Pub Date : 2023-10-31DOI: 10.3389/fviro.2023.1324885
Eva G. Álvarez, Paula Otero, Bernardo Rodríguez-Martín, Ana Pequeño-Valtierra, Iago Otero, André Vidal-Capón, Jorge Rodríguez-Castro, Juan J. Pasantes, Carmen Rivas, Jose M.C. Tubío, Daniel García-Souto
• please read through all the templates before choosing • pick the most relevant text template(s) from the following page and delete all others.• edit the text as necessary, ensuring that the original incorrect text is included for the record, please see the below. • please do not use any extra formatting when editing the templates, and only modify the red text unless absolutely necessary • submit to Frontiers following the instructions on this page.When the original text contained incorrect information, to preserve the scientific record, please include that text when editing the below templates. For example:There was a mistake in the Funding statement, an incorrect number was used. The correct number is "2015C03Bd051.". The publisher apologizes for this mistake.The original version of this article has been updated. In the published article, there was an error in the author list, and author Jose M.C. Tubío should share correspondence for this brief research report article with Daniel García-Souto. The corrected author list appears below.Eva G. Álvarez 1,2,3 † Paula Otero 1,2,3 † Bernardo Rodríguez-Martín 1 Ana Pequeño-Valtierra 1,3 Iago Otero 1,2,3 André Vidal-Capón 4 Jorge Rodríguez-Castro 1,3 Juan J. Pasantes 4 Carmen Rivas 5 Jose M.C. Tubío 1,2,3* ‡ Daniel García-Souto 1,2,3* ‡
•请在选择之前通读所有模板•从以下页面中选择最相关的文本模板并删除所有其他文本模板。•根据需要编辑文本,确保原始的错误文本包括在记录中,请参见下文。•请勿在编辑模板时使用任何额外的格式,除非绝对必要,请仅修改红色文本•按照本页的说明提交到前沿。当原始文本包含不正确的信息时,为了保存科学记录,请在编辑以下模板时包含该文本。在资金报表中有一个错误,使用了一个不正确的数字。正确的号码是“2015C03Bd051.”出版商为这个错误道歉。本文的原始版本已更新。在发表的文章中,作者列表中有一个错误,作者Jose M.C. Tubío应该与Daniel García-Souto分享这篇简短的研究报告文章的通信。更正后的作者名单如下所示。Eva G. Álvarez 1,2,3†Paula Otero 1,2,3†Bernardo Rodríguez-Martín 1 Ana Pequeño-Valtierra 1,3 Iago Otero 1,2,3 andr Vidal-Capón 4 Jorge Rodríguez-Castro 1,3 Juan J. Pasantes 4 Carmen Rivas 5 Jose M.C. Tubío 1,2,3*‡Daniel García-Souto 1,2,3*‡
{"title":"Corrigendum: Characterization of Human Herpesvirus 8 genomic integration and amplification events in a primary effusion lymphoma cell line","authors":"Eva G. Álvarez, Paula Otero, Bernardo Rodríguez-Martín, Ana Pequeño-Valtierra, Iago Otero, André Vidal-Capón, Jorge Rodríguez-Castro, Juan J. Pasantes, Carmen Rivas, Jose M.C. Tubío, Daniel García-Souto","doi":"10.3389/fviro.2023.1324885","DOIUrl":"https://doi.org/10.3389/fviro.2023.1324885","url":null,"abstract":"• please read through all the templates before choosing • pick the most relevant text template(s) from the following page and delete all others.• edit the text as necessary, ensuring that the original incorrect text is included for the record, please see the below. • please do not use any extra formatting when editing the templates, and only modify the red text unless absolutely necessary • submit to Frontiers following the instructions on this page.When the original text contained incorrect information, to preserve the scientific record, please include that text when editing the below templates. For example:There was a mistake in the Funding statement, an incorrect number was used. The correct number is \"2015C03Bd051.\". The publisher apologizes for this mistake.The original version of this article has been updated. In the published article, there was an error in the author list, and author Jose M.C. Tubío should share correspondence for this brief research report article with Daniel García-Souto. The corrected author list appears below.Eva G. Álvarez 1,2,3 † Paula Otero 1,2,3 † Bernardo Rodríguez-Martín 1 Ana Pequeño-Valtierra 1,3 Iago Otero 1,2,3 André Vidal-Capón 4 Jorge Rodríguez-Castro 1,3 Juan J. Pasantes 4 Carmen Rivas 5 Jose M.C. Tubío 1,2,3* ‡ Daniel García-Souto 1,2,3* ‡","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"127 40","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135863453","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}
Pub Date : 2023-10-30DOI: 10.3389/fviro.2023.1291996
Shuntai Zhou, Nathan Long, Ronald Swanstrom
HIV-1 generates remarkable intra- and inter-host viral diversity during infection. In the response to the dynamic selective pressures of the host’s environment, HIV-1 evolves distinct phenotypes—biological features that provide fitness advantages. The transmitted form of HIV-1 has been shown to require a high density of CD4 on the target cell surface (as found on CD4+ T cells) and typically uses C–C chemokine receptor type 5 (CCR5) as a coreceptor during entry. This phenotype is referred to as R5T cell-tropic (or R5 T-tropic); however, HIV-1 can switch to a secondary coreceptor, C–X–C chemokine receptor type 4 (CXCR4), resulting in a X4T cell-tropic phenotype. Macrophage-tropic (or M-tropic) HIV-1 can evolve to efficiently enter cells expressing low densities of CD4 on their surface (such as macrophages/microglia). So far only CCR5-using M-tropic viruses have