Miguel Lança, Vânia Gaio, Ana Paula Rodrigues, Camila Henriques, Licínia Gomes, Daniela Dias, Maria de Jesus Chasqueira, Raquel Guiomar, Aryse Melo
Background
Respiratory syncytial virus (RSV) is the leading cause of acute respiratory infection (ARI) in young children, but its genetic diversity requires ongoing surveillance.
Methods
From 2021 to 2023, a total of 619 and 94 RSV-positive samples from the National Respiratory Syncytial Virus Surveillance Network (VigiRSV) and the Sentinel Influenza and other respiratory viruses surveillance network (Sentinel ISN), respectively, were analysed. The RSV A and RSV B typing was assessed by a multiplex real-time RT-PCR. Sanger sequencing was performed on a subset of samples (n = 495). Phylogenetic analysis was carried out on partial glycoprotein G sequences. Clinical and epidemiological data were compared through Pearson Chi-Square tests.
Results
RSV Subgroup A was more prevalent (53.5%, 85/159) in the 2021/2022 season, whereas in the 2022/2023 season, it was RSV Subgroup B (82.1%, 435/530) in both networks. RSV A strains in VigiRSV clustered mainly to A.D.1 (39.0%, 39/100), whereas in Sentinel ISN, they clustered in A.D.5 (30.0%, 3/10). RSV Type B clustered mainly to B.D.E.1 (96.6%, 372/385) in both networks. All lineages cocirculated during the study period and in both surveillance networks. Regional clusters were identified for both subgroups.
Conclusions
This study provides new insights into RSV genetic variability in Portugal, namely, the cocirculation of lineages and intravariability among lineages within both subgroups during the study period and in all Portuguese regions. However, our study is based on partial sequencing of the G gene, and because of this limitation, our results should be considered with great caution.
{"title":"Genetic and Epidemiological Insights Into Respiratory Syncytial Virus Infections: A Comparative Study of Hospitalized Versus Community Cases in Portugal (2021–2023)","authors":"Miguel Lança, Vânia Gaio, Ana Paula Rodrigues, Camila Henriques, Licínia Gomes, Daniela Dias, Maria de Jesus Chasqueira, Raquel Guiomar, Aryse Melo","doi":"10.1111/irv.70147","DOIUrl":"10.1111/irv.70147","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Respiratory syncytial virus (RSV) is the leading cause of acute respiratory infection (ARI) in young children, but its genetic diversity requires ongoing surveillance.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>From 2021 to 2023, a total of 619 and 94 RSV-positive samples from the National Respiratory Syncytial Virus Surveillance Network (VigiRSV) and the Sentinel Influenza and other respiratory viruses surveillance network (Sentinel ISN), respectively, were analysed. The RSV A and RSV B typing was assessed by a multiplex real-time RT-PCR. Sanger sequencing was performed on a subset of samples (<i>n</i> = 495). Phylogenetic analysis was carried out on partial glycoprotein G sequences. Clinical and epidemiological data were compared through Pearson Chi-Square tests.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>RSV Subgroup A was more prevalent (53.5%, 85/159) in the 2021/2022 season, whereas in the 2022/2023 season, it was RSV Subgroup B (82.1%, 435/530) in both networks. RSV A strains in VigiRSV clustered mainly to <span>A.D</span>.1 (39.0%, 39/100), whereas in Sentinel ISN, they clustered in <span>A.D</span>.5 (30.0%, 3/10). RSV Type B clustered mainly to B.D.E.1 (96.6%, 372/385) in both networks. All lineages cocirculated during the study period and in both surveillance networks. Regional clusters were identified for both subgroups.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This study provides new insights into RSV genetic variability in Portugal, namely, the cocirculation of lineages and intravariability among lineages within both subgroups during the study period and in all Portuguese regions. However, our study is based on partial sequencing of the G gene, and because of this limitation, our results should be considered with great caution.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12516350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280119","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}
Zimmerman, RK, Balasubramani, GK, D'Agostino, HEA, et al., Population-Based Hospitalization Burden Estimates for Respiratory Viruses, 2015–2019. Influenza Other Respi Viruses.2022; 16(6): 1133–1140. https://doi.org/10.1111/irv.13040.
