Jean-Baka Domelevo Entfellner, Edward Abworo Okoth, Cynthia Kavulani Onzere, Chris Upton, Emma Peter Njau, Dirk Höper, Sonal P. Henson, Samuel O. Oyola, Edwina Bochere, Eunice M. Machuka, Richard P. Bishop
African swine fever virus (ASFV) is endemic to African wild pigs (Phacochoerus and Potamochoerus), in which viral infection is asymptomatic, and Ornithodoros soft ticks. However, ASFV causes a lethal disease in Eurasian domestic pigs (Sus scrofa). While Sub-Saharan Africa is believed to be the original home of ASFV, publicly available whole-genome ASFV sequences show a strong bias towards p72 Genotypes I and II, which are responsible for domestic pig pandemics outside Africa. To reduce this bias, we hereby describe nine novel East African complete genomes in p72 Genotype IX and present the phylogenetic analysis of all 16 available Genotype IX genomes compared with other ASFV p72 clades. We also document genome-level differences between one specific novel Genotype IX genome sequence (KE/2013/Busia.3) and a wild boar cell-passaged derivative. The Genotype IX genomes clustered with the five available Genotype X genomes. By contrast, Genotype IX and X genomes were strongly phylogenetically differentiated from all other ASFV genomes. The p72 gene region, on which the p72-based virus detection primers are derived, contains consistent SNPs in Genotype IX, potentially resulting in reduced sensitivity of detection. In addition to the abovementioned cell-adapted variant, eight novel ASFV Genotype IX genomes were determined: five from viruses passaged once in primary porcine peripheral blood monocytes and three generated from DNA isolated directly from field-sampled kidney tissues. Based on this methodological simplification, genome sequencing of ASFV field isolates should become increasingly routine and result in a rapid expansion of knowledge pertaining to the diversity of African ASFV at the whole-genome level.
非洲猪瘟病毒（ASFV）是非洲野猪（Phacochoerus 和 Potamochoerus）和软蜱（Ornithodoros soft ticks）的地方性传染病。然而，ASFV 会导致欧亚家猪（Sus scrofa）患上致命疾病。虽然撒哈拉以南非洲地区被认为是 ASFV 的原产地，但公开的 ASFV 全基因组序列显示，p72 基因型 I 和 II 有很强的偏向性，而这两种基因型是非洲以外地区家猪大流行的罪魁祸首。为了减少这种偏差，我们在此描述了 p72 基因型 IX 中的九个新的东非完整基因组，并将所有 16 个可用的基因型 IX 基因组与其他 ASFV p72 支系进行了系统发育分析。我们还记录了一个特定的新基因型 IX 基因组序列（KE/2013/Busia.3）与野猪细胞传代衍生物在基因组水平上的差异。基因型 IX 基因组与现有的五个基因型 X 基因组聚集在一起。相比之下，基因型 IX 和 X 基因组在系统发育上与所有其他 ASFV 基因组有很大区别。基于 p72 的病毒检测引物所基于的 p72 基因区在基因九型中含有一致的 SNP，可能导致检测灵敏度降低。除上述细胞适应变体外，还测定了 8 个新型 ASFV 基因型 IX 基因组：5 个来自在原代猪外周血单核细胞中传代一次的病毒，3 个来自直接从现场取样的肾组织中分离的 DNA。基于这种方法学上的简化，ASFV 现场分离物的基因组测序应该会越来越常规化，从而在全基因组水平上迅速扩展有关非洲 ASFV 多样性的知识。
{"title":"Complete Genome Sequencing and Comparative Phylogenomics of Nine African Swine Fever Virus (ASFV) Isolates of the Virulent East African p72 Genotype IX without Viral Sequence Enrichment","authors":"Jean-Baka Domelevo Entfellner, Edward Abworo Okoth, Cynthia Kavulani Onzere, Chris Upton, Emma Peter Njau, Dirk Höper, Sonal P. Henson, Samuel O. Oyola, Edwina Bochere, Eunice M. Machuka, Richard P. Bishop","doi":"10.3390/v16091466","DOIUrl":"https://doi.org/10.3390/v16091466","url":null,"abstract":"African swine fever virus (ASFV) is endemic to African wild pigs (Phacochoerus and Potamochoerus), in which viral infection is asymptomatic, and Ornithodoros soft ticks. However, ASFV causes a lethal disease in Eurasian domestic pigs (Sus scrofa). While Sub-Saharan Africa is believed to be the original home of ASFV, publicly available whole-genome ASFV sequences show a strong bias towards p72 Genotypes I and II, which are responsible for domestic pig pandemics outside Africa. To reduce this bias, we hereby describe nine novel East African complete genomes in p72 Genotype IX and present the phylogenetic analysis of all 16 available Genotype IX genomes compared with other ASFV p72 clades. We also document genome-level differences between one specific novel Genotype IX genome sequence (KE/2013/Busia.3) and a wild boar cell-passaged derivative. The Genotype IX genomes clustered with the five available Genotype X genomes. By contrast, Genotype IX and X genomes were strongly phylogenetically differentiated from all other ASFV genomes. The p72 gene region, on which the p72-based virus detection primers are derived, contains consistent SNPs in Genotype IX, potentially resulting in reduced sensitivity of detection. In addition to the abovementioned cell-adapted variant, eight novel ASFV Genotype IX genomes were determined: five from viruses passaged once in primary porcine peripheral blood monocytes and three generated from DNA isolated directly from field-sampled kidney tissues. Based on this methodological simplification, genome sequencing of ASFV field isolates should become increasingly routine and result in a rapid expansion of knowledge pertaining to the diversity of African ASFV at the whole-genome level.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255511","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}