been found. M-tropic HIV-1 is most frequently found within the central nervous system (CNS), and infection of the CNS has been associated with neurologic impairment. It has been shown that interferon-resistant phenotypes have a selective advantage during transmission, but the underlying mechanism of this is still unclear. During untreated infection, HIV-1 evolves under selective pressure from both the humoral/antibody response and CD8+ T-cell killing. Sufficiently potent antiviral therapy can suppress viral replication, but if the antiviral drugs are not powerful enough to stop replication, then the replicating virus will evolve drug resistance. HIV-1 phenotypes are highly relevant to treatment efforts, clinical outcomes, vaccine studies, and cure strategies. Therefore, it is critical to understand the dynamics of the host environment that drive these phenotypes and how they affect HIV-1 pathogenesis. This review will provide a comprehensive discussion of HIV-1 entry and transmission, and drug-resistant phenotypes. Finally, we will assess the methods used in previous and current research to characterize these phenotypes.
{"title":"Evolution driven by a varying host environment selects for distinct HIV-1 entry phenotypes and other informative variants","authors":"Shuntai Zhou, Nathan Long, Ronald Swanstrom","doi":"10.3389/fviro.2023.1291996","DOIUrl":"https://doi.org/10.3389/fviro.2023.1291996","url":null,"abstract":"<p>HIV-1 generates remarkable intra- and inter-host viral diversity during infection. In the response to the dynamic selective pressures of the host’s environment, HIV-1 evolves distinct phenotypes—biological features that provide fitness advantages. The transmitted form of HIV-1 has been shown to require a high density of CD4 on the target cell surface (as found on CD4<sup>+</sup> T cells) and typically uses C–C chemokine receptor type 5 (CCR5) as a coreceptor during entry. This phenotype is referred to as R5T cell-tropic (or R5 T-tropic); however, HIV-1 can switch to a secondary coreceptor, C–X–C chemokine receptor type 4 (CXCR4), resulting in a X4T cell-tropic phenotype. Macrophage-tropic (or M-tropic) HIV-1 can evolve to efficiently enter cells expressing low densities of CD4 on their surface (such as macrophages/microglia). So far only CCR5-using M-tropic viruses have been found. M-tropic HIV-1 is most frequently found within the central nervous system (CNS), and infection of the CNS has been associated with neurologic impairment. It has been shown that interferon-resistant phenotypes have a selective advantage during transmission, but the underlying mechanism of this is still unclear. During untreated infection, HIV-1 evolves under selective pressure from both the humoral/antibody response and CD8<sup>+</sup> T-cell killing. Sufficiently potent antiviral therapy can suppress viral replication, but if the antiviral drugs are not powerful enough to stop replication, then the replicating virus will evolve drug resistance. HIV-1 phenotypes are highly relevant to treatment efforts, clinical outcomes, vaccine studies, and cure strategies. Therefore, it is critical to understand the dynamics of the host environment that drive these phenotypes and how they affect HIV-1 pathogenesis. This review will provide a comprehensive discussion of HIV-1 entry and transmission, and drug-resistant phenotypes. Finally, we will assess the methods used in previous and current research to characterize these phenotypes.</p>","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138531597","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}
Pub Date : 2023-10-26DOI: 10.3389/fviro.2023.1111619
Gisele Cassão, Krist Helen Antunes, João Ismael Budelon Gonçalvez, Leonardo Duarte Santos, Bruno Lopes Abbadi, Cristiano Valim Bizarro, Pablo Machado, Luiz Augusto Basso, Christian Pasquali, Renato T. Stein, Ana Paula Duarte de Souza
OM-85 is a bacterial lysate from common respiratory tract pathogens, with an excellent safety profile, widely used to prevent recurrent respiratory tract infections. Several studies have been reporting the immunomodulating properties and antiviral roles of OM-85. The COVID-19 pandemic, originating in 2019, has presented a significant global public health crisis. While effective vaccines have been developed, vaccination rates vary considerably, and numerous concerning viral variants continue to emerge. The challenge persists in creating early interventions to halt the progression of the disease to its severe stages. To examine the therapeutic effect of OM-85 after SARS-CoV-2 infection and compared to recombinant human (rhINF-β) we collected nasopharyngeal cells from COVID-19 patients. The cells were treated ex-vivo with OM-85 or hrINF-β and the response was analyzed after 24h for gene expression by real-time PCR. We found that OM-85 decreased the SARS-CoV-2 N1 gene expression and increased RIG-I (DDX58) in these cells. The expression of ACE2 was undetected in these samples. These data support the antiviral effect of OM-85 against SARS-CoV-2.