In Table 3, fifth row, the heading ‘Annual virus specific detections and burden per 100,000 population’ is incorrect and should have been “Combined 4 Years Virus-Specific Detections and Burden per 100,000 Population.” The corrected Table 3 for annual burden is shown below.
In the discussion, third paragraph, the sentence “We found influenza burden to range from 372/100,000 for 18–64 year-olds to 1964/100,000 for those ≥65 years” is correct for a 4-year cumulative estimate but would be better understood with annual estimates: “We found the annual influenza burden to range from 36/100,000 for 18-49 year-olds to 150/100,000 for 50-64 year-olds to 491/100,000 for those ≥65 years.”
{"title":"Correction to “Population-Based Hospitalization Burden Estimates for Respiratory Viruses, 2015–2019. Influenza Other Respir Viruses”","authors":"","doi":"10.1111/irv.70168","DOIUrl":"10.1111/irv.70168","url":null,"abstract":"<p>\u0000 <span>Zimmerman, RK</span>, <span>Balasubramani, GK</span>, <span>D'Agostino, HEA</span>, et al., <span>Population-Based Hospitalization Burden Estimates for Respiratory Viruses, 2015–2019</span>. <i>Influenza Other Respi Viruses.</i> <span>2022</span>; <span>16</span>(<span>6</span>): <span>1133</span>–<span>1140</span>. https://doi.org/10.1111/irv.13040.\u0000 </p><p>In Table 3, fifth row, the heading ‘Annual virus specific detections and burden per 100,000 population’ is incorrect and should have been “Combined 4 Years Virus-Specific Detections and Burden per 100,000 Population.” The corrected Table 3 for annual burden is shown below.</p><p>In the discussion, third paragraph, the sentence “We found influenza burden to range from 372/100,000 for 18–64 year-olds to 1964/100,000 for those ≥65 years” is correct for a 4-year cumulative estimate but would be better understood with annual estimates: “We found the annual influenza burden to range from 36/100,000 for 18-49 year-olds to 150/100,000 for 50-64 year-olds to 491/100,000 for those ≥65 years.”</p><p>We apologize for these errors.</p>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12516252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280118","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}
Sarah F. Hak, Joanne G. Wildenbeest, Sara Bracaloni, Michela Scarpaci, Tommaso Cosci, Enrica Esposito, Maria Chironna, Donatella Panatto, Giancarlo Icardi, Melissa Torrisi, Leonardo Bonaldo, Eugenio Mammolenti, Emma te Bogt, Jacqueline Vlaskamp-Smit, Louis J. Bont, Caterina Rizzo, Roderick P. Venekamp
Introduction
Respiratory syncytial virus (RSV) is increasingly recognized as an important cause of acute respiratory infections (ARI) in older adults. However, primary care data on RSV infections are scarce.
Methods
We conducted a prospective cohort study over two winter seasons (2022–2023 and 2023–2024) in Italy and the Netherlands (NCT06318936). Older adults (≥ 60 years) presenting to primary care with ARI were tested for RSV and influenza. Clinical and socioeconomic burden was assessed through questionnaires on Days 1, 14, and 30. In secondary analyses, we compared between RSV- and influenza-positive patients and estimated RSV-ARI incidence in Dutch primary care.
Results
Of 703 older adults tested, 93 (13.2%) were RSV-positive and 100 (14.2%) influenza-positive. In RSV patients (mean age: 76 years [SD: 8], 63% ≥ 1 comorbidity), mean illness duration was 17 days (SD: 10). Repeat primary care visits occurred in 38% (33/87), emergency department referral in 5% (4/88), and hospitalization in 2% (2/88) of RSV patients. The mean costs per RSV episode were €78.1 (95%CI: 74.4–81.8) and €279.7 (95%CI: 245.5–318.2) from a healthcare system and societal perspective, respectively. The annual RSV-ARI incidence rate was 10.3 episodes per 1000 person-years. RSV patients were significantly older, and had less often fever, muscle pain, and fatigue than influenza patients, but clinical and socioeconomic burdens were comparable.
