B. Aneesh, Swapna K. Pillai, P. S. Chippy, Megha Chandran, Arun V. Jose, Lalitha Kailas, M. Neziya, S. Aswathyraj, E. Sreekumar
{"title":"Human bocavirus infections in paediatric patients in a tertiary care hospital in Kerala, India","authors":"B. Aneesh, Swapna K. Pillai, P. S. Chippy, Megha Chandran, Arun V. Jose, Lalitha Kailas, M. Neziya, S. Aswathyraj, E. Sreekumar","doi":"10.1007/s00705-024-06218-w","DOIUrl":"10.1007/s00705-024-06218-w","url":null,"abstract":"<div><p>Human bocaviruses (HBoVs) can cause respiratory illness in young children. Although the first HBoV infection in India was reported in 2010, very little information is available about its prevalence, clinical features, or geographic distribution in this country. This study was conducted using 136 respiratory samples from paediatric patients in a tertiary care hospital in Kerala, 21 of which tested positive for HBoV1 and were further characterized through VP1/VP2 gene sequencing. We found that different strains of HBoV1 are co-circulating in the region and that HBoV1 can be detected in children with severe acute respiratory infections, either alone or coinfections with other pathogens, without any significant differences in their clinical characteristics.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Forgia, M. Vallino, M. Marra, P. Mussano, A. P. Lanteri, G. P. Accotto, M Ciuffo
{"title":"Characterization of mint virus C, a new member of the genus Carlavirus","authors":"M. Forgia, M. Vallino, M. Marra, P. Mussano, A. P. Lanteri, G. P. Accotto, M Ciuffo","doi":"10.1007/s00705-025-06222-8","DOIUrl":"10.1007/s00705-025-06222-8","url":null,"abstract":"<div><p>Here, we report the complete genome sequence of a new carlavirus causing mosaic on mint plants in Italy, which we have tentatively named \"mint virus C\" (MVC). Flexuous particles of around 600 nm were observed using transmission electron microscopy, and next-generation sequencing was performed to determine the nucleotide sequence of the MVC genome, which was found to be 8558 nt long, excluding the poly(A) tail, and shows the typical organization of a carlavirus. The putative proteins encoded by MVC are 44–56% identical to the closest matches in the NCBI database, suggesting that MVC should be considered a member of a new species in the genus <i>Carlavirus</i>. MVC was detected in independent mint samples from different regions of Italy, collected in 2023 and 2024. Two MVC isolates, identified in 2023 (Me1) and in 2024 (Me2), have been included in the Plant Virus Italy (PLAVIT) collection.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A new capulavirus infecting sugar beet (Beta vulgaris L.) in France","authors":"Zhixiang Zhang, Chantal Faure, Armelle Marais, Amélie Monteiro, Thierry Candresse","doi":"10.1007/s00705-025-06223-7","DOIUrl":"10.1007/s00705-025-06223-7","url":null,"abstract":"<div><p>A novel capulavirus was identified by high-throughput sequencing in four sugar beet (<i>Beta vulgaris</i> L.) plants collected in April 2023 in Normandy (France). The complete genome of 2744 nucleotides (nt) was sequenced and found to have an organization similar to that of known capulaviruses, with which it showed close phylogenetic relationships. In addition, data mining of a publicly available <i>Thalictrum thalictroides</i> whole-genome shotgun sequence assembly allowed the identification of a contig (JABWDY010003008.1) representing a longer-than-unit length, likely episomal, genome with 99.4% nt sequence identity to the genome of the French beet isolate. The genome of the novel virus shares only 60.7–66.9% nt sequence identity with known capulaviruses, which is well below the species demarcation threshold of 78%, suggesting that a new species should be created to accommodate it. The common name \"beet capulavirus 1\" (BCV1) is proposed for this novel virus. Given that BCV1 was identified in plants that were coinfected with beet yellows virus, no conclusions can be drawn at this stage about its potential pathogenicity.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Long-term immune responses induced by low-dose infection with high pathogenicity avian influenza viruses can protect mallards from reinfection with a heterologous strain","authors":"Saki Sakuma, Junki Mine, Yuko Uchida, Asuka Kumagai, Yoshihiro Takadate, Ryota Tsunekuni, Hayate Nishiura, Kohtaro Miyazawa","doi":"10.1007/s00705-024-06209-x","DOIUrl":"10.1007/s00705-024-06209-x","url":null,"abstract":"<div><p>Migratory water birds are considered to be carriers of high pathogenicity avian influenza viruses (HPAIVs). In Japan, mallards are often observed during winter, and HPAIV-infected mallards often shed viruses asymptomatically. In this study, we focused on mallards as potential carriers of HPAIVs and investigated