{"title":"Brief research report: OM-85 reduces SARS-COV-2 viral RNA expression in nasopharyngeal cells from COVID-19 patients","authors":"Gisele Cassão, Krist Helen Antunes, João Ismael Budelon Gonçalvez, Leonardo Duarte Santos, Bruno Lopes Abbadi, Cristiano Valim Bizarro, Pablo Machado, Luiz Augusto Basso, Christian Pasquali, Renato T. Stein, Ana Paula Duarte de Souza","doi":"10.3389/fviro.2023.1111619","DOIUrl":"https://doi.org/10.3389/fviro.2023.1111619","url":null,"abstract":"OM-85 is a bacterial lysate from common respiratory tract pathogens, with an excellent safety profile, widely used to prevent recurrent respiratory tract infections. Several studies have been reporting the immunomodulating properties and antiviral roles of OM-85. The COVID-19 pandemic, originating in 2019, has presented a significant global public health crisis. While effective vaccines have been developed, vaccination rates vary considerably, and numerous concerning viral variants continue to emerge. The challenge persists in creating early interventions to halt the progression of the disease to its severe stages. To examine the therapeutic effect of OM-85 after SARS-CoV-2 infection and compared to recombinant human (rhINF-β) we collected nasopharyngeal cells from COVID-19 patients. The cells were treated ex-vivo with OM-85 or hrINF-β and the response was analyzed after 24h for gene expression by real-time PCR. We found that OM-85 decreased the SARS-CoV-2 N1 gene expression and increased RIG-I (DDX58) in these cells. The expression of ACE2 was undetected in these samples. These data support the antiviral effect of OM-85 against SARS-CoV-2.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136376467","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}
Pub Date : 2023-10-24DOI: 10.3389/fviro.2023.1227317
Ashraf Elbahrawy, Hassan Atalla, Abdulla A. Mahmoud, Ahmed Eliwa, Alaa Alsawak, Mohamed Alboraie, Ali Madian, Ahmed Alashker, Sadek Mostafa, Ahmed Alwassief, Hussein H. Aly
The risk of hepatocellular carcinoma (HCC) diminishes in patients with hepatitis C virus (HCV)-related advanced chronic liver disease after virological cure. However, despite viral clearance, HCV-induced epigenetic alterations, immune dysregulations, and hepatic parenchymal injuries remain, contributing to de novo HCC occurrence. While HCC incidence is low (0.45 – 0.5%) in patients with advanced fibrosis (F3), the presence of liver cirrhosis and clinically significant portal hypertension increases the HCC risk. The cost-effectiveness of lifelong HCC surveillance in patients with compensated advanced chronic liver disease (cACLD) has sparked debate, raising questions about the most reliable noninvasive tests and stratification models for predicting HCC in patients with sustained virological response (SVR). Furthermore, identifying cACLD patients who may not require long-term HCC surveillance after SVR remains crucial. Several HCC risk stratification scores have been suggested for patients with cACLD, and emerging evidence supports individualized care based on personalized risk assessments. This review focuses on revising the pretreatment and posttreatment predictors of HCC, as well as the indications for HCC surveillance in cACLD patients treated with direct-acting antivirals.