Conclusions
This prospective study is the first sufficiently large to demonstrate that the primary care burden of RSV infections among older adults is substantial and comparable with influenza. These findings are highly relevant for informing public health decisions on novel RSV vaccines.
{"title":"Clinical and Socioeconomic Burden of RSV Infections Among Older Adults in Primary Care: An International Prospective Cohort Study","authors":"Sarah F. Hak, Joanne G. Wildenbeest, Sara Bracaloni, Michela Scarpaci, Tommaso Cosci, Enrica Esposito, Maria Chironna, Donatella Panatto, Giancarlo Icardi, Melissa Torrisi, Leonardo Bonaldo, Eugenio Mammolenti, Emma te Bogt, Jacqueline Vlaskamp-Smit, Louis J. Bont, Caterina Rizzo, Roderick P. Venekamp","doi":"10.1111/irv.70174","DOIUrl":"https://doi.org/10.1111/irv.70174","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Introduction</h3>\u0000 \u0000 <p>Respiratory syncytial virus (RSV) is increasingly recognized as an important cause of acute respiratory infections (ARI) in older adults. However, primary care data on RSV infections are scarce.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We conducted a prospective cohort study over two winter seasons (2022–2023 and 2023–2024) in Italy and the Netherlands (NCT06318936). Older adults (≥ 60 years) presenting to primary care with ARI were tested for RSV and influenza. Clinical and socioeconomic burden was assessed through questionnaires on Days 1, 14, and 30. In secondary analyses, we compared between RSV- and influenza-positive patients and estimated RSV-ARI incidence in Dutch primary care.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Of 703 older adults tested, 93 (13.2%) were RSV-positive and 100 (14.2%) influenza-positive. In RSV patients (mean age: 76 years [SD: 8], 63% ≥ 1 comorbidity), mean illness duration was 17 days (SD: 10). Repeat primary care visits occurred in 38% (33/87), emergency department referral in 5% (4/88), and hospitalization in 2% (2/88) of RSV patients. The mean costs per RSV episode were €78.1 (95%CI: 74.4–81.8) and €279.7 (95%CI: 245.5–318.2) from a healthcare system and societal perspective, respectively. The annual RSV-ARI incidence rate was 10.3 episodes per 1000 person-years. RSV patients were significantly older, and had less often fever, muscle pain, and fatigue than influenza patients, but clinical and socioeconomic burdens were comparable.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This prospective study is the first sufficiently large to demonstrate that the primary care burden of RSV infections among older adults is substantial and comparable with influenza. These findings are highly relevant for informing public health decisions on novel RSV vaccines.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.70174","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272710","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}
Marcela Safratova, Yu-Li Chen, Anna Hostalkova, Jakub Chlebek, Chung-Fan Hsieh, Bing-Hung Chen, Lucie Cahlikova, Stefan Kosturko, Anders Backlund, Jim-Tong Horng, Tsong-Long Hwang, Michal Korinek
Background
Natural alkaloids are a structurally diverse class of bioactive compounds with significant therapeutic potential. This study aimed to evaluate the in vitro antiviral activity of various natural alkaloids against coronaviruses, clarify molecular effects via bioassays and docking, and explore structure–activity relationships. Tested compounds included a wide variety of isoquinoline and Amaryllidaceae-type alkaloids.
Methodology
Antiviral activity was assessed using HCoV-229E and pseudotyped lentivirus assays for different strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cytotoxicity was evaluated with the WST-1 assay. AutoDock was used for molecular docking, online tools assessed drug-likeness, and ChemGPS-NP analyzed physicochemical properties correlated to antiviral clinical drugs.
Results
Several bis-benzylisoquinoline alkaloids, especially from Berberis vulgaris L., and specific Amaryllidaceae alkaloids showed protective activity against HCoV-229E (EC50 = 4.1–8.1 μM). Active compounds were further tested against SARS-CoV-2 variants. Aromoline (Compound 16) exhibited strong antiviral activity, inhibiting D614G, Delta, and Omicron variants in pseudovirus assays with IC50 values of 0.47–0.66 μM. Other bis-benzylisoquinoline analogues showed moderate activity (IC50 = 1.24–2.86 μM). Docking studies revealed aromoline's favorable interaction at the SARS-CoV-2 spike/ACE2 interface, forming hydrogen bonds with Gln493 and Ser494 (binding energy −5.34 kcal/mol). ChemGPS-NP analysis highlighted a distinct cluster of active bis-benzylisoquinolines (Compounds 16–19) in chemical space.