Jinjin Yang, Rongnian Zhu, Nan Li, Yanyan Zhang, Xintao Zhou, Huixian Yue, Qixuan Li, Yu Wang, Faming Miao, Teng Chen, Fei Zhang, Shoufeng Zhang, Aidong Qian, Rongliang Hu
African swine fever (ASF) is an acute infectious disease with a high mortality rate in both domestic and wild boars. Commercial vaccines or antiviral drugs for ASF were not available due to the complex diversity of the structure and genome of its pathogen African swine fever virus (ASFV). In recent years, there have been many reports on candidate strains of attenuated vaccines for ASFV. In this study, we obtained a recombinant virus named SY18ΔL60LΔCD2v by simultaneously deleting the L60L gene and CD2v gene from highly virulent strain SY18. In vitro, SY18ΔL60LΔCD2v displayed a decreased growth kinetic compared to that of parental SY18. In vivo, high doses (105 TCID50) of SY18ΔL60LΔCD2v can protect pigs (5/5) from attacks by the parental SY18 strain (102 TCID50). Low doses (102 TCID50) of SY18ΔL60LΔCD2v only protected 20% of pigs (1/5) from attacks by the parental SY18 strain (102 TCID50). The results indicated that the absence of these two genes in SY18 could induce protection against the homologous parental strain, and there were no obvious clinical symptoms or viremia. These results indicate that the SY18ΔL60LΔCD2v strain can serve as a new live attenuated vaccine candidate for the prevention and control of ASFV infection.
{"title":"Protection Evaluation of a New Attenuated ASFV by Deletion of the L60L and CD2v Genes against Homologous Challenge","authors":"Jinjin Yang, Rongnian Zhu, Nan Li, Yanyan Zhang, Xintao Zhou, Huixian Yue, Qixuan Li, Yu Wang, Faming Miao, Teng Chen, Fei Zhang, Shoufeng Zhang, Aidong Qian, Rongliang Hu","doi":"10.3390/v16091464","DOIUrl":"https://doi.org/10.3390/v16091464","url":null,"abstract":"African swine fever (ASF) is an acute infectious disease with a high mortality rate in both domestic and wild boars. Commercial vaccines or antiviral drugs for ASF were not available due to the complex diversity of the structure and genome of its pathogen African swine fever virus (ASFV). In recent years, there have been many reports on candidate strains of attenuated vaccines for ASFV. In this study, we obtained a recombinant virus named SY18ΔL60LΔCD2v by simultaneously deleting the L60L gene and CD2v gene from highly virulent strain SY18. In vitro, SY18ΔL60LΔCD2v displayed a decreased growth kinetic compared to that of parental SY18. In vivo, high doses (105 TCID50) of SY18ΔL60LΔCD2v can protect pigs (5/5) from attacks by the parental SY18 strain (102 TCID50). Low doses (102 TCID50) of SY18ΔL60LΔCD2v only protected 20% of pigs (1/5) from attacks by the parental SY18 strain (102 TCID50). The results indicated that the absence of these two genes in SY18 could induce protection against the homologous parental strain, and there were no obvious clinical symptoms or viremia. These results indicate that the SY18ΔL60LΔCD2v strain can serve as a new live attenuated vaccine candidate for the prevention and control of ASFV infection.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255510","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}
Doris Villanueva-Pérez, Luis Tataje-Lavanda, Angela Montalván-Avalos, Diego Paredes-Inofuente, Suly Montoya-Ortiz, Gisela Isasi-Rivas, María F. Fernández, Manolo Fernández-Sánchez, Manolo Fernández-Díaz
Infectious Bronchitis Virus (IBV) is a major threat to the poultry industry worldwide, causing significant economic losses. While the virus’s genetic structure is well understood, the specific strains circulating in Bolivia have remained uncharacterized until now. This study aimed to identify and characterize new IBV strains in Bolivia. Tissue samples from broilers exhibiting clinical signs of Infectious Bronchitis were screened to detect IBV using real-time RT-PCR (RT-qPCR). Positive samples with low cycle threshold (Ct) values were selected for sequencing the full S1 gene. Of the 12 samples analyzed, 10 were determined to be positive for IBV. However, only four samples yielded sufficient genetic material for sequencing and subsequent phylogenetic analysis. The results revealed the presence of GI-1 and GI-23 lineages, both belonging to genotype I (GI). The GI-1 lineage showed >99% sequence identity to the H120 and Massachusetts vaccine strains, suggesting a close relationship. In contrast, the GI-23 lineage clustered with other IBV strains, showing a distinct subclade that is genetically distant from Brazilian strains. No evidence of recombination was found. Furthermore, amino acid substitution analysis identified specific mutations in the S1 subunit, particularly in the hypervariable regions 1, 2, and 3. These mutations could potentially alter the virus’s antigenicity, leading to reduced vaccine efficacy. The findings of this study highlight the importance of continued and broad genomic surveillance of circulating IBV strains and the need to improve vaccination strategies in Bolivia.