{"title":"Prediction and surveillance of de novo HCC in patients with compensated advanced chronic liver disease after hepatitis C virus eradication with direct antiviral agents","authors":"Ashraf Elbahrawy, Hassan Atalla, Abdulla A. Mahmoud, Ahmed Eliwa, Alaa Alsawak, Mohamed Alboraie, Ali Madian, Ahmed Alashker, Sadek Mostafa, Ahmed Alwassief, Hussein H. Aly","doi":"10.3389/fviro.2023.1227317","DOIUrl":"https://doi.org/10.3389/fviro.2023.1227317","url":null,"abstract":"The risk of hepatocellular carcinoma (HCC) diminishes in patients with hepatitis C virus (HCV)-related advanced chronic liver disease after virological cure. However, despite viral clearance, HCV-induced epigenetic alterations, immune dysregulations, and hepatic parenchymal injuries remain, contributing to de novo HCC occurrence. While HCC incidence is low (0.45 – 0.5%) in patients with advanced fibrosis (F3), the presence of liver cirrhosis and clinically significant portal hypertension increases the HCC risk. The cost-effectiveness of lifelong HCC surveillance in patients with compensated advanced chronic liver disease (cACLD) has sparked debate, raising questions about the most reliable noninvasive tests and stratification models for predicting HCC in patients with sustained virological response (SVR). Furthermore, identifying cACLD patients who may not require long-term HCC surveillance after SVR remains crucial. Several HCC risk stratification scores have been suggested for patients with cACLD, and emerging evidence supports individualized care based on personalized risk assessments. This review focuses on revising the pretreatment and posttreatment predictors of HCC, as well as the indications for HCC surveillance in cACLD patients treated with direct-acting antivirals.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"2017 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135266251","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}
Pub Date : 2023-10-12DOI: 10.3389/fviro.2023.1202742
Edith A. Ogalo, Edwin Gudu, Thomas Andale, Daisy Korir, Samson Ndege, Tabu Simiyu, Richard Olekuyo, Henry Mwangi, Sylvester Kimaiyo, Wilson Aruasa
Introduction We describe the clinical spectrum of COVID-19 cases in western Kenya from 6 April 2020 to 31 May 2021, providing baseline data for further studies into COVID-19 in Kenya. Methods We did a retrospective chart review of laboratory and inpatient files of patients diagnosed and managed for COVID-19 at the Moi Teaching and Referral Hospital in Kenya and analyzed the data using Stata ® version 16 (StataCorp LP, College Station, TX, USA) and calculated measures of association at 95% CI. Results The patients ( n = 1,770) had a mean age of 43 years (SD 20 years) and 55.4% were male. Close to 70% had asymptomatic disease, with the symptomatic cases largely being respiratory in nature. One-quarter had comorbidities. The case fatality rate was 13.6% ( n = 240). Male sex increased the odds of mortality by 1.69 (95% CI 1.27–2.25; p ≤ 0.001), and the presence of comorbidities increased the odds of mortality by 3.16 (95% CI 2.38–4.18; p ≤ 0.001). Those aged 59 years and above were 18 times more likely to die from COVID-19 than those below 15 years of age (95% CI 1.61–90.66; p = 0.015). Conclusion COVID-19 had a significantly high mortality rate in western Kenya. Male sex and the presence of comorbidities increased the risk of severe disease and mortality.
我们描述了2020年4月6日至2021年5月31日肯尼亚西部COVID-19病例的临床谱,为肯尼亚进一步研究COVID-19提供基线数据。方法我们对肯尼亚Moi教学和转诊医院诊断和治疗的COVID-19患者的实验室和住院档案进行回顾性图表回顾,并使用Stata®version 16 (StataCorp LP, College Station, TX, USA)分析数据,并计算95% CI的关联度量。结果1770例患者平均年龄43岁(SD 20岁),男性55.4%。近70%无症状,有症状的病例以呼吸道为主。四分之一有合并症。病死率为13.6% (n = 240)。男性使死亡率增加1.69 (95% CI 1.27-2.25;p≤0.001),合并症的存在使死亡率增加3.16 (95% CI 2.38-4.18;P≤0.001)。59岁及以上人群死于COVID-19的可能性是15岁以下人群的18倍(95% CI 1.61-90.66;P = 0.015)。结论新型冠状病毒病死率在肯尼亚西部地区较高。男性和合并症的存在增加了严重疾病和死亡的风险。
{"title":"Clinical spectrum of COVID-19 at a national referral hospital in western Kenya during the period 2020–2021","authors":"Edith A. Ogalo, Edwin Gudu, Thomas Andale, Daisy Korir, Samson Ndege, Tabu Simiyu, Richard Olekuyo, Henry Mwangi, Sylvester Kimaiyo, Wilson Aruasa","doi":"10.3389/fviro.2023.1202742","DOIUrl":"https://doi.org/10.3389/fviro.2023.1202742","url":null,"abstract":"Introduction We describe the clinical spectrum of COVID-19 cases in western Kenya from 6 April 2020 to 31 May 2021, providing baseline data for further studies into COVID-19 in Kenya. Methods We did a retrospective chart review of laboratory and inpatient files of patients diagnosed and managed for COVID-19 at the Moi Teaching and Referral Hospital in Kenya and analyzed the data using Stata ® version 16 (StataCorp LP, College Station, TX, USA) and calculated measures of association at 95% CI. Results The patients ( n = 1,770) had a mean age of 43 years (SD 20 years) and 55.4% were male. Close to 70% had asymptomatic disease, with the symptomatic cases largely being respiratory in nature. One-quarter had comorbidities. The case fatality rate was 13.6% ( n = 240). Male sex increased the odds of mortality by 1.69 (95% CI 1.27–2.25; p ≤ 0.001), and the presence of comorbidities increased the odds of mortality by 3.16 (95% CI 2.38–4.18; p ≤ 0.001). Those aged 59 years and above were 18 times more likely to die from COVID-19 than those below 15 years of age (95% CI 1.61–90.66; p = 0.015). Conclusion COVID-19 had a significantly high mortality rate in western Kenya. Male sex and the presence of comorbidities increased the risk of severe disease and mortality.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135968675","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}
Pub Date : 2023-10-12DOI: 10.3389/fviro.2023.1208853
Nidhi Kumari, Vivek Sharma, Priyankaben Patel, P. N. Sharma