Conclusion
This study highlights the antiviral potential of bis-benzylisoquinoline and Amaryllidaceae alkaloids, particularly aromoline. The findings support their relevance as scaffolds for developing novel anticoronavirus agents and advance the understanding of their structure–activity relationships.
{"title":"Anticoronavirus Isoquinoline Alkaloids: Unraveling the Secrets of Their Structure–Activity Relationship","authors":"Marcela Safratova, Yu-Li Chen, Anna Hostalkova, Jakub Chlebek, Chung-Fan Hsieh, Bing-Hung Chen, Lucie Cahlikova, Stefan Kosturko, Anders Backlund, Jim-Tong Horng, Tsong-Long Hwang, Michal Korinek","doi":"10.1111/irv.70166","DOIUrl":"10.1111/irv.70166","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Natural alkaloids are a structurally diverse class of bioactive compounds with significant therapeutic potential. This study aimed to evaluate the in vitro antiviral activity of various natural alkaloids against coronaviruses, clarify molecular effects via bioassays and docking, and explore structure–activity relationships. Tested compounds included a wide variety of isoquinoline and Amaryllidaceae-type alkaloids.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methodology</h3>\u0000 \u0000 <p>Antiviral activity was assessed using HCoV-229E and pseudotyped lentivirus assays for different strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cytotoxicity was evaluated with the WST-1 assay. AutoDock was used for molecular docking, online tools assessed drug-likeness, and ChemGPS-NP analyzed physicochemical properties correlated to antiviral clinical drugs.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Several bis-benzylisoquinoline alkaloids, especially from <i>Berberis vulgaris</i> L., and specific Amaryllidaceae alkaloids showed protective activity against HCoV-229E (EC<sub>50</sub> = 4.1–8.1 μM). Active compounds were further tested against SARS-CoV-2 variants. Aromoline (Compound <b>16</b>) exhibited strong antiviral activity, inhibiting D614G, Delta, and Omicron variants in pseudovirus assays with IC<sub>50</sub> values of 0.47–0.66 μM. Other bis-benzylisoquinoline analogues showed moderate activity (IC<sub>50</sub> = 1.24–2.86 μM). Docking studies revealed aromoline's favorable interaction at the SARS-CoV-2 spike/ACE2 interface, forming hydrogen bonds with Gln493 and Ser494 (binding energy −5.34 kcal/mol). ChemGPS-NP analysis highlighted a distinct cluster of active bis-benzylisoquinolines (Compounds <b>16</b>–<b>19</b>) in chemical space.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>This study highlights the antiviral potential of bis-benzylisoquinoline and Amaryllidaceae alkaloids, particularly aromoline. The findings support their relevance as scaffolds for developing novel anticoronavirus agents and advance the understanding of their structure–activity relationships.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12497685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232512","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}