{"title":"Detection and Molecular Characterization of GI-1 and GI-23 Avian Infectious Bronchitis Virus in Broilers Indicate the Emergence of New Genotypes in Bolivia","authors":"Doris Villanueva-Pérez, Luis Tataje-Lavanda, Angela Montalván-Avalos, Diego Paredes-Inofuente, Suly Montoya-Ortiz, Gisela Isasi-Rivas, María F. Fernández, Manolo Fernández-Sánchez, Manolo Fernández-Díaz","doi":"10.3390/v16091463","DOIUrl":"https://doi.org/10.3390/v16091463","url":null,"abstract":"Infectious Bronchitis Virus (IBV) is a major threat to the poultry industry worldwide, causing significant economic losses. While the virus’s genetic structure is well understood, the specific strains circulating in Bolivia have remained uncharacterized until now. This study aimed to identify and characterize new IBV strains in Bolivia. Tissue samples from broilers exhibiting clinical signs of Infectious Bronchitis were screened to detect IBV using real-time RT-PCR (RT-qPCR). Positive samples with low cycle threshold (Ct) values were selected for sequencing the full S1 gene. Of the 12 samples analyzed, 10 were determined to be positive for IBV. However, only four samples yielded sufficient genetic material for sequencing and subsequent phylogenetic analysis. The results revealed the presence of GI-1 and GI-23 lineages, both belonging to genotype I (GI). The GI-1 lineage showed >99% sequence identity to the H120 and Massachusetts vaccine strains, suggesting a close relationship. In contrast, the GI-23 lineage clustered with other IBV strains, showing a distinct subclade that is genetically distant from Brazilian strains. No evidence of recombination was found. Furthermore, amino acid substitution analysis identified specific mutations in the S1 subunit, particularly in the hypervariable regions 1, 2, and 3. These mutations could potentially alter the virus’s antigenicity, leading to reduced vaccine efficacy. The findings of this study highlight the importance of continued and broad genomic surveillance of circulating IBV strains and the need to improve vaccination strategies in Bolivia.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255508","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}
Camilla Biba, Lia Fiaschi, Ilenia Varasi, Chiara Paletti, Niccolò Bartolini, Maurizio Zazzi, Ilaria Vicenti, Francesco Saladini
Background: Next-generation sequencing (NGS) kits are needed to finalise the transition from Sanger sequencing to NGS in HIV-1 genotypic drug resistance testing. Materials and Methods: We compared a homemade NGS amplicon-based protocol and the AD4SEQ HIV-1 Solution v2 (AD4SEQ) NGS kit from Arrow Diagnostics for identifying resistance-associated mutations (RAMs) above the 5% threshold in 28 plasma samples where Sanger sequencing previously detected at least one RAM. Results: The samples had a median 4.8 log [IQR 4.4–5.2] HIV-1 RNA copies/mL and were mostly subtype B (61%) and CRF02_AG (14%). Homemade NGS had a lower rate of samples with low-coverage regions (2/28) compared with AD4SEQ (13/28) (p < 0.001). Homemade NGS and AD4SEQ identified additional mutations with respect to Sanger sequencing in 13/28 and 9/28 samples, respectively. However, there were two and eight cases where mutations detected by Sanger sequencing were missed by homemade NGS and AD4SEQ-SmartVir, respectively. The discrepancies between NGS and Sanger sequencing resulted in a few minor differences in drug susceptibility interpretation, mostly for NNRTIs. Conclusions: Both the NGS systems identified additional mutations with respect to Sanger sequencing, and the agreement between them was fair. However, AD4SEQ should benefit from technical adjustments allowing higher sequence coverage.
