Frontiers in virology最新文献

{"title":"Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling","authors":"Colby T. Ford, Shirish Yasa, Denis Jacob Machado, Richard Allen White, Daniel A. Janies","doi":"10.3389/fviro.2023.1172027","DOIUrl":"https://doi.org/10.3389/fviro.2023.1172027","url":null,"abstract":"The SARS-CoV-2 variant XBB.1.5 is of concern as it has high transmissibility. XBB.1.5 currently accounts for upwards of 30% of new infections in the United States. One year after our group published the predicted structure of the Omicron (B.1.1.529) variant’s receptor binding domain (RBD) and antibody binding affinity, we return to investigate the new mutations seen in XBB.1.5 which is a descendant of Omicron. Using in silico modeling approaches against newer neutralizing antibodies that are shown effective against B.1.1.529, we predict the immune consequences of XBB.1.5’s mutations and show that there is no statistically significant difference in overall antibody evasion when comparing to the B.1.1.529 and other related variants (e.g., BJ.1 andBM.1.1.1). However, noticeable changes in antibody binding affinity were seen due to specific amino acid changes of interest in the newer variants.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136380012","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":"Molecular characterization of dengue virus serotype 1 infections in French travelers from Africa between 2013 and 2019","authors":"T. Fourié, G. Durand, F. Touret, G. Piorkowski, A. Dubot-Pérès, X. D. de Lamballerie, I. Leparc-Goffart, G. Grard","doi":"10.3389/fviro.2023.1124848","DOIUrl":"https://doi.org/10.3389/fviro.2023.1124848","url":null,"abstract":"Laboratory-confirmed dengue virus (DENV) infections in Africa are rarely reported. In this study, we report 18 DENV serotype 1 (DENV-1) infections, diagnosed by the French National Reference Center for Arboviruses, in patients who had histories of recent travel in Africa. Our analyses revealed two cases, one from Niger in 2018 and one from the Republic of the Congo in 2016, where dengue fever had not been previously reported, and one case from Mauritania in 2015, where DENV-1 had not been previously reported. These cases support the reported spread of DENV outside its well-established tropical and subtropical environment toward the arid deserts of the Sahel. Phylogenetic analyses suggest that a single monophyletic DENV-1 lineage is currently in circulation in West Africa, having spread from East Africa after its original importation from Asia. Our study provides an improved understanding of DENV dynamics in Africa and underlines the importance of surveillance of travel-acquired infections.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42287196","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":"Regulation of viral RNA-dependent RNA polymerases by phosphorylation","authors":"Camille Duflos, T. Michiels","doi":"10.3389/fviro.2023.1176840","DOIUrl":"https://doi.org/10.3389/fviro.2023.1176840","url":null,"abstract":"RNA viruses encode an RNA-dependent RNA polymerase (RdRp), which is essential for transcription and replication of their genome since host cells lack equivalent enzymes. RdRp residues were shown to be phosphorylated by host kinases in several human, animal or plant viruses including flaviviruses, picornaviruses, coronaviruses, influenza viruses and tymoviruses. RdRps can be phosphorylated on several residues by distinct host kinases. Phosphomimetic mutations of identified phosphorylated residues either positively or negatively regulate RNA synthesis or association of RdRps with RNA or other proteins. Interestingly, some RdRps evolved to recruit cellular kinases through direct protein-protein interaction, likely to promote or to tightly control their own phosphorylation. Given the essential nature of RdRps for RNA virus replication, a better knowledge of RdRps’ phosphorylation is expected to facilitate the design of future drugs that strongly affect polymerase activity.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42688221","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":"Co-detection of respiratory syncytial virus with other respiratory viruses across all age groups before and during the COVID-19 pandemic","authors":"Haya Hayek, Justin Z. Amarin, Yasmeen Z. Qwaider, A. Khanfar, Tess Stopczynski, J. Schmitz, J. Chappell, J. Wrenn, A. Spieker, N. Halasa, L. Howard","doi":"10.3389/fviro.2023.1156012","DOIUrl":"https://doi.org/10.3389/fviro.2023.1156012","url":null,"abstract":"Background Patterns of respiratory syncytial virus (RSV) co-detection with other viruses may have been disrupted during the coronavirus disease 2019 (COVID-19) pandemic, but the clinical impact of viral co-detections with RSV is not well-established. We aimed to explore the frequency and clinical outcomes associated with RSV single detection and co-detection before and during the pandemic. Methods We conducted a single-center retrospective cohort study of all children and adults with respiratory samples tested using a respiratory pathogen panel (RPP; 01/01/2018–11/30/2022), a provider-ordered polymerase chain reaction–based assay that detects respiratory pathogens. We stratified our cohort into age groups: 0–4, 5–17, 18–64, and ≥65 years old. Among RSV-positive samples, we compared the proportion of samples with single RSV detection before and during the pandemic and the patterns of specific viral co-detections. We compared the odds of hospitalization, oxygen use, intensive care unit admission, and intubation between individuals with RSV single detection and those with