Francisco M. Guerra Jr, Emily M. Edgar, Judith U. Oguzie, Lyudmyla V. Marushchak, Morgan Pattillo, Gregory C. Gray
<p>Recent investigations have demonstrated that influenza C (ICV) is associated with symptomatic bovine respiratory disease (BRD) and that seroprevalence in cattle can be as high as 27% [<span>1</span>]. Prior studies of US cattle in Northwestern and Western states from 2011 to 2014 showed a prevalence of 7.84% [<span>2</span>]. More recently, from areas near North Dakota, the ICV prevalence among cattle decreased to 5.99% [<span>3</span>]. In the present study of Southern US cattle, the ICV prevalence is found to be 0.2%, marking a significant shift. One positive ICV sample from a Texas bovine nasal specimen demonstrated a mixing event between human and bovine ICVs.</p><p>Influenza viruses present significant public health and veterinary health concerns due to their genetic variability and potential for widespread transmission through animals and humans [<span>1, 3, 4</span>]. Previously, ICV has primarily affected humans with sporadic spillover to swine and dogs [<span>5-7</span>]. As humans, we are becoming more connected with farm animals through the food we eat, the people who work with or next to farm animals, and the proximity of farms to cities in the farm-to-table movement. These interactions increase the possibility of reservoirs for influenza in multiple species [<span>8</span>]. The One Health concept has demonstrated the interconnected network of health between humans, animals, and the environment [<span>9</span>]. Currently, highly pathogenic avian influenza H5N1, “bird flu,” is raging in wild birds and has jumped species to numerous domestic and wild mammals. As ICV is known to cause infections in humans and pigs, being on the forefront of an outbreak in cattle would well position public health practitioners to prepare for and prevent any potential human pandemics. Investigations of data from Japan from 2020 to 2023 show that ICV had an overall cattle seroprevalence of 27.0% [<span>1</span>]. From 2010 to 2011, 2.32% of children under 10 years of age from 474 mixed human respiratory samples were found to have C/Kanagawa and C/Sao Paulo [<span>10</span>]. In 2009, a novel <i>influenza A</i> virus emerged after a reassortment of viruses from different sources including pigs, birds, and humans, which resulted in an influenza pandemic. There is little attention drawn to ICV due to its lower human pathogenicity and prevalence compared to influenza A or B [<span>8</span>]. Consequently, there are no vaccines or effective antiviral treatments currently available for this type of influenza, despite the currently approved polymerase inhibitor baloxavir possessing some antiviral activity against ICV [<span>8, 11</span>]. This study utilizes nasal swab samples collected by the UTMB One Health Team in three US states and one region in Mexico from 2024 to 2025 to estimate the current prevalence of ICV in cattle in North America.</p><p>In this study, we conducted qRT-PCR assays on nasal swabs collected from cattle from dairy farms across three U