Viruses are one of the major restraining factors in pepper cultivation globally. Among different viruses, pepper mild mottle virus (PMMoV) is one of the most detrimental plant viruses infecting Capsicum spp. belonging to the genus Tobamovirus and Virgaviridae family. It has a monopartite positive-sense single-stranded RNA genome of 6.35 kb size. On an average, PMMoV results in 15%–40% losses in capsicum fruit yield. However, the incidence of PMMoV can reach as high as 95%, leading to substantial yield losses ranging from 75% to 95%. The virus is transmitted via contact, soil, and seeds rather than via insect vectors. PMMoV, because of its seed-borne nature, now occurs worldwide. PMMoV mainly infects Capsicum spp. under natural conditions; however, it can experimentally be transmitted to other plants species belonging to the families Solanaceae, Cucurbitaceae, Labiatae, Chenopodiaceae, and Plantaginaceae. The resistance to tobamoviruses in capsicum is conferred by L locus. Mutations in the coat protein of PMMoV are responsible for the emergence of L -mediated resistance-breaking pathotypes. The highly contagious nature of the virus, seed transmission behavior, and the emergence of virulence complicate its management through a single approach. Therefore, efforts are directed towards providing a more practical and efficient integrated management solution using the RNA interference approach; exploitation of the L gene for resistance breeding; and the inhibitory potential of natural products, systemic resistance-inducing antagonistic bacteria, and chemically synthesized silver nanoparticles. Markers linked to L alleles have been observed to accelerate capsicum breeding programs through marker-assisted selection. In this study, an attempt has been made to compile the recent developments in PMMoV biology, pathogenic variability, genomic organization, and management strategies.
{"title":"Pepper mild mottle virus: a formidable foe of capsicum production—a review","authors":"Nidhi Kumari, Vivek Sharma, Priyankaben Patel, P. N. Sharma","doi":"10.3389/fviro.2023.1208853","DOIUrl":"https://doi.org/10.3389/fviro.2023.1208853","url":null,"abstract":"Viruses are one of the major restraining factors in pepper cultivation globally. Among different viruses, pepper mild mottle virus (PMMoV) is one of the most detrimental plant viruses infecting Capsicum spp. belonging to the genus Tobamovirus and Virgaviridae family. It has a monopartite positive-sense single-stranded RNA genome of 6.35 kb size. On an average, PMMoV results in 15%–40% losses in capsicum fruit yield. However, the incidence of PMMoV can reach as high as 95%, leading to substantial yield losses ranging from 75% to 95%. The virus is transmitted via contact, soil, and seeds rather than via insect vectors. PMMoV, because of its seed-borne nature, now occurs worldwide. PMMoV mainly infects Capsicum spp. under natural conditions; however, it can experimentally be transmitted to other plants species belonging to the families Solanaceae, Cucurbitaceae, Labiatae, Chenopodiaceae, and Plantaginaceae. The resistance to tobamoviruses in capsicum is conferred by L locus. Mutations in the coat protein of PMMoV are responsible for the emergence of L -mediated resistance-breaking pathotypes. The highly contagious nature of the virus, seed transmission behavior, and the emergence of virulence complicate its management through a single approach. Therefore, efforts are directed towards providing a more practical and efficient integrated management solution using the RNA interference approach; exploitation of the L gene for resistance breeding; and the inhibitory potential of natural products, systemic resistance-inducing antagonistic bacteria, and chemically synthesized silver nanoparticles. Markers linked to L alleles have been observed to accelerate capsicum breeding programs through marker-assisted selection. In this study, an attempt has been made to compile the recent developments in PMMoV biology, pathogenic variability, genomic organization, and management strategies.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"128 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135968661","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}
Pub Date : 2023-10-02DOI: 10.3389/fviro.2023.1253416
Eva G. Álvarez, Paula Otero, Bernardo Rodríguez-Martín, Ana Pequeño-Valtierra, Iago Otero, André Vidal-Capón, Jorge Rodríguez-Castro, Juan J. Pasantes, Carmen Rivas, Jose M.C. Tubío, Daniel García-Souto
In this study, we investigated the integration of Human Herpesvirus 8 (HHV-8) into the human genome using the primary effusion lymphoma (PEL) cell line BC-3. Through next-generation sequencing (NGS) data from multiple independent sequencing runs, we identified two highly supported HHV-8 integrants. These integrants encompassed a region of human chromosome 12 that was amplified approximately 16-fold between the junctions. Significantly, these events could represent the first known instance of HHV-8 integration into a hybrid human-viral extrachromosomal chimeric circular DNA (eccDNA). The amplified fragment contained partial or complete copies of various human genes, including SELPLG and CORO1C. Analysis of long-read Nanopore data indicated that the CpGs at the SELPLG promoter were mostly unmethylated, suggesting that the additional copies of SELPLG within this eccDNA are likely transcriptionally active. Our findings suggest that viral insertion and eccDNA amplification could be crucial mechanisms in the development of HHV-8-related cancers. In conclusion, our study provides valuable insights into the molecular mechanisms involved in HHV-8-induced oncogenesis and emphasizes the importance of investigating viral integration and eccDNAs in cancer development. Furthermore, we highlight the necessity of employing multiple independent sequencing approaches to validate integration events and avoid false positives derived from library construction artifacts.
