Frontiers in virology最新文献

{"title":"Rapid and Affordable High Throughput Screening of SARS-CoV-2 Variants Using Denaturing High-Performance Liquid Chromatography Analysis","authors":"M. Turba, D. Mion, S. Papadimitriou, F. Taddei, G. Dirani, V. Sambri, F. Gentilini","doi":"10.3389/fviro.2022.889592","DOIUrl":"https://doi.org/10.3389/fviro.2022.889592","url":null,"abstract":"Mutations in the receptor binding domain (RBD) of SARS-CoV-2 alter the infectivity, pathogenicity, and transmissibility of new variants of concern (VOCs). In addition, those mutations cause immune escape, undermining the population immunity induced by ongoing mass vaccination programs. There is an urgent need for novel strategies and techniques aimed at the surveillance of the active emergence and spread of the VOCs. The aim of this study was to provide a quick, cheap and straightforward denaturing high-performance liquid chromatography (DHPLC) method for the prompt identification of the SARS-CoV-2 VOCs. Two PCRs were designed to target the RBD region, spanning residues N417 through N501 of the Spike protein. Furthermore, a DHPLC screening analysis was set up. The screening consisted of mixing the unknown sample with a standard sample of a known variant, denaturing at high temperature, renaturing at room temperature followed by a 2-minute run using the WAVE DHPLC system to detect the heteroduplexes which invariably form whenever the unknown sample has a nucleotide difference with respect to the standard used. The workflow was able to readily detect all the variants including B.1.1.7, P.1, B.1.585 B.1. 617.2 and lineages at a very affordable cost. The DHPLC analysis was robust being able to identify variants, even in the case of samples with very unbalanced target concentrations including those samples at the limit of detection. This approach has the potential of greatly expediting surveillance of the SARS-CoV-2 variants.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47956060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 and the Missing Link of Intermediate Hosts in Viral Emergence - What We Can Learn From Other Betacoronaviruses","authors":"B. Schindell, Meagan Allardice, Jessica A.M. McBride, Brendan Dennehy, J. Kindrachuk","doi":"10.3389/fviro.2022.875213","DOIUrl":"https://doi.org/10.3389/fviro.2022.875213","url":null,"abstract":"The emergence of SARS-CoV-2 in 2019 has resulted in a global pandemic with devastating human health and economic consequences. The development of multiple vaccines, antivirals and supportive care modalities have aided in our efforts to gain control of the pandemic. However, the emergence of multiple variants of concern and spillover into numerous nonhuman animal species could protract the pandemic. Further, these events also increase the difficulty in simultaneously monitoring viral evolution across multiple species and predicting future spillback potential into the human population. Here, we provide historic context regarding the roles of reservoir and intermediate hosts in coronavirus circulation and discuss current knowledge of these for SARS-CoV-2. Increased understanding of SARS-CoV-2 zoonoses are fundamental for efforts to control the global health and economic impacts of COVID-19.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48774820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes in Symptoms Experienced by SARS-CoV-2-Infected Individuals – From the First Wave to the Omicron Variant","authors":"H. Schulze, W. Bayer","doi":"10.3389/fviro.2022.880707","DOIUrl":"https://doi.org/10.3389/fviro.2022.880707","url":null,"abstract":"The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic and public health crisis since the beginning of 2020. First recognized for the induction of severe disease, the virus also causes asymptomatic infections or infections with mild symptoms that can resemble common colds. To provide better understanding of these mild SARS-CoV-2 infections and to monitor the development of symptoms over time, we performed a detailed analysis of self-reported symptoms of SARS-CoV-2 positive and SARS-CoV-2 negative individuals. In an online-based survey, a total of 2117 individuals provided information on symptoms associated with an acute respiratory infection, 1925 of the participants had tested positive for SARS-CoV-2 infection, and 192 had tested negative. The symptoms reported most frequently during the early phases of the pandemic by SARS-CoV-2 infected individuals were tiredness, headache, impairment of smell or taste and dry cough. With the spread of the alpha and delta variants, the frequency of nose symptoms such as blocked or runny nose and sneezing increased to being reported by almost 60% of infected individuals. Interestingly, the spread of the omicron variant brought a sharp decrease in the incidence of impaired sense of smell or taste, which was reported by only 24% in this phase of the pandemic. The constellation of symptoms should be monitored closely in the months ahead, since future SARS-CoV-2 variants are likely to bring about more changes.