{"title":"A Comparison of Sanger Sequencing and Amplicon-Based Next Generation Sequencing Approaches for the Detection of HIV-1 Drug Resistance Mutations","authors":"Camilla Biba, Lia Fiaschi, Ilenia Varasi, Chiara Paletti, Niccolò Bartolini, Maurizio Zazzi, Ilaria Vicenti, Francesco Saladini","doi":"10.3390/v16091465","DOIUrl":"https://doi.org/10.3390/v16091465","url":null,"abstract":"Background: Next-generation sequencing (NGS) kits are needed to finalise the transition from Sanger sequencing to NGS in HIV-1 genotypic drug resistance testing. Materials and Methods: We compared a homemade NGS amplicon-based protocol and the AD4SEQ HIV-1 Solution v2 (AD4SEQ) NGS kit from Arrow Diagnostics for identifying resistance-associated mutations (RAMs) above the 5% threshold in 28 plasma samples where Sanger sequencing previously detected at least one RAM. Results: The samples had a median 4.8 log [IQR 4.4–5.2] HIV-1 RNA copies/mL and were mostly subtype B (61%) and CRF02_AG (14%). Homemade NGS had a lower rate of samples with low-coverage regions (2/28) compared with AD4SEQ (13/28) (p < 0.001). Homemade NGS and AD4SEQ identified additional mutations with respect to Sanger sequencing in 13/28 and 9/28 samples, respectively. However, there were two and eight cases where mutations detected by Sanger sequencing were missed by homemade NGS and AD4SEQ-SmartVir, respectively. The discrepancies between NGS and Sanger sequencing resulted in a few minor differences in drug susceptibility interpretation, mostly for NNRTIs. Conclusions: Both the NGS systems identified additional mutations with respect to Sanger sequencing, and the agreement between them was fair. However, AD4SEQ should benefit from technical adjustments allowing higher sequence coverage.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255509","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}
Crystal G. Roux, Shayne Mason, Louise D. V. du Toit, Jan-Gert Nel, Theresa M. Rossouw, Helen C. Steel
Antiretroviral therapy (ART) has reduced the mortality and morbidity associated with HIV. However, irrespective of treatment, people living with HIV remain at a higher risk of developing non-AIDS-associated diseases. In 2019, the World Health Organization recommended the transition from efavirenz (EFV)- to dolutegravir (DTG)-based ART. Data on the impact of this transition are still limited. The current study therefore investigated the metabolic profiles, cytokine inflammatory responses, and platelet activation before and after the treatment transition. Plasma samples from nine virally suppressed adults living with HIV and sixteen healthy, HIV-uninfected individuals residing in Gauteng, South Africa were compared. Metabolite and cytokine profiles, and markers associated with platelet activation, were investigated with untargeted proton magnetic resonance metabolomics, multiplex suspension bead array immunoassays, and sandwich enzyme-linked immunosorbent assays, respectively. In those individuals with normal C-reactive protein levels, the transition to a DTG-based ART regimen resulted in decreased concentrations of acetoacetic acid, creatinine, adenosine monophosphate, 1,7-dimethylxanthine, glycolic acid, 3-hydroxybutyric acid, urea, and lysine. Moreover, increased levels of formic acid, glucose, lactic acid, myo-inositol, valine, glycolic acid, and 3-hydroxybutyric acid were observed. Notably, levels of interleukin-6, platelet-derived growth factor-BB, granulocyte-macrophage colony-stimulating factor, tumor necrosis factor–alpha, soluble cluster of differentiation 40 ligand, as well as regulated on activation, normal T-cell expressed and secreted (RANTES) reached levels close to those observed in the healthy control participants. The elevated concentration of macrophage inflammatory protein-1 alpha was the only marker indicative of elevated levels of inflammation associated with DTG-based treatment. The transition from EFV- to DTG-based regimens therefore appears to be of potential benefit with metabolic and inflammatory markers, as well as those associated with cardiovascular disease and other chronic non-AIDS-related diseases, reaching levels similar to those observed in individuals not living with HIV.