{"title":"Characterization of Human Herpesvirus 8 genomic integration and amplification events in a primary effusion lymphoma cell line","authors":"Eva G. Álvarez, Paula Otero, Bernardo Rodríguez-Martín, Ana Pequeño-Valtierra, Iago Otero, André Vidal-Capón, Jorge Rodríguez-Castro, Juan J. Pasantes, Carmen Rivas, Jose M.C. Tubío, Daniel García-Souto","doi":"10.3389/fviro.2023.1253416","DOIUrl":"https://doi.org/10.3389/fviro.2023.1253416","url":null,"abstract":"In this study, we investigated the integration of Human Herpesvirus 8 (HHV-8) into the human genome using the primary effusion lymphoma (PEL) cell line BC-3. Through next-generation sequencing (NGS) data from multiple independent sequencing runs, we identified two highly supported HHV-8 integrants. These integrants encompassed a region of human chromosome 12 that was amplified approximately 16-fold between the junctions. Significantly, these events could represent the first known instance of HHV-8 integration into a hybrid human-viral extrachromosomal chimeric circular DNA (eccDNA). The amplified fragment contained partial or complete copies of various human genes, including SELPLG and CORO1C. Analysis of long-read Nanopore data indicated that the CpGs at the SELPLG promoter were mostly unmethylated, suggesting that the additional copies of SELPLG within this eccDNA are likely transcriptionally active. Our findings suggest that viral insertion and eccDNA amplification could be crucial mechanisms in the development of HHV-8-related cancers. In conclusion, our study provides valuable insights into the molecular mechanisms involved in HHV-8-induced oncogenesis and emphasizes the importance of investigating viral integration and eccDNAs in cancer development. Furthermore, we highlight the necessity of employing multiple independent sequencing approaches to validate integration events and avoid false positives derived from library construction artifacts.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"240 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135895518","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}
Pub Date : 2023-09-29DOI: 10.3389/fviro.2023.1267692
Cesar Escalante, Surasak Khankhum, Rodrigo A. Valverde
Peppers ( Capsicum spp.) are native plants to the Americas. They are cultivated worldwide for direct human consumption and industrial purposes. Peppers can be infected by acute plant viruses, which cause a variety of diseases and crop losses. However, many Capsicum species can also be infected by persistent viruses. These are emerging viruses and they do not cause apparent disease and are transmitted only vertically. Using two near-isogenic lines of bell pepper cv. Marengo, biological and molecular interactions between the persistent virus bell pepper endornavirus (BPEV) and two acute viruses, pepper mild mottle virus (PMMoV) and tobacco mild green mosaic virus (TMGMV), were evaluated by symptom expression, enzyme-linked immunosorbent assay, and RT-qPCR. The relative titer of BPEV decreased at least two-fold at 14 days after infection when BPEV-infected plants were single infected with TMGMV or in mixed infection of PMMoV and TMGMV. The presence of BPEV was associated with symptom reduction in pepper plants infected with single and mixed infections of PMMoV and TMGMV. This suggests that the ubiquitous infection of BPEV may trigger the plant immune response, and therefore, BPEV is active when the plant is infected with PMMoV and/or TMGMV.