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44592947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strand-Specific Patterns of Codon Usage Bias Across Cressdnaviricota","authors":"Alvin Crespo-Bellido, S. Duffy","doi":"10.3389/fviro.2022.899608","DOIUrl":"https://doi.org/10.3389/fviro.2022.899608","url":null,"abstract":"The rapidly expanding phylum Cressdnaviricota contains circular, Rep-encoding single-stranded (CRESS) DNA viruses that are organized within seven established families, but many CRESS DNA virus sequences are not taxonomically defined. We hypothesized that genes in CRESS DNA virus ambisense genomes exhibit strand-specific signatures due to a cytosine to thymine transition bias that can help determine the orientation of the genome: which strand is packaged and is in the “virion sense”. To identify broad strand-specific patterns across genera, we performed compositional analyses of codon usage across the two major opposite sense open reading frames of 712 reference viruses. Additionally, we developed a statistical test to identify relative codon overrepresentation between ambisense sequence pairs for each classified virus exemplar and an additional 137 unclassified CRESS DNA viruses. Codons clustered by the identity of their third-position nucleotide, displaying both strand- and genus-specific patterns across Cressdnaviricota. Roughly 70% of virion-sense sequences have a relative overrepresentation of thymine-ending codons while ~80% of anti-sense sequences display a relative overrepresentation of adenine-ending codons (corresponding to a relative overrepresentation of thymine in these genes as packaged). Thirteen of the 137 unclassified viruses show strong evidence of having the rarer circovirus-like genome orientation, and likely represent novel genera or families within Cressdnaviricota. Given the strong strand-specific patterns of relative codon overrepresentation, the results suggest that the relative codon overrepresentation test can serve as a tool to help corroborate the genome organization of unclassified CRESS DNA viruses.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49581400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brief Research Report: Ebola Virus Differentially Infects Human Iris and Retinal Pigment Epithelial Cells","authors":"S. Todd, Yuefang Ma, Liam M Ashander, B. Appukuttan, M. Michael, Timothy A. Blenkinsop, S. Yeh, G. Marsh, Justine R. Smith","doi":"10.3389/fviro.2022.892394","DOIUrl":"https://doi.org/10.3389/fviro.2022.892394","url":null,"abstract":"Uveitis is a common manifestation of post-Ebola syndrome, associated with persistence of Ebola virus (EBOV; Zaire ebolavirus) inside the eye. The iris and retinal pigment epithelia are key components of the blood-ocular barriers, but have the capacity to act as hosts for microorganisms. We investigated the ability of EBOV to productively infect these cell populations. Donor-matched human iris and retinal pigment epithelial isolates (n = 5) were infected with EBOV at a multiplicity of infection of 1 for up to 72 hours. Parallel cultures were infected with Reston virus (RESTV; Reston ebolavirus) or Zika virus (ZIKV), or held uninfected under the same conditions. Viral transcript expression by RT-qPCR on total cellular RNA, cytoimmunofluorescence, and assays of 50% tissue culture infected dose of culture supernatant showed that both iris and retinal pigment epithelial isolates were permissive to infection, and supported replication and release of EBOV, as well as RESTV and ZIKV. However, in comparison to cells isolated from iris, those from retina demonstrated obvious EBOV-induced cytopathic effect, had higher intracellular EBOV nucleoprotein transcript, expressed intracellular EBOV protein more widely, and released EBOV at higher titer. Comparable results were obtained for isolates infected with RESTV and ZIKV. Consistent with observations of retinal pigment epithelial scars in Ebola survivors, our results suggest that an early event in post-Ebola uveitis is infection of the retinal pigment epithelium. Relative susceptibility of retinal pigment epithelial cells to infection with RESTV and ZIKV, as well as EBOV, implies this phenomenon may relate to a cell-specific attribute, such as high phagocytic activity.