抗逆转录病毒疗法（ART）降低了与艾滋病毒相关的死亡率和发病率。然而，无论治疗与否，艾滋病毒感染者罹患非艾滋病相关疾病的风险仍然较高。2019 年，世界卫生组织建议从依非韦伦（EFV）为基础的抗逆转录病毒疗法过渡到多罗替拉韦（DTG）为基础的抗逆转录病毒疗法。有关这一过渡影响的数据仍然有限。因此，本研究调查了治疗过渡前后的代谢概况、细胞因子炎症反应和血小板活化情况。研究人员比较了居住在南非豪登省的九名病毒已被抑制的成年艾滋病病毒感染者和十六名健康的未感染艾滋病病毒者的血浆样本。分别采用非靶向质子磁共振代谢组学、多重悬浮珠阵列免疫分析法和夹心酶联免疫吸附分析法对代谢物和细胞因子谱以及与血小板活化相关的标记物进行了研究。在 C 反应蛋白水平正常的患者中，转用以 DTG 为基础的抗逆转录病毒疗法后，乙酰乙酸、肌酐、单磷酸腺苷、1,7-二甲基黄嘌呤、乙醇酸、3-羟丁酸、尿素和赖氨酸的浓度均有所下降。此外，还观察到甲酸、葡萄糖、乳酸、肌醇、缬氨酸、乙醇酸和 3-羟基丁酸的含量增加。值得注意的是，白细胞介素-6、血小板衍生生长因子-BB、粒细胞-巨噬细胞集落刺激因子、肿瘤坏死因子-α、可溶性分化簇 40 配体以及正常 T 细胞表达和分泌的活化调节因子（RANTES）的水平达到了接近健康对照组参与者的水平。巨噬细胞炎症蛋白-1α浓度的升高是唯一表明与 DTG 治疗相关的炎症水平升高的标志物。因此，从以 EFV 为基础的治疗方案过渡到以 DTG 为基础的治疗方案似乎具有潜在的益处，其代谢和炎症标志物以及与心血管疾病和其他非艾滋病相关慢性疾病有关的标志物达到了与未感染艾滋病毒的人相似的水平。
{"title":"Comparative Effects of Efavirenz and Dolutegravir on Metabolomic and Inflammatory Profiles, and Platelet Activation of People Living with HIV: A Pilot Study","authors":"Crystal G. Roux, Shayne Mason, Louise D. V. du Toit, Jan-Gert Nel, Theresa M. Rossouw, Helen C. Steel","doi":"10.3390/v16091462","DOIUrl":"https://doi.org/10.3390/v16091462","url":null,"abstract":"Antiretroviral therapy (ART) has reduced the mortality and morbidity associated with HIV. However, irrespective of treatment, people living with HIV remain at a higher risk of developing non-AIDS-associated diseases. In 2019, the World Health Organization recommended the transition from efavirenz (EFV)- to dolutegravir (DTG)-based ART. Data on the impact of this transition are still limited. The current study therefore investigated the metabolic profiles, cytokine inflammatory responses, and platelet activation before and after the treatment transition. Plasma samples from nine virally suppressed adults living with HIV and sixteen healthy, HIV-uninfected individuals residing in Gauteng, South Africa were compared. Metabolite and cytokine profiles, and markers associated with platelet activation, were investigated with untargeted proton magnetic resonance metabolomics, multiplex suspension bead array immunoassays, and sandwich enzyme-linked immunosorbent assays, respectively. In those individuals with normal C-reactive protein levels, the transition to a DTG-based ART regimen resulted in decreased concentrations of acetoacetic acid, creatinine, adenosine monophosphate, 1,7-dimethylxanthine, glycolic acid, 3-hydroxybutyric acid, urea, and lysine. Moreover, increased levels of formic acid, glucose, lactic acid, myo-inositol, valine, glycolic acid, and 3-hydroxybutyric acid were observed. Notably, levels of interleukin-6, platelet-derived growth factor-BB, granulocyte-macrophage colony-stimulating factor, tumor necrosis factor–alpha, soluble cluster of differentiation 40 ligand, as well as regulated on activation, normal T-cell expressed and secreted (RANTES) reached levels close to those observed in the healthy control participants. The elevated concentration of macrophage inflammatory protein-1 alpha was the only marker indicative of elevated levels of inflammation associated with DTG-based treatment. The transition from EFV- to DTG-based regimens therefore appears to be of potential benefit with metabolic and inflammatory markers, as well as those associated with cardiovascular disease and other chronic non-AIDS-related diseases, reaching levels similar to those observed in individuals not living with HIV.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255473","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}
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady Verkhivker
The most recent wave of SARS-CoV-2 Omicron variants descending from BA.2 and BA.2.86 exhibited improved viral growth and fitness due to convergent evolution of functional hotspots. These hotspots operate in tandem to optimize both receptor binding for effective infection and immune evasion efficiency, thereby maintaining overall viral fitness. The lack of molecular details on structure, dynamics and binding energetics of the latest FLiRT and FLuQE variants with the ACE2 receptor and antibodies provides a considerable challenge that is explored in this study. We combined AlphaFold2-based atomistic predictions of structures and conformational ensembles of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the most dominant Omicron variants JN.1, KP.1, KP.2 and KP.3 to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and computations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. The results suggested the existence of epistatic interactions between convergent mutational sites at L455, F456, Q493 positions that protect and restore ACE2-binding affinity while conferring beneficial immune escape. To examine immune escape mechanisms, we performed structure-based mutational profiling of the spike protein binding with several classes of antibodies that displayed impaired neutralization against BA.2.86, JN.1, KP.2 and KP.3. The results confirmed the experimental data that JN.1, KP.2 and KP.3 harboring the L455S and F456L mutations can significantly impair the neutralizing activity of class 1 monoclonal antibodies, while the epistatic effects mediated by F456L can facilitate the subsequent convergence of Q493E changes to rescue ACE2 binding. Structural and energetic analysis provided a rationale to the experimental results showing that BD55-5840 and BD55-5514 antibodies that bind to different binding epitopes can retain neutralizing efficacy against all examined variants BA.2.86, JN.1, KP.2 and KP.3. The results support the notion that evolution of Omicron variants may favor emergence of lineages with beneficial combinations of mutations involving mediators of epistatic couplings that control balance of high ACE2 affinity and immune evasion.