co-detection. Results Among 57,940 samples collected during the study period, 3,986 (6.9%) were RSV-positive. RSV was co-detected with at least one other virus in 1,231/3,158 (39.0%), 104/348 (29.9%), 49/312 (15.7%), and 21/168 (12.5%) of samples from individuals 0–4, 5–17, 18–64, and ≥65 years old, respectively. The relative frequencies of RSV single detection and co-detection were comparable before and during the pandemic except in children 0–4 years old, in whom single RSV detections were more prevalent before (63.7%) than during (59.5%) the pandemic (p=0.021). In children 0–4 years old, RSV co-detection was associated with lower odds of hospitalization compared to single RSV detection, and RSV co-detection with parainfluenza viruses or human rhinovirus/enterovirus was associated with significantly lower odds of hospitalization, while RSV/SARS-CoV-2 co-detection was associated with higher odds of ICU admission. In adults ≥65 years old, RSV co-detection was associated with lower odds of oxygen use. Conclusion The proportion of RSV co-detection did not appreciably vary before and during the pandemic, except in young children, though the combinations of co-detected viruses did vary. Our findings suggest that the clinical impact of RSV co-detection with other viruses may be age-associated and virus-specific.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41584954","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":"Identification of surfactin as an anti-severe fever with thrombocytopenia syndrome virus multi-target compound extracted from the culture broth of marine microbes","authors":"Shuzo Urata, Jun Takouda, Yoshihiro Watanabe, M. Sakaguchi, Yasuteru Sakurai, Y. Inahashi, M. Iwatsuki, J. Yasuda, Yoshimasa Tanaka, K. Takeda","doi":"10.3389/fviro.2022.1064265","DOIUrl":"https://doi.org/10.3389/fviro.2022.1064265","url":null,"abstract":"Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne virus first identified in China in 2011 and later reported in other Asian countries. Significant efforts have been made to develop anti-SFTSV compounds; however, there are no approved vaccines or antivirals against SFTSV infections. Marine organisms provide nearly unlimited biological resources to produce therapeutic drugs for the treatment and control of disease. In this study, we aimed to identify anti-SFTSV chemical compounds from the culture broth extracts of marine microbes collected from the coasts of the Nagasaki Prefecture, Japan. Of the 80 extracts, two showed an anti-SFTSV effect. One of them, which exhibited low cell toxicity, was used for further characterization. Chemical analysis combined with the anti-SFTSV effect identified surfactin as one of the main components of the selected extract. Our study showed a proof-of-concept to identify novel antiviral compounds from marine microbes against the virus of interest. Further analysis showed that surfactin affected the integrity of the virion membrane and inhibited SFTSV infection-induced membrane fusion at low pH conditions. Furthermore, surfactin inhibits the post-entry step of viral replication in the cell, which is a novel mode of antiviral action of surfactin. These results indicate that surfactin can target multiple steps of SFTSV replication in cells.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41581046","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":"Oral intake of heat-killed Lactiplantibacillus pentosus ONRICb0240 partially protects mice against SARS-CoV-2 infection","authors":"Maki Kiso, R. Uraki, Mutsumi Ito, S. Yamayoshi, Yoshifumi Kotani, M. Imai, N. Kohda, Y. Kawaoka","doi":"10.3389/fviro.2023.1137133","DOIUrl":"https://doi.org/10.3389/fviro.2023.1137133","url":null,"abstract":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing coronavirus pandemic. Besides vaccines and antiviral drugs, probiotics have attracted attention for prevention of SARS-CoV-2 infection. Here, we examined the efficacy of heat-killed Lactiplantibacillus pentosus ONRICb0240 (b240) against SARS-CoV-2 infection in mice. We observed that oral intake of heat-killed b240 did not affect virus titers in the respiratory organs of SARS-CoV-2-infected mice, but did provide partial protection against SARS-CoV-2 infection. In addition, heat-killed b240 treatment suppressed the expression of IL-6, a key proinflammatory cytokine, on Day 2 post-infection. Our results highlight the promising protective role of heat-killed b240 and suggest a possible mechanism by which heat-killed b240 partially protects against SARS-CoV-2 infection by modulating host responses.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47231200","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":"Epitope mapping of SARS-CoV-2 spike protein differentiates the antibody binding activity in vaccinated and infected individuals","authors":"Nathaniel Felbinger, D. Trudil, L. Loomis, R. Ascione, G. Siragusa, S. Haba, Shruti Rastogi, Aidan Mucci, Mark Claycomb, Sebastian Snowberger, B. Luke, S. Francesconi, Shirley Tsang","doi":"10.3389/fviro.2023.988109","DOIUrl":"https://doi.org/10.3389/fviro.2023.988109","url":null,"abstract":"Previous studies have attempted to characterize the antibody response of individuals to the SARS-CoV-2 virus on a linear peptide level by utilizing peptide microarrays. These studies have helped to identify epitopes that have potential to be used for diagnostic tests to identify infected individuals. The immunological responses of individuals who have received the two most popular vaccines available in the US, the Moderna mRNA-1273 or the Pfizer BNT162b2 mRNA vaccines, have not been characterized. We aimed to identify linear peptides of the SARS-CoV-2 spike protein that elicited high IgG or IgA binding activity and to compare the immunoreactivity of infected individuals to those who received both doses of either vaccine by utilizing peptide microarrays. Our results revealed peptide epitopes of significant IgG binding among recently infected individuals. Some of these peptides are located near variable regions of the receptor binding domains as well as the conserved region in the c-terminal of the spike protein implicated in the high infectivity of SARS-CoV-2. Vaccinated individuals lacked a response to these distinct markers despite the overall antibody binding activity being similar.