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45571832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intricacy of Mitochondrial Dynamics and Antiviral Response During RNA Virus Infection","authors":"Sneha Singh, Karim Dirani, Ajay Kumar","doi":"10.3389/fviro.2022.918806","DOIUrl":"https://doi.org/10.3389/fviro.2022.918806","url":null,"abstract":"Viruses are known to hijack the intracellular organelles, including mitochondria, endoplasmic reticulum, lipid droplets, and cytoskeleton to promote its replication. The host responds to invading viruses by mounting antiviral responses and rearrangement of its organelles. In particular, the mitochondria are one of the target organelles exploited by viruses and their proteins to suppress the host antiviral response. In this review, we have comprehensively summarized the impact of mitochondrial dynamics in modulating antiviral response during emerging and re-emerging RNA virus infections caused by genus Flavivirus (Dengue virus, Zika virus, Hepatitis C virus), and SARS-CoV-2, the causative agent of COVID-19 pandemic. In addition to knowledge gaps in mitochondria-virus interaction studies, we discuss recent advancements in therapeutics regulating the mitochondrial dynamics to combat viral infections.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46424268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Host Immune Responses to Retroviral Infections","authors":"M. Miyazawa, M. Clerici","doi":"10.3389/fviro.2022.945530","DOIUrl":"https://doi.org/10.3389/fviro.2022.945530","url":null,"abstract":"Upon infection, retroviruses reverse transcribe their genome and integrate it into host chromosomes as proviruses; as such retroviruses are one of the greatest threats to the genetic integrity of all cellular organisms. At this point proviruses can hide inside host cells in a latent phase; however, when they are expressed and viral proteins are translated, their presence is recognized by the adaptive immune system. Thus, when inoculated into immunocompetent hosts, retroviruses can be rapidly eliminated and cause no pathology (1). To establish a long enough period of productive infection that allows interindividual transmission, retroviruses must overcome and/or evade host immune responses. Acutely transforming retroviruses overcome immune attacks by inducing rapid proliferation of infected cells, while non-acute retroviruses elaborate several different mechanisms to evade host immune responses and establish persistent infection. These mechanisms work through camouflaging viral particles, suppressing gene expression within infected cells, and inducing central and peripheral immune non-responsiveness. In this Research Topic, four groups of authors provide new insights into the different strategies that retroviruses have developed in the attempt to evade host immune responses and establish persistent infection. It has been known for a long time that when egressing from infected cells retroviruses incorporate host cell proteins into their envelope (reviewed in 2). This process is not just passive but some particular groups of host cell proteins are selectively incorporated from the plasma membrane into budding virions through interactions with viral proteins. Immunologically relevant examples of host cell proteins that are enriched in retroviral envelopes are MHC proteins, cell adhesion molecules and complement regulating factors (2). Using newly developed technique offlow virometry, Maltseva and Langlois have shown that the incorporation of tetraspanins and lipid raft-associated Thy1.2 andCD45 into Moloney murine leukemia virus (MuLV) particles is influenced by the presence or absence of the viral accessory protein, glycosylated Gag (glycoGag). GlycoGag is unnecessary for in vitro replication of MuLVs but is required for their efficient proliferation and pathogenicity in vivo, and glycoGag-deficient MuLV revert to glycoGag-expressing ones during in vivo propagation and tumorigenesis (3–5). GlycoGag is also implicated in the resistance of reverse transcription to the host restriction factor APOBEC3 (6). Thus, the paper by Maltseva and Langlois suggests that glycoGag may affect MuLV replication and pathogenesis not only through resistance to restriction factors but also by modulating incorporation of host-derived proteins into budding virions. As described above, non-acute retrovirusesmust evade host immune responses to establish persistent infection. Results by Higuchi et al. summarize HTLV-1’s strategies for evading immune responses,","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47254854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interferon Alpha-Inducible Protein 27 Expression Is Linked to Disease Severity in Chronic Infection of Both HIV-1 and HIV-2","authors":"A. Palm, Srinivas Veerla, Jacob Lindman, P. Isberg, Emil Johansson, Antonio J. Biague, F. Månsson, H. Norrgren, J. Esbjörnsson, P. Medstrand, M. Jansson","doi":"10.3389/fviro.2022.929053","DOIUrl":"https://doi.org/10.3389/fviro.2022.929053","url":null,"abstract":"Disease progression is slower in HIV-2, as compared with HIV-1 infection, in accordance with low or undetectable plasma viremia at viral setpoint. However, it is unclear why most HIV-2 infected individuals are still at risk of developing AIDS. To explore if specific host responses are linked to HIV disease severity, we have compared blood gene expression profiles between HIV seronegative and HIV-1, HIV-2 or dually HIV-1/HIV-2 