for more than 15 days [29]. Since the COVID-19 outbreak lasted only several months, an extremely large number of SNVs suggested a low accuracy of the method. ...
Background
Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified.
Results
In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references).
Conclusions
Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).
... It was reported that TMV could enter and persist in mouse lungs, raising questions about the potential interactions between the virus and human host. 40 Accordingly, a further investigation was necessary. Our BALF metatranscriptome results detailed the species in the lungs of COVID-19 patients and shed light on the complex interactions between SARS-CoV-2 and other microbes in the lungs. ...
Introduction: With the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the interaction between the host and SARS-CoV-2 was widely studied. However, it is unclear whether and how SARS-CoV-2 infection affects lung microflora, which contribute to COVID-19 complications.
Methods: Here, we analyzed the metatranscriptomic data of bronchoalveolar lavage fluid (BALF) of 19 COVID-19 patients and 23 healthy controls from 6 independent projects and detailed the active microbiota landscape in both healthy individuals and COVID-19 patients.
Results: The infection of SARS-CoV-2 could deeply change the lung microbiota, evidenced by the α-diversity, β-diversity, and species composition analysis based on bacterial microbiota and virome. Pathogens (e.g., Klebsiella oxytoca causing pneumonia as well), immunomodulatory probiotics (e.g., lactic acid bacteria and Faecalibacterium prausnitzii, a butyrate producer), and Tobacco mosaic virus (TMV) were enriched in the COVID-19 group, suggesting a severe microbiota dysbiosis. The significant correlation between Rothia mucilaginosa, TMV, and SARS-CoV-2 revealed drastic inflammatory battles between the host, SARS-CoV-2, and other microbes in the lungs. Notably, TMV only existed in the COVID-19 group, while human respirovirus 3 (HRV 3) only existed in the healthy group. Our study provides insights into the active microbiota in the lungs of COVID-19 patients and would contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications.
Conclusion: SARS-COV-2 infection deeply altered the lung microbiota of COVID-19 patients. The enrichment of several other pathogens, immunomodulatory probiotics (lactic acid or butyrate producers), and TMV in the COVID-19 group suggests a complex and active lung microbiota disorder.
... All samples had at least one virus, and a maximum of three human RNA viruses were identified (average two viruses/sample), which included, for example, RSV, CoV, HRV, enteroviruses (EVs), and influenza. Interestingly, plant viruses were also identified in almost all samples, which has been reported before in human and mice lungs (Balique et al., 2013;Nakamura et al., 2009). With a stringent cutoff of >90% genome coverage, and minimum 5× coverage, we identified two plant viruses, rehmannia mosaic virus NcaS (ReMV-NcaS) and tobacco mosaic virus ( Figure 1B; Table S2). ...
We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that H. influenzae was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.
... A High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA, USA) was used to synthesize 70 μL of cDNA using 35 μL of the extracted RNA, following the manufacturer's protocol. Taq-Man (MGB)-based qPCR was performed using 2.5 μL of cDNA/DNA with a Thermal Cycler Dice Real-Time System TP800 (Takara Bio, Kusatsu, Japan) for eight enteric viruses [AiV-1 ( Kitajima et al., 2011 ), BKPyVs and JCPyVs ( Pal et al., 2006 ), EVs ( Katayama et al., 2002 ;Shieh et al., 1995 ), HCoSV ( Stöcker et al., 2012 ), HAdVs ( Heim et al., 2003 ), NoVs-GI ( Kageyama et al., 2003 ), RVAs ( Jothikumar et al., 2009 )], including two indicator viruses [PMMoV ( Haramoto et al., 2013 ;Zhang et al., 2005 ), TMV ( Balique et al., 2013 )], and MNV ( Kitajima et al., 2010 ). As described previously ( Tandukar et al., 2020a ), all samples were tested in duplicate and a standard curve was drawn using 10-fold serial dilutions of artificially synthesized plasmid DNA containing the amplification region sequences. ...
Continuous discharge of enteric viruses through treated wastewater is a potential threat to the environment and humans. This study aimed to investigate the occurrence and reduction of enteric viruses at two wastewater treatment plants (WWTPs) in the Kathmandu Valley, Nepal. Twenty-two samples (from the influent samples and effluent samples, n = 11 each) were collected at two WWTPs (WWTP A and WWTP B, installing oxidation ditch and non-aerated lagoon systems, respectively) between April and August 2018. Human adenoviruses, JC and BK polyomaviruses, Aichi virus 1, enteroviruses, noroviruses of genogroup I (NoVs-GI), group A rotaviruses, and human cosavirus, along with plant viruses (pepper mild mottle and tobacco mosaic viruses), were detected using quantitative PCR. The most prevalent enteric virus was NoVs-GI (100%), followed by human adenoviruses (95%), and enteroviruses and JC polyomaviruses (91%). Log10 reduction values of all tested viruses were found to be lower than those of fecal indicator bacteria. Both WWTPs were less efficient for the reduction of pathogens (p < 0.05). A significant positive correlation was found in the concentrations between indicator viruses (JC and BK polyomaviruses) and total enteric viruses in the effluents (p < 0.05). Both WWTPs were not adequately effective to reduce enteric viruses and indicator viruses. Our findings suggested that advanced treatment processes are needed for both WWTPs to achieve better reduction efficiency in the future.