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46550990","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":"Willingness to accept COVID-19 vaccine and its determinants in Ethiopia: A systematic review and meta-analysis","authors":"Tadesse Tolossa, Getahun Fetensa, Bikila Regassa Feyisa, B. Wakuma, Matiyos Lema","doi":"10.3389/fviro.2023.1065991","DOIUrl":"https://doi.org/10.3389/fviro.2023.1065991","url":null,"abstract":"Introduction Vaccination is one of the most crucial strategies in the control of pandemics such as COVID-19. Although a couple of research has been conducted to assess the willingness of the population to accept the COVID-19 vaccine, the findings are inconsistent and inconclusive. This study aimed to assess the pooled willingness to uptake the COVID-19 vaccine and its determinants in Ethiopia. Methods Published and unpublished articles were accessed from various electronic databases and digital libraries. A random-effects model was used to estimate the pooled effect size with a 95% confidence interval. Inverse variance (I2) was used to visualize the presence of heterogeneity. Publication bias was assessed using funnel plots and Egger’s statistical test. Results A total of 2345 studies were identified from several databases and 16 studies fulfilled the eligibility criteria and were included in the final meta-analysis. The pooled magnitude of willingness to accept the COVID-19 vaccine in Ethiopia was 55.19% (95% CI: 42.91, 67.48). The current meta-analysis indicated that age greater than 25 years (OR=1.49, 95% CI: 1.12, 1.98) and having a good attitude towards the COVID-19 vaccine (3.57, 95% CI: 1.46, 8.72) were significantly associated with the COVID-19 vaccine uptake. Conclusions and recommendations In general, the magnitude of the COVID-19 vaccine acceptance rate among the public is unacceptably low in Ethiopia. Therefore, there is a need to build public trust through the provision of reliable and consistent information about vaccines using different media outlets.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42909130","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":"Visualisation of microalgal-viral interactions by high-speed atomic force microscopy","authors":"Christopher T Evans, O. Payton, L. Picco, M. Allen","doi":"10.3389/fviro.2023.1111335","DOIUrl":"https://doi.org/10.3389/fviro.2023.1111335","url":null,"abstract":"Visualization of viruses and their hosts has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. This study demonstrates progress that has been made in exploiting the capabilities offered by HS-AFM to characterise the interactions between coccolithoviruses and their globally important coccolithophore hosts. We observe whole Emiliania huxleyi Virus capsids, transient binding to Emiliania huxleyi derived supported lipid bilayers, and host-virus binding in real-time in an environmentally relevant, aqueous environment.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41920640","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":"Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.","authors":"Pradeepa Pushparaj,&nbsp;Andrea Nicoletto,&nbsp;Xaquin Castro Dopico,&nbsp;Daniel J Sheward,&nbsp;Sungyong Kim,&nbsp;Simon Ekström,&nbsp;Ben Murrell,&nbsp;Martin Corcoran,&nbsp;Gunilla B Karlsson Hedestam","doi":"10.3389/fviro.2023.1128253","DOIUrl":"https://doi.org/10.3389/fviro.2023.1128253","url":null,"abstract":"<p><p>The antibody response to SARS-CoV-2 shows biased immunoglobulin heavy chain variable (IGHV) gene usage, allowing definition of genetic signatures for some classes of neutralizing antibodies. We investigated IGHV gene usage frequencies by sorting spike-specific single memory B cells from individuals infected with SARS-CoV-2 early in the pandemic. From two study participants and 703 spikespecific B cells, the most used genes were IGHV1-69, IGHV3-30-3, and IGHV3-30. Here, we focused on the IGHV3-30 group of genes and an IGHV3-30-3-using ultrapotent neutralizing monoclonal antibody, CAB-F52, which displayed broad neutralizing activity also in its germline-reverted form. IGHV3-30-3 is encoded by a region of the IGH locus that is highly variable at both the allelic and structural levels. Using personalized IG genotyping, we found that 4 of 14 study participants lacked the IGHV3-30-3 gene on both chromosomes, raising the question if other, highly similar IGHV genes could substitute for IGHV3-30-3 in persons lacking this gene. In the context of CAB-F52, we found that none of the tested IGHV3-33 alleles, but several IGHV3-30 alleles could substitute for IGHV3-30-3, suggesting functional redundancy between the highly homologous IGHV3-30 and IGHV3-30-3 genes for this antibody.</p>","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"3 ","pages":"1128253"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9302856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}