{"title":"AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance","authors":"Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady Verkhivker","doi":"10.3390/v16091458","DOIUrl":"https://doi.org/10.3390/v16091458","url":null,"abstract":"The most recent wave of SARS-CoV-2 Omicron variants descending from BA.2 and BA.2.86 exhibited improved viral growth and fitness due to convergent evolution of functional hotspots. These hotspots operate in tandem to optimize both receptor binding for effective infection and immune evasion efficiency, thereby maintaining overall viral fitness. The lack of molecular details on structure, dynamics and binding energetics of the latest FLiRT and FLuQE variants with the ACE2 receptor and antibodies provides a considerable challenge that is explored in this study. We combined AlphaFold2-based atomistic predictions of structures and conformational ensembles of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the most dominant Omicron variants JN.1, KP.1, KP.2 and KP.3 to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and computations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. The results suggested the existence of epistatic interactions between convergent mutational sites at L455, F456, Q493 positions that protect and restore ACE2-binding affinity while conferring beneficial immune escape. To examine immune escape mechanisms, we performed structure-based mutational profiling of the spike protein binding with several classes of antibodies that displayed impaired neutralization against BA.2.86, JN.1, KP.2 and KP.3. The results confirmed the experimental data that JN.1, KP.2 and KP.3 harboring the L455S and F456L mutations can significantly impair the neutralizing activity of class 1 monoclonal antibodies, while the epistatic effects mediated by F456L can facilitate the subsequent convergence of Q493E changes to rescue ACE2 binding. Structural and energetic analysis provided a rationale to the experimental results showing that BD55-5840 and BD55-5514 antibodies that bind to different binding epitopes can retain neutralizing efficacy against all examined variants BA.2.86, JN.1, KP.2 and KP.3. The results support the notion that evolution of Omicron variants may favor emergence of lineages with beneficial combinations of mutations involving mediators of epistatic couplings that control balance of high ACE2 affinity and immune evasion.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206863","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}
Maria Nannyonjo, Jonah Omooja, Daniel Lule Bugembe, Nicholas Bbosa, Sandra Lunkuse, Stella Esther Nabirye, Faridah Nassolo, Hamidah Namagembe, Andrew Abaasa, Anne Kazibwe, Pontiano Kaleebu, Deogratius Ssemwanga
We assessed the performance and clinical relevance of Illumina MiSeq next-generation sequencing (NGS) for HIV-1 genotyping compared with Sanger sequencing (SS). We analyzed 167 participants, 45 with virologic failure (VL ≥ 1000 copies/mL), i.e., cases, and 122 time-matched participants with virologic suppression (VL < 1000 copies/mL), i.e., controls, 12 months post-ART initiation. Major surveillance drug resistance mutations (SDRMs) detected by SS were all detectable by NGS. Among cases at 12 months, SS identified SDRMs in 32/45 (71.1%) while NGS identified SDRMs among 35/45 (77.8%), increasing the number of cases with SDRMs by 3/45 (6.7%). Participants identified with, and proportions of major SDRMs increased when NGS was used. NGS vs. SS at endpoint revealed for NNRTIs: 36/45 vs. 33/45; Y181C: 26/45 vs. 24/45; K103N: 9/45 vs. 6/45 participants with SDRMs, respectively. At baseline, NGS revealed major SDRMs in 9/45 (20%) cases without SDRMs by SS. Participant MBL/043, among the nine, the following major SDRMs existed: L90M to PIs, K65R and M184V to NRTIs, and Y181C and K103N to NNRTIs. The SDRMs among the nine increased SDRMs to NRTIs, NNRTIs, and PIs. Only 43/122 (25.7%) of participants had pre-treatment minority SDRMs. Also, 24.4% of the cases vs. 26.2 of controls had minority SDRMs (p = 0.802); minority SDRMs were not associated with virologic failure. NGS agreed with SS in HIV-1 genotyping but detected additional major SDRMs and identified more participants harboring major SDRMs, expanding the HIV DRM profile of this cohort. NGS could improve HIV genotyping to guide treatment decisions for enhancing ART efficacy, a cardinal pre-requisite in the pursuit of the UNAIDS 95-95-95 targets.