whether individual wild mallards are repeatedly infected with HPAIVs and act as HPAIV carriers multiple times within a season. Mallards were experimentally infected with H5N1 and H5N8 HPAIVs that were isolated recently in Japan and phylogenetically belong to different hemagglutinin groups (G2a, G2b, and G2d). All of these strains are more infectious to mallards than to chickens, and the infected mallards shed enough virus to infect others, regardless of whether they exhibited clinical signs. Serum antibodies to the homologous antigen, induced by a single infection with a low virus dose (10 times the 50% mallard infectious dose), were maintained at detectable levels for 84 days. Immunity at 84 days post-inoculation fully protected the mallards from a challenge with the homologous strain, as demonstrated by a lack of viral shedding, and antibody levels did not increase significantly in most of these birds. Protection against heterologous challenge was also observed despite undetectable levels of antibodies to the challenge strain. Our findings suggest that repeated infections with homologous and heterologous HPAIV strains do not occur frequently in individual wild mallards within a season, particularly at low viral doses, and the frequency with which they act as carriers may be limited.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-024-06209-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bernard Bergey, Armelle Marais, Chantal Faure, Thierry Candresse
{"title":"Complete genome sequence of a new beny-like virus from winter wheat (Triticum aestivum L.) in France","authors":"Bernard Bergey, Armelle Marais, Chantal Faure, Thierry Candresse","doi":"10.1007/s00705-025-06221-9","DOIUrl":"10.1007/s00705-025-06221-9","url":null,"abstract":"<div><p>Here, we report the discovery of a new beny-like virus in winter wheat (<i>Triticum aestivum</i> L.) plants collected in the Brittany and Burgundy regions of France in spring 2022, using a high-throughput sequencing approach. A complete genome sequence, comprising two genomic RNAs of 6734 nt (RNA1) and 4856 nt (RNA2) was obtained. This genome shows a typical benyvirus organization, with the RNA1 encoding a large replication-associated protein and the RNA2 encoding, from 5' to 3', the coat protein and its readthrough domain and a triple gene block. Pairwise sequence comparisons and phylogenetic analysis showed that the new virus is a member of the family <i>Benyviridae</i> and that its closest relatives are the recently described beny-like virus wheat stripe mosaic virus and, somewhat more distantly, other recognized benyviruses. Creation of a new species to accommodate the new virus, with the proposed common name \"wheat beny-like virus 1\" (WBLV1), is suggested, either in the genus <i>Benyvirus</i> or in another genus to be created within the family <i>Benyviridae</i>. Given that WBLV1 was identified in plants that were coinfected by other viruses, no conclusions can be drawn at this stage on its potential pathogenicity.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zaira Rehman, Katherine Edington, Zunera Jamal, Angelika Kritz-Wilson, Gytis Dudas, Samuel Sims, Richard Myers, Babak Afrough, Leena Inamdar, Syed Adnan Haider, Aamer Ikram, Muhammad Salman, Massab Umair
{"title":"The introduction of the SARS-CoV-2 BA.4 lineage into Pakistan","authors":"Zaira Rehman, Katherine Edington, Zunera Jamal, Angelika Kritz-Wilson, Gytis Dudas, Samuel Sims, Richard Myers, Babak Afrough, Leena Inamdar, Syed Adnan Haider, Aamer Ikram, Muhammad Salman, Massab Umair","doi":"10.1007/s00705-024-06211-3","DOIUrl":"10.1007/s00705-024-06211-3","url":null,"abstract":"<div><p>Pakistan has experienced a total of six COVID-19 waves throughout the pandemic, each driven by distinct SARS-CoV-2 lineages. This study explores the introduction of Omicron lineage BA.4 into Pakistan, which contributed to the sixth wave between June and September 2022. A discrete phylogeographic reconstruction was conducted on a global dataset of 443 samples across 49 countries, of which 92 samples were collected in Pakistan. Samples collected in Pakistan were from 10 locations across the country: Balochistan, Gilgit Baltistan, Islamabad, Jhelum, Karachi, Khyber Pakhtunkhwa, Lahore, Mirpur, Punjab, and Swat. This analysis identified eight distinct introductions into Pakistan between May 2022 and January 2023. The majority of BA.4 cases in Pakistan descended from one introduction, indicating that most transmission occurred within the country rather than through multiple importations. Two exportation events were also identified. During this time, there were reduced public health interventions in place, following the lifting of international travel restrictions in March 2022. This work stems from a collaboration between the UKHSA New Variant Assessment Platform and the National Institute of Health of Pakistan to strengthen genomic surveillance in front-line public health laboratories for global pandemic preparedness and response. The benefit of such partnerships has been evidenced throughout the COVID-19 pandemic, where scientific collaboration through data sharing and knowledge exchange has facilitated risk assessment and action. As a result of this collaboration, we have conducted the first Bayesian phylodynamic analysis of SARS-CoV-2 in Pakistan. This work can lend evidence to support understanding of SARS-CoV-2 variant transmission patterns and inform public health containment measures for virus spread.