... Interestingly, plant viruses were also found in almost all samples, which has been reported before in human and mice lungs 14,15 . With a stringent cut off of >90% genome coverage, and minimum 5X coverage, we identi ed two plant viruses, Rehmannia mosaic virus NcaS (ReMV-NcaS), and Tobacco mosaic virus (TMV) (Figure 1b, Supplementary Table S2). ...
... as of November 18, 2019) 14 . To this end, sequences were grouped into amplicon sequence variants (ASVs) and taxonomy was assigned using the SILVA reference database 15 . Sequences were subsequently processed through the R package decontam 16 to remove any suspected contaminants that were found in the negative control samples. ...
We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low-biomass clinical samples. Using nasal swab samples, we have demonstrated that this method captures the comprehensive RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high-frequency of Respiratory Syncytial Virus (RSV) and Coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-infections in children with symptomatic RSV. In addition, we have characterized commensal and pathogenic bacteria, and fungi at the species-level. Functional analysis of bacterial transcripts revealed H. influenzae was highly active in symptomatic RSV subjects. Host transcriptome shows upregulation of the innate immune system, antiviral response and inflammasome pathway, and down regulation of fatty-acids pathway. This method is broadly applicable to infer transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.
... In-vivo experiments show that anti-TMV antibodies are produced both by mice after intratracheal inoculation [7] and by humans after exposure to tobacco products [8]. ...
An hypothesis for the putative protective role of tobacco smoking on Covid-19, based on the immune adjuvant action of tobacco mosaic virus
... In-vivo experiments show that anti-TMV antibodies are produced both by mice after intratracheal inoculation [7] and by humans after exposure to tobacco products [8]. ...
Reports from various countries suggest that tobacco smoking might protect from SARS-CoV-2 infection, since the prevalence of smoking in COVID-19 hospitalized patients is lower than in the respective general population. Apart from nicotine or other chemicals contained in tobacco smoke, we propose that a single-stranded RNA virus that infects tobacco leaves, tobacco mosaic virus (TMV), might be implicated in this effect. TMV, though non-pathogenic, is found in smokers’ airways, and stimulates adaptive and innate immunity, with release of specific antibodies and interferons. The latter may have preventive and/or therapeutic effects against COVID-19.
If confirmed by epidemiological and interventional studies, this might lead to the use of TMV as an immunological adjuvant against SARS-CoV-2 infection and COVID-19 disease.
(Full text from PubMed Central in https://pubmed.ncbi.nlm.nih.gov/32763662/ )
... Collected water samples were subjected to virus concentration using an electronegative membrane filter (Katayama et al. 2002) with slight modifications (Tandukar et al. 2020). Subsequently, the concentrated samples were used for viral RNA extraction using a ZR Viral DNA/RNA Kit (Zymo Research, Irvine, USA), followed by reverse transcription and quantitative polymerase chain reaction (qPCR) for four human enteric viruses [AiV-1 (Kitajima et al. 2011), EVs (Shieh et al. 1995;Katayama et al. 2002), and NoVs-GI and NoVs-GII (Kageyama et al. 2003)] and two indicator viruses [PMMoV (Zhang et al. 2005;Haramoto et al. 2007) and TMV (Balique et al. 2013)] as described previously (Tandukar et al. 2020). As recommended , the level of qPCR inhibition was monitored using artificially synthesized plasmid DNA which contained sequences amplified by qPCR assay for chicken parvovirus (82 bp) (Carratalà et al. 2012) as qPCR-control DNA. ...
This study assessed wastewater quality through the quantification of four human enteric viruses and the applicability of pepper mild mottle virus (PMMoV) and tobacco mosaic virus (TMV) as indicators of viral reduction during wastewater treatment. Thirty-three samples were collected from three steps of a wastewater treatment plant in Southern Louisiana, USA for a year between March 2017 and February 2018. Noroviruses of genogroup I were the most prevalent human enteric viruses in influent samples. The concentrations of PMMoV in influent samples (5.9 ± 0.7 log10 copies/L) and biologically treated effluent samples (5.9 ± 0.5 log10 copies/L) were significantly higher than those of TMV (P < 0.05), and the reduction ratio of PMMoV (1.0 ± 0.8 log10) was found comparable to those of TMV and Aichi virus 1. Because of the high prevalence, high correlations with human enteric viruses, and lower reduction ratios, PMMoV was deemed an appropriate indicator of human enteric viral reduction during wastewater treatment process.