最近的调查表明，丙型流感（ICV）与有症状的牛呼吸道疾病（BRD）有关，牛的血清患病率可高达27%。2011年至2014年对美国西北部和西部各州的牛进行的先前研究显示，流行率为7.84%。最近，在北达科他州附近地区，ICV在牛中的流行率下降到5.99%。在目前对美国南部牛的研究中，发现ICV患病率为0.2%，这标志着一个重大转变。一份来自德克萨斯牛鼻标本的ICV阳性样本显示了人类和牛ICV的混合事件。流感病毒由于其遗传变异性和通过动物和人类广泛传播的潜力，引起了重大的公共卫生和兽医卫生问题[1,3,4]。以前，ICV主要影响人类，零星地向猪和狗传播[5-7]。作为人类，我们与农场动物的联系越来越紧密，通过我们吃的食物，与农场动物一起工作或在农场动物旁边工作的人，以及农场到餐桌运动中农场与城市的距离。这些相互作用增加了流感在多个物种中存在宿主的可能性。“同一个健康”概念展示了人类、动物和环境之间相互关联的健康网络。目前，高致病性禽流感H5N1，即“禽流感”正在野生鸟类中肆虐，并已跨越物种传染给许多家养和野生哺乳动物。由于已知ICV会在人类和猪中引起感染，因此站在牛中爆发疫情的最前沿，将使公共卫生从业人员能够为任何可能的人类大流行做好准备并加以预防。对日本2020年至2023年数据的调查显示，ICV的牛血清总体患病率为27.0%。2010 - 2011年，在474份混合呼吸道样本中发现2.32%的10岁以下儿童患有C/神奈川和C/圣保罗[10]。2009年，来自猪、鸟和人等不同来源的病毒重新组合后，出现了一种新型甲型流感病毒，导致流感大流行。由于与甲型流感或乙型流感相比，ICV的人类致病性和流行率较低，因此很少引起人们的注意。因此，尽管目前批准的聚合酶抑制剂baloxavir对ICV具有一定的抗病毒活性，但目前还没有针对这种流感的疫苗或有效的抗病毒治疗方法[8,11]。本研究利用UTMB One Health团队从2024年至2025年在美国三个州和墨西哥一个地区收集的鼻拭子样本来估计目前北美牛中ICV的流行情况。在这项研究中，我们对2024年1月至2025年6月期间从美国三个州（印第安纳州、肯塔基州和德克萨斯州）和墨西哥一个州的奶牛场收集的牛鼻拭子进行了qRT-PCR分析，以估计奶牛中ICV的当前流行情况。我们使用了两组不同的引物，一组用于检测基质(M)蛋白，一组用于检测ICV的核蛋白（NP）。大多数样本是通过农场和实地考察收集的。其余的样本分别进行了测试。每次访问每个农场收集大约20头牛的鼻腔样本，等待牛的供应。鼻拭子标本保存在病毒运输介质（VTM）中，冷链保存在冷却器中。在实验室中，样品迅速转移到- 80°C。按照制造商的说明，在QIAcube Connect自动提取系统（Qiagen）上使用QIAamp病毒RNA迷你试剂盒（Qiagen, Valencia， CA）进行RNA提取。采用AgPath-ID一步RT-PCR试剂盒（Cat # AM1005），用两组引物（M或NP基因）中的一组对提取的牛鼻拭子样本进行qRT-PCR一步检测。提取的RNA池样品（5 μL）（或单个样品）以0.2 μM探针和0.8-μM正向/反向引物最终浓度加入终体积为25 μL的M蛋白检测；剩余的数量是根据制造商的说明。提取的RNA池样品（3.5 μL）（或单个样品）以0.29 μ m探针和0.60-μM正向/反向引物最终浓度加入终体积为21 μL的NP蛋白检测；剩余的数量是根据制造商的说明。M蛋白检测循环条件为：50℃10 min， 95℃10 min, 95℃45 s, 60℃15 s，循环45次。NP实验类似于48°C 10分钟，95°C 10分钟，95°C 15秒，60°C 45秒的45个循环。从qRT-PCR检测中检测到的单个阳性样品被分离并在MDCK细胞中生长。从单个实验室复制阳性样本中提取RNA并准备用于下一代测序（NGS）。 测序文库使用Illumina （New England Biolabs, Ipswich， MA）的NEB Next Ultra II RNA文库准备试剂盒，按照制造商对ICV阳性样品的说明制作。在Element Biosciences的AVITI Sequencer平台上进行75-bp的配对端NGS，该平台可在https://www.elementbiosciences.com/上获得。原始测序读数在Chan Zuckerberg ID宏基因组平台（CZ ID平台）上进行分析，该平台可在https://czid.org/上获得。经过分类单元分类和宿主细化，构建了单个ICV阳性样本的一致基因组。利用1000个HEF基因进行系统发育分析。从2024年到2025年，我们对美国三个州和墨西哥一个州的农场的433头牛进行了qRT-PCR检测，发现了一例牛ICV阳性病例，患病率为0.2%。对ICV阳性牛鼻拭子样本的NGS分析显示，片段1 ~ 6与C/ bovine /Montana/12/2016的核苷酸序列一致性为96% ~ 98%。另一方面，编码NS1和NS2的第7片段与人类衍生的ICV变体C/Mississippi/80的核苷酸序列一致性约为98%（表1）。根据第4段的血凝素-酯酶融合（HEF）基因序列，我们的基因组总体上与C/Bovine/Montana/12/2016最接近（表1）。ICV包含7个片段，编码9个蛋白质[5]。ICV有一个表面糖蛋白HEF，它将血凝素和神经氨酸酶的功能结合在一个单一的融合蛋白[1]上。ICV与显示9- o -乙酰- n -乙酰神经氨酸受体[6]的受体结合。唾液酸α-2,3-和α-2,6-半乳糖宿主受体是禽流感和人甲型流感的受体靶点，已在牛乳腺中发现。本研究监测的433份牛鼻拭子样本中发现0.2%。相比之下，对2019年至2020年提交给南达科他州立大学的217份牛尸体肺炎阳性肺样本进行均质化和病毒RNA提取后，发现ICV患病率为5.99%[3]。在另一项研究中，包括2011年至2014年来自新墨西哥州，科罗拉多州和西澳州的农场，在599人中检测到7.84%的总患病率。目前的研究显示，ICV患病率为0.2%，表明ICV患病率降低了10倍。同时进行的研究（由UTMB One Health Gray实验室单独发表）中的D型流感（IDV）病例显示，与ICV相比，IDV的患病率更高。本研究取样的农场（墨西哥、德克萨斯州、肯塔基州和印第安纳州）与其他研究中美国西南部和西北部各州之间存在地理差异。其他研究也是在5-14岁之间进行的，这可能意味着ICV数量有足够的时间减少。对C/Bovine/Texas/2024牛鼻拭子样本的NGS分析显示，第7片段（编码NS1和NS2）与C/Mississippi/80序列同源性为98%。非结构蛋白1 （NS1）是一种含有约230个氨基酸的干扰素拮抗剂，具有多种功能。非结构蛋白2 （NS2）是一种含有121个氨基酸的RNP核输出蛋白（NEP），参与调控RNA合成。已知NS1可抑制1型干扰素γ (IFN)的产生，而IFN可抑制宿主对呼吸道病毒感染的先天免疫反应[13,14]。序列分析显示，C/Bovine/Texas/202