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Characterization and genomic analysis of a jumbo phage, PG216, with broad lytic activity against several Vibrio species","authors":"Shenao Li, Xixi Li, Chen Zhang, Xuefeng Xu, Sixuan Liang, Zhe Zhao","doi":"10.1007/s00705-024-06215-z","DOIUrl":"10.1007/s00705-024-06215-z","url":null,"abstract":"<div><p>In this study, a lytic phage, named PG216, was obtained from seawater collected in Qingdao, using <i>Vibrio parahaemolyticus</i> strain G299 as its host. Transmission electron microscopy revealed that phage PG216 has an icosahedral head with a diameter of 100 ± 6.7 nm and a contractible tail with a length of 126 ± 6.7 nm. The spot assay and EOP assay for host range testing revealed that the phage displayed extensive lytic activity against five <i>Vibrio</i> species: <i>V. alginolyticus</i>, <i>V. parahaemolyticus</i>, <i>V. vulnificus</i>, <i>V. mimicus</i>, and <i>V. harveyi</i>. The one-step growth curve indicated that the phage has a latent period of 25 min, a lysis duration of 115 min, and an average burst size of 135 ± 02 PFU/cell. The genome of PG216 is 244,027 bp in length with a GC content of 42.89%, and itcontains383 ORFs and encodes 28 tRNAs. Phylogenetic analysis suggested that PG216 belongs to the genus <i>Schizotequatrovirus</i> within the family <i>Straboviridae</i>. Phage PG216 was found to be able to eradicate mature biofilms produced by <i>V. parahaemolyticus</i> G299. Phage PG216 demonstrates notable lytic activity while lacking virulence and antibiotic-resistance genes and therefore might be a viable candidate for use in phage therapy of vibriosis.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Dhanalakshmi, Himani Dhanze, Akash Mote, N. Narmatha, K. Sibi Thomas, R. Nithiaselvi, Deepa Mehta, M. Suman Kumar, K. N. Bhilegaonkar
{"title":"Unique humoral immune response of pigs to repeated natural Japanese encephalitis virus infections: an amplifying host perspective","authors":"M. Dhanalakshmi, Himani Dhanze, Akash Mote, N. Narmatha, K. Sibi Thomas, R. Nithiaselvi, Deepa Mehta, M. Suman Kumar, K. N. Bhilegaonkar","doi":"10.1007/s00705-024-06208-y","DOIUrl":"10.1007/s00705-024-06208-y","url":null,"abstract":"<div><p>Japanese encephalitis virus (JEV) is the leading cause of viral encephalitis in the Asia-Pacific region. Amplification of JEV in pigs is a potent driver for spillover of the infection to humans, and hence monitoring of virus dynamics in pigs can provide insights into JEV ecology. To study the dynamics of natural JEV infection in a tropical region, two groups of immunologically naïve pigs consisting of six animals per group were kept as sentinels on two different farms in the district of Thanjavur, Tamil Nadu, India. In a longitudinal study conducted from May 2022 to October 2023, nested RT-PCR and indirect ELISA were used to track the dynamics of JEV and the humoral response in pigs. Synchronous and asynchronous seroconversion in pigs was recorded on two different farms with different management practices. Repeated infections with JEV were recorded in all of the sentinel animals throughout the study period, irrespective of the season. Phylogenetic analysis revealed the presence of JEV genotype III in the region. It was observed that the IgG response to natural JEV infection did not last long, which might have been the reason for repeated infections in the sentinel animals. The longest period during which IgG was present at detectable levels in this study was two months, after which the pigs could once again amplify the virus. A significant positive correlation was found between wind speed and JEV incidence in sentinel animals. Our results offer a different perspective on the relationship between JEV and its amplifying host that contradicts the assumption that pre-immune pigs are resistant to JEV amplification. Our findings could have a major impact on our understanding of the ecology of JEV in tropical regions, where there is a high burden of JE despite coordinated prevention efforts that have relied on achieving a long-lasting immune response.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muhammad Awais Ashraf, Muhammad Asif Raza, Azka Imran, Muhammad Nabeel Amjad