{"title":"Next-Generation Sequencing Reveals a High Frequency of HIV-1 Minority Variants and an Expanded Drug Resistance Profile among Individuals on First-Line ART","authors":"Maria Nannyonjo, Jonah Omooja, Daniel Lule Bugembe, Nicholas Bbosa, Sandra Lunkuse, Stella Esther Nabirye, Faridah Nassolo, Hamidah Namagembe, Andrew Abaasa, Anne Kazibwe, Pontiano Kaleebu, Deogratius Ssemwanga","doi":"10.3390/v16091454","DOIUrl":"https://doi.org/10.3390/v16091454","url":null,"abstract":"We assessed the performance and clinical relevance of Illumina MiSeq next-generation sequencing (NGS) for HIV-1 genotyping compared with Sanger sequencing (SS). We analyzed 167 participants, 45 with virologic failure (VL ≥ 1000 copies/mL), i.e., cases, and 122 time-matched participants with virologic suppression (VL < 1000 copies/mL), i.e., controls, 12 months post-ART initiation. Major surveillance drug resistance mutations (SDRMs) detected by SS were all detectable by NGS. Among cases at 12 months, SS identified SDRMs in 32/45 (71.1%) while NGS identified SDRMs among 35/45 (77.8%), increasing the number of cases with SDRMs by 3/45 (6.7%). Participants identified with, and proportions of major SDRMs increased when NGS was used. NGS vs. SS at endpoint revealed for NNRTIs: 36/45 vs. 33/45; Y181C: 26/45 vs. 24/45; K103N: 9/45 vs. 6/45 participants with SDRMs, respectively. At baseline, NGS revealed major SDRMs in 9/45 (20%) cases without SDRMs by SS. Participant MBL/043, among the nine, the following major SDRMs existed: L90M to PIs, K65R and M184V to NRTIs, and Y181C and K103N to NNRTIs. The SDRMs among the nine increased SDRMs to NRTIs, NNRTIs, and PIs. Only 43/122 (25.7%) of participants had pre-treatment minority SDRMs. Also, 24.4% of the cases vs. 26.2 of controls had minority SDRMs (p = 0.802); minority SDRMs were not associated with virologic failure. NGS agreed with SS in HIV-1 genotyping but detected additional major SDRMs and identified more participants harboring major SDRMs, expanding the HIV DRM profile of this cohort. NGS could improve HIV genotyping to guide treatment decisions for enhancing ART efficacy, a cardinal pre-requisite in the pursuit of the UNAIDS 95-95-95 targets.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206859","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}
Hunter Spencer, Devin Gregoire, Gillian Leichtling, Megan Herink, Andrew Seaman, P. Todd Korthuis, Ryan Cook
Hepatitis C (HCV) treatment for people who use drugs (PWUD) decreases injection drug use and injection equipment sharing. We examined changes in injection drug use and injection equipment sharing following HCV treatment in a randomized trial comparing peer-assisted telemedicine for HCV treatment (TeleHCV) versus peer-assisted usual care in rural PWUD. We hypothesize that TeleHCV reduces risky behaviors and peers facilitate this change. We used mixed-effects logistic regression to describe participant-level (n = 203) associations between both injection drug use and injection equipment sharing and randomized groups, frequency of peer contact, HCV treatment initiation, HCV cure, and time. Risky behaviors were surveyed at baseline and 12 and 36 weeks after HCV treatment completion. Injection drug use declined more over time in TeleHCV participants vs. control at 12 weeks (adjusted odds ratio [aOR] = 0.42, 95% CI 0.20–0.87, p = 0.02) and 36 weeks (aOR = 0.48, 95% CI 0.21–1.08, p = 0.076). Injection drug use decreased more with a greater number of peer interactions, with reductions among participants in the 3rd quartile exceeding those in the 1st quartile of peer interactions at 12 weeks (aOR = 0.75, 95% CI 0.57–0.99, p = 0.04). Similarly, injection equipment sharing decreased over time, with reductions among participants in the 3rd quartile exceeding those in the 1st quartile of peer interactions at 36 weeks (aOR = 0.08, 95% CI 0.01–0.97, p = 0.047). Peer-assisted telemedicine for HCV treatment decreases injection drug use and injection equipment sharing; peers contribute to this effect.