{"title":"Sparse Evidence of Influenza C on US Dairy and Beef Cattle Farms","authors":"Francisco M. Guerra Jr, Emily M. Edgar, Judith U. Oguzie, Lyudmyla V. Marushchak, Morgan Pattillo, Gregory C. Gray","doi":"10.1111/irv.70167","DOIUrl":"10.1111/irv.70167","url":null,"abstract":"<p>Recent investigations have demonstrated that influenza C (ICV) is associated with symptomatic bovine respiratory disease (BRD) and that seroprevalence in cattle can be as high as 27% [<span>1</span>]. Prior studies of US cattle in Northwestern and Western states from 2011 to 2014 showed a prevalence of 7.84% [<span>2</span>]. More recently, from areas near North Dakota, the ICV prevalence among cattle decreased to 5.99% [<span>3</span>]. In the present study of Southern US cattle, the ICV prevalence is found to be 0.2%, marking a significant shift. One positive ICV sample from a Texas bovine nasal specimen demonstrated a mixing event between human and bovine ICVs.</p><p>Influenza viruses present significant public health and veterinary health concerns due to their genetic variability and potential for widespread transmission through animals and humans [<span>1, 3, 4</span>]. Previously, ICV has primarily affected humans with sporadic spillover to swine and dogs [<span>5-7</span>]. As humans, we are becoming more connected with farm animals through the food we eat, the people who work with or next to farm animals, and the proximity of farms to cities in the farm-to-table movement. These interactions increase the possibility of reservoirs for influenza in multiple species [<span>8</span>]. The One Health concept has demonstrated the interconnected network of health between humans, animals, and the environment [<span>9</span>]. Currently, highly pathogenic avian influenza H5N1, “bird flu,” is raging in wild birds and has jumped species to numerous domestic and wild mammals. As ICV is known to cause infections in humans and pigs, being on the forefront of an outbreak in cattle would well position public health practitioners to prepare for and prevent any potential human pandemics. Investigations of data from Japan from 2020 to 2023 show that ICV had an overall cattle seroprevalence of 27.0% [<span>1</span>]. From 2010 to 2011, 2.32% of children under 10 years of age from 474 mixed human respiratory samples were found to have C/Kanagawa and C/Sao Paulo [<span>10</span>]. In 2009, a novel <i>influenza A</i> virus emerged after a reassortment of viruses from different sources including pigs, birds, and humans, which resulted in an influenza pandemic. There is little attention drawn to ICV due to its lower human pathogenicity and prevalence compared to influenza A or B [<span>8</span>]. Consequently, there are no vaccines or effective antiviral treatments currently available for this type of influenza, despite the currently approved polymerase inhibitor baloxavir possessing some antiviral activity against ICV [<span>8, 11</span>]. This study utilizes nasal swab samples collected by the UTMB One Health Team in three US states and one region in Mexico from 2024 to 2025 to estimate the current prevalence of ICV in cattle in North America.</p><p>In this study, we conducted qRT-PCR assays on nasal swabs collected from