{"title":"Biological and molecular interactions between bell pepper endornavirus and two tobamoviruses","authors":"Cesar Escalante, Surasak Khankhum, Rodrigo A. Valverde","doi":"10.3389/fviro.2023.1267692","DOIUrl":"https://doi.org/10.3389/fviro.2023.1267692","url":null,"abstract":"Peppers ( Capsicum spp.) are native plants to the Americas. They are cultivated worldwide for direct human consumption and industrial purposes. Peppers can be infected by acute plant viruses, which cause a variety of diseases and crop losses. However, many Capsicum species can also be infected by persistent viruses. These are emerging viruses and they do not cause apparent disease and are transmitted only vertically. Using two near-isogenic lines of bell pepper cv. Marengo, biological and molecular interactions between the persistent virus bell pepper endornavirus (BPEV) and two acute viruses, pepper mild mottle virus (PMMoV) and tobacco mild green mosaic virus (TMGMV), were evaluated by symptom expression, enzyme-linked immunosorbent assay, and RT-qPCR. The relative titer of BPEV decreased at least two-fold at 14 days after infection when BPEV-infected plants were single infected with TMGMV or in mixed infection of PMMoV and TMGMV. The presence of BPEV was associated with symptom reduction in pepper plants infected with single and mixed infections of PMMoV and TMGMV. This suggests that the ubiquitous infection of BPEV may trigger the plant immune response, and therefore, BPEV is active when the plant is infected with PMMoV and/or TMGMV.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"95 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135245981","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}
Pub Date : 2023-09-26DOI: 10.3389/fviro.2023.1160078
Malowane H. Ngoato, Edina Amponsah-Dacosta, Ntombifuthi Blose, Selokela G. Selabe, Thembeni L. Msibi, Mojakgomo H. Motswaledi, Andrew M. Musyoki
Introduction Reactivation of hepatitis B virus (HBV) infection induced by immunosuppressive cancer therapy is associated with fulminant liver disease and death. While national guidelines recommend HBV screening and antiviral prophylaxis for patients with cancer prior to initiating immunosuppressive therapy, compliance with these measures is unclear. This study characterized the burden of HBV infection among patients diagnosed with gynecological or dermatological cancers, with or without underlying HIV infection, before initiating immunosuppressive therapy. Methods Between 2016 – 2018, we recruited study patients from the Dr George Mukhari Academic Hospital in Tshwane, South Africa. Demographic (age, sex) and clinical data (HIV test results, HIV antiviral regimen, type of cancer) were recorded using a standardized data collection form. All participants were tested for HBV surface antigen (HBsAg), and antibodies to the surface (anti-HBs) and core antigens (anti-HBc). For detection of HBV DNA, a nested polymerase chain reaction was used to amplify polymerase gene fragments which were Sanger-sequenced and analyzed using bioinformatics software. All statistical analyses were performed using R version 4.1.0 (2021-05-18) and R studio version 2022.07.2. Results Study participants were predominantly female (96.3%, 103/107) with a median (IQR) age of 50 (17.5) years. Cervical cancer was the most frequent cancer diagnosis (72%). Over half (52.3%; 56/107) of the participants were HIV positive and all but four (92.9%) on highly active antiretroviral therapy at the time of enrollment. The prevalence of chronic hepatitis B in the study population was 11.2% [95% CI:6.2-19.1], increasing to 14.3% [95% CI:6.8-26.8] in the HIV positive sub-population. The overall prevalence of occult HBV infection was 20% [95% CI:12.8-29.7], 57.9% [95% CI:33.97-78.9] of whom tested negative for all serological markers. Phylogenetic inference showed that all polymerase gene sequences generated in this study were sub-genotype A2. Mutational analysis did not reveal any drug resistance-associated amino acid variations in this study. Conclusion These findings suggest that chronic and occult HBV infections are more prevalent among cancer patients with or without underlying HIV infection compared to what has previously been reported for the general South African population. This underscores the need to scale-up universal HBV serological and molecular screening with timely institution of prophylaxis prior to initiating immunosuppressive cancer therapy.