{"title":"Next-generation vaccines for influenza B virus: advancements and challenges","authors":"Muhammad Awais Ashraf, Muhammad Asif Raza, Azka Imran, Muhammad Nabeel Amjad","doi":"10.1007/s00705-024-06210-4","DOIUrl":"10.1007/s00705-024-06210-4","url":null,"abstract":"<div><p>To battle seasonal outbreaks of influenza B virus infection, which continue to pose a major threat to world health, new and improved vaccines are urgently needed. In this article, we discuss the current state of next-generation influenza B vaccine development, including both advancements and challenges. This review covers the shortcomings of existing influenza vaccines and stresses the need for more-effective and broadly protective vaccines and more-easily scalable manufacturing processes. New possibilities for vaccine development have emerged due to recent technical developments such as virus-like particle (VLP) platforms, recombinant DNA technologies, and reverse genetics. By using these methods, vaccines can be developed that elicit stronger and longer-lasting immune responses against various strains of influenza B virus. Vaccines may be more effective and immunogenic when adjuvants and new delivery mechanisms are used. Progress has been made in the development of influenza B vaccine mRNA vaccines, nanoparticle-based vaccines, and vector-based vaccines. However, there are still several obstacles to overcome before next-generation influenza B vaccines can be widely used, including the challenge of antigenic drift, the extinction of the B/Yamagata lineage, and difficulties in strain selection. There are also other challenges related to public acceptance, vaccine distribution, manufacturing complexity, and regulations. To overcome these challenges, scientists, politicians, and pharmaceutical firms must work together to expedite the development and licensing of vaccines and the establishment of immunization programs. The need for constant monitoring and quick adaptation of vaccines to match the currently circulating strains is further highlighted by the appearance of novel influenza B virus variants. To be ready for future pandemics and influenza B outbreaks, we need better vaccines and better monitoring systems.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"High-resolution melting analysis for detection of nucleotide mutation markers in the polymerase-acidic (PA) gene of influenza virus that are associated with baloxavir marboxil resistance","authors":"Rosaria Arvia, Arianna Rocca, Benedetta Casciato, Maria Alfreda Stincarelli, Simone Giannecchini","doi":"10.1007/s00705-024-06214-0","DOIUrl":"10.1007/s00705-024-06214-0","url":null,"abstract":"<div><p>The I38T substitution in the influenza virus polymerase-acidic (PA) subunit is a resistance marker of concern for treatment with the antiviral baloxavir marboxil (BXM). Thus, monitoring PA/I38T mutations is of clinical importance. Here, we developed three rapid and sensitive assays for the detection and monitoring of the PA/I38T mutation. In addition, we updated our previously developed methods to monitor the D197N mutation in the neuraminidase (NA) of influenza B virus, which is associated with resistance to oseltamivir. Real-time PCR high-resolution melting analysis (HRMA) was developed for the rapid detection of the PA/I38T and NA/D197N mutations using oligonucleotides with substitutions of interest and influenza viruses isolated in our laboratory. HRMA was subsequently performed on 94 clinical samples that were positive for A/H1N1pdm09, A/H3N2, and type-B influenza viruses and on viruses that were selected <i>in vitro</i> to grow in the presence of BXA (baloxavir acid, BXM active compound). The HRMAs were able to discriminate PA/I38 from the PA/I38T mutation and NA substitutions in synthetic oligonucleotides. However, the I38T mutation and NA mutations were not detected in any of our clinical samples, indicating the absence of these resistance markers in the circulating viruses examined. Only one out of 43 A/H3N2 clinical samples analyzed contained a virus with mutations associated with resistance to oseltamivir. All the HRMA results were confirmed by sequencing. Finally, HRMA was performed on A/H1N1pdm09 and A/H3N2 influenza viruses following BXA selection <i>in vitro</i>. The presence of the I38T mutation in the BXA-selected A/H3N2 variant, but not in the A/H1N1pdm09 variant, was identified by HRMA after 12 passages. Overall, these findings indicate that HRMA could be a powerful tool for rapidly monitoring BXM resistance in influenza viruses during seasonal circulation.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}