infected individuals. In this study the gene encoding Interferon alpha-inducible protein 27 (IFI27) was found to be the most differentially expressed. Detailed expression analysis revealed significantly higher IFI27 expression in HIV infected individuals compared with seronegative individuals, irrespectively of HIV type. Moreover, IFI27 expression was higher in HIV-1 than in HIV-2 infected individuals. Multiple linear regression analysis, adjusting for age and sex, showed also that plasma viral load was the strongest predictor of IFI27 expression, followed by CD4% and HIV type. In line with this, IFI27 expression was found to be higher in HIV-2 viremic, compared with HIV-2 aviremic individuals. Still, HIV-2 aviremic individuals displayed elevated IFI27 expression compared with seronegative individuals. Furthermore, in HIV-2 infected individuals, IFI27 expression was also correlated with plasma markers previously linked to inflammation and disease progression in HIV infection. Taken together, our findings suggest that sustained elevation of type I interferon signaling, here reflected by elevated IFI27 expression in the chronic infection phase, is a key pathogenic feature of both HIV-1 and HIV-2.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43695783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mimiviruses Interfere With IκBα Degradation","authors":"Juliana dos Santos Oliveira, D. F. Oliveira, Victor Alejandro Essus, Gabriel Henrique Pereira Nunes, L. Honorato, J. M. Peralta, L. Nimrichter, A. Guimarães, D. Foguel, A. Filardy, Juliana R. Cortines","doi":"10.3389/fviro.2022.908704","DOIUrl":"https://doi.org/10.3389/fviro.2022.908704","url":null,"abstract":"Many aspects of giant viruses biology still eludes scientists, with viruses such as Acanthamoeba polyphaga mimivirus (APMV) and Tupanvirus (TPV) possessing large virions covered by fibrils and are cultivated in laboratories using Acanthamoeba cells as hosts. However, little is known about the infectivity of these giant viruses in vertebrate cells. In the present study, we investigated the consequences of the incubation of APMV and Tupanvirus with mammalian cells. These cells express Toll-like receptors (TLR) that are capable of recognizing lipopolysaccharides, favoring the internalization of the antigen and activation of the inflammatory system. By using a lineage of human lung adenocarcinoma cells (A549), we found that APMV and TPV virus particles interact and are internalized by these cells. Furthermore, when treating cells with a fibriless variant of APMV, the M4 strain, there was no significant loss of cell viability, reinforcing the roles of fibrils in cell activation. In addition, we found an upregulation of TLR4 expression and an expected down regulation of IκBα in A549 APMV or TPV-infected cells compared to non-infected cells. Our results suggest that mimiviruses are able to interact with innate immune components such as TLR4, inducing their downstream signaling pathway, which ultimately active proinflammatory responses in lung cells.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47973390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype F Mumps Viruses Continue to Circulate in China, From 1995 to 2019","authors":"Yao Su, Jianyang Liu, Mingchen Liu, Meng Li, Fan Gao, Changgui Li, Zhenglun Liang, Xing Wu, Q. Mao, Qian Wang, Lian-lian Bian","doi":"10.3389/fviro.2022.901618","DOIUrl":"https://doi.org/10.3389/fviro.2022.901618","url":null,"abstract":"Mumps, a disease caused by the mumps virus (MuV), has been spread widely across the world, especially among children and adolescents. Recent frequent local mumps outbreaks were reported worldwide, which may be caused by the decline in the neutralization ability of the existing attenuated live mumps vaccines against circulating MuV strains which were different from the genotype A or B vaccine strains. There is an urgent need to understand the genotypes of MuV strains currently circulated globally and in China. The gene sequences of MuV strains circulated globally were collected and phylogenetic trees were constructed using different strategies. The results showed that the MuV strains previously circulated globally were predominantly genotype G, while genotype F was predominantly circulated in China, followed by genotype G. The molecular evolution of genotype F MuV strains circulated in China is at a low genetic mutation rate, and the analysis of population dynamics pattern indicates that the incidence of genotype F mumps in China showed a rebound trend. These findings provide a basis for the selection or design of vaccine strains, and the decision of the evaluation strains for immunogenicity and protective efficacy, which laid the foundation for the research and development, as well as the application of next-generation MuV vaccines.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47901827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}