{"title":"Hepatitis B virus infection in patients presenting for immunosuppressive cancer therapy with and without underlying HIV infection","authors":"Malowane H. Ngoato, Edina Amponsah-Dacosta, Ntombifuthi Blose, Selokela G. Selabe, Thembeni L. Msibi, Mojakgomo H. Motswaledi, Andrew M. Musyoki","doi":"10.3389/fviro.2023.1160078","DOIUrl":"https://doi.org/10.3389/fviro.2023.1160078","url":null,"abstract":"Introduction Reactivation of hepatitis B virus (HBV) infection induced by immunosuppressive cancer therapy is associated with fulminant liver disease and death. While national guidelines recommend HBV screening and antiviral prophylaxis for patients with cancer prior to initiating immunosuppressive therapy, compliance with these measures is unclear. This study characterized the burden of HBV infection among patients diagnosed with gynecological or dermatological cancers, with or without underlying HIV infection, before initiating immunosuppressive therapy. Methods Between 2016 – 2018, we recruited study patients from the Dr George Mukhari Academic Hospital in Tshwane, South Africa. Demographic (age, sex) and clinical data (HIV test results, HIV antiviral regimen, type of cancer) were recorded using a standardized data collection form. All participants were tested for HBV surface antigen (HBsAg), and antibodies to the surface (anti-HBs) and core antigens (anti-HBc). For detection of HBV DNA, a nested polymerase chain reaction was used to amplify polymerase gene fragments which were Sanger-sequenced and analyzed using bioinformatics software. All statistical analyses were performed using R version 4.1.0 (2021-05-18) and R studio version 2022.07.2. Results Study participants were predominantly female (96.3%, 103/107) with a median (IQR) age of 50 (17.5) years. Cervical cancer was the most frequent cancer diagnosis (72%). Over half (52.3%; 56/107) of the participants were HIV positive and all but four (92.9%) on highly active antiretroviral therapy at the time of enrollment. The prevalence of chronic hepatitis B in the study population was 11.2% [95% CI:6.2-19.1], increasing to 14.3% [95% CI:6.8-26.8] in the HIV positive sub-population. The overall prevalence of occult HBV infection was 20% [95% CI:12.8-29.7], 57.9% [95% CI:33.97-78.9] of whom tested negative for all serological markers. Phylogenetic inference showed that all polymerase gene sequences generated in this study were sub-genotype A2. Mutational analysis did not reveal any drug resistance-associated amino acid variations in this study. Conclusion These findings suggest that chronic and occult HBV infections are more prevalent among cancer patients with or without underlying HIV infection compared to what has previously been reported for the general South African population. This underscores the need to scale-up universal HBV serological and molecular screening with timely institution of prophylaxis prior to initiating immunosuppressive cancer therapy.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135719306","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}
Pub Date : 2023-09-25DOI: 10.3389/fviro.2023.1253661
Doreen Kamori, Godfrey Barabona
In sub-Saharan Africa (SSA) the burden of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance (HIVDR) has been high over the years. Therefore, in 2018 the World Health Organization (WHO) recommended a regimen based on a integrase strand transfer inhibitor (INSTI), dolutegravir, as the default first-line antiretroviral therapy (ART) in countries in SSA. The scale-up of DTG-based regimens in SSA has gained significant momentum since 2018 and has continued to expand across multiple countries in recent years. However, whether or not the DTG robustness experienced in the developed world will also be achieved in SSA settings is still an important question. Evidence generated from in vitro and in vivo studies suggests that the emergence of DTG HIVDR is HIV-1 subtype dependent. These findings demonstrate that the extensive HIV-1 diversity in SSA can influence DTG effectiveness and the emergence of drug resistance. In addition, the programmatic approach to the transition to DTG adopted by many countries in the SSA region potentially exposes individuals to DTG functional monotherapy, which is associated with the emergence of DTG resistance. In this mini review, we describe the current trends of the effectiveness of DTG as reflected by viral suppression and DTG resistance. Furthermore, we explore how HIV-1 diversity and the programmatic approach in SSA could shape DTG effectiveness and DTG HIVDR in the region.
{"title":"Dolutegravir resistance in sub-Saharan Africa: should resource-limited settings be concerned for future treatment?","authors":"Doreen Kamori, Godfrey Barabona","doi":"10.3389/fviro.2023.1253661","DOIUrl":"https://doi.org/10.3389/fviro.2023.1253661","url":null,"abstract":"In sub-Saharan Africa (SSA) the burden of non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV drug resistance (HIVDR) has been high over the years. Therefore, in 2018 the World Health Organization (WHO) recommended a regimen based on a integrase strand transfer inhibitor (INSTI), dolutegravir, as the default first-line antiretroviral therapy (ART) in countries in SSA. The scale-up of DTG-based regimens in SSA has gained significant momentum since 2018 and has continued to expand across multiple countries in recent years. However, whether or not the DTG robustness experienced in the developed world will also be achieved in SSA settings is still an important question. Evidence generated from in vitro and in vivo studies suggests that the emergence of DTG HIVDR is HIV-1 subtype dependent. These findings demonstrate that the extensive HIV-1 diversity in SSA can influence DTG effectiveness and the emergence of drug resistance. In addition, the programmatic approach to the transition to DTG adopted by many countries in the SSA region potentially exposes individuals to DTG functional monotherapy, which is associated with the emergence of DTG resistance. In this mini review, we describe the current trends of the effectiveness of DTG as reflected by viral suppression and DTG resistance. Furthermore, we explore how HIV-1 diversity and the programmatic approach in SSA could shape DTG effectiveness and DTG HIVDR in the region.","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135864646","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}