{"title":"Harm Reduction in Peer-Assisted Telemedicine for Hepatitis C: Secondary Outcomes of a Randomized Controlled Trial","authors":"Hunter Spencer, Devin Gregoire, Gillian Leichtling, Megan Herink, Andrew Seaman, P. Todd Korthuis, Ryan Cook","doi":"10.3390/v16091455","DOIUrl":"https://doi.org/10.3390/v16091455","url":null,"abstract":"Hepatitis C (HCV) treatment for people who use drugs (PWUD) decreases injection drug use and injection equipment sharing. We examined changes in injection drug use and injection equipment sharing following HCV treatment in a randomized trial comparing peer-assisted telemedicine for HCV treatment (TeleHCV) versus peer-assisted usual care in rural PWUD. We hypothesize that TeleHCV reduces risky behaviors and peers facilitate this change. We used mixed-effects logistic regression to describe participant-level (n = 203) associations between both injection drug use and injection equipment sharing and randomized groups, frequency of peer contact, HCV treatment initiation, HCV cure, and time. Risky behaviors were surveyed at baseline and 12 and 36 weeks after HCV treatment completion. Injection drug use declined more over time in TeleHCV participants vs. control at 12 weeks (adjusted odds ratio [aOR] = 0.42, 95% CI 0.20–0.87, p = 0.02) and 36 weeks (aOR = 0.48, 95% CI 0.21–1.08, p = 0.076). Injection drug use decreased more with a greater number of peer interactions, with reductions among participants in the 3rd quartile exceeding those in the 1st quartile of peer interactions at 12 weeks (aOR = 0.75, 95% CI 0.57–0.99, p = 0.04). Similarly, injection equipment sharing decreased over time, with reductions among participants in the 3rd quartile exceeding those in the 1st quartile of peer interactions at 36 weeks (aOR = 0.08, 95% CI 0.01–0.97, p = 0.047). Peer-assisted telemedicine for HCV treatment decreases injection drug use and injection equipment sharing; peers contribute to this effect.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206862","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}
While Mammarenavirus Wenzhouense (WENV) is broadly distributed across Asia, the dynamics of WENV infection remain unclear. In this study, a field-derived strain of WENV was used to inoculate Sprague Dawley (SD) rats by intramuscular injection, and the process of viral infection was observed over the course of 28 d. Viral RNA became detectable in the blood at 3 dpi and remained detectable for about 12 d. In most organ tissues, viral RNA peaked at 7 dpi, and then began to decline by 14 d, but remained detectable in intestine and brain tissues at 21 and 28 dpi. Viral shedding was detected from fecal samples for 5 d, from 6 to 11 dpi using qRT-PCR, and was recovered from feces collected at 8 dpi. Horizontal contact infection occurred among cage-mates at 14 and 21 dpi. Antibodies against the nucleocapsid were detected at 5 dpi, and then increased and persisted until the end of the experiment. These results enabled us to determine the kinetics of viremic response, viral shedding in feces, and horizontal transmission dynamics, as well as the potential sites for WENV replication and viral maintenance in nature.
{"title":"Dynamics of Acute Infection with Mammarenavirus Wenzhouense in Rattus norvegicus","authors":"Shanshan Du, Xuefei Deng, Xiaoxia Huang, Tiezhu Liu, Aqian Li, Qin Wang, Tingting Tian, Chuan Li, Zhangqi Zheng, Qihan Lin, Zhuowei Li, Shiwen Wang, Jiandong Li","doi":"10.3390/v16091459","DOIUrl":"https://doi.org/10.3390/v16091459","url":null,"abstract":"While Mammarenavirus Wenzhouense (WENV) is broadly distributed across Asia, the dynamics of WENV infection remain unclear. In this study, a field-derived strain of WENV was used to inoculate Sprague Dawley (SD) rats by intramuscular injection, and the process of viral infection was observed over the course of 28 d. Viral RNA became detectable in the blood at 3 dpi and remained detectable for about 12 d. In most organ tissues, viral RNA peaked at 7 dpi, and then began to decline by 14 d, but remained detectable in intestine and brain tissues at 21 and 28 dpi. Viral shedding was detected from fecal samples for 5 d, from 6 to 11 dpi using qRT-PCR, and was recovered from feces collected at 8 dpi. Horizontal contact infection occurred among cage-mates at 14 and 21 dpi. Antibodies against the nucleocapsid were detected at 5 dpi, and then increased and persisted until the end of the experiment. These results enabled us to determine the kinetics of viremic response, viral shedding in feces, and horizontal transmission dynamics, as well as the potential sites for WENV replication and viral maintenance in nature.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"63 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226351","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}
Juliana Osse de Souza, Vicki Klaassen, Kristian Stevens, Teresa M. Erickson, Claire Heinitz, Maher Al Rwahnih
The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.
{"title":"Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay","authors":"Juliana Osse de Souza, Vicki Klaassen, Kristian Stevens, Teresa M. Erickson, Claire Heinitz, Maher Al Rwahnih","doi":"10.3390/v16091457","DOIUrl":"https://doi.org/10.3390/v16091457","url":null,"abstract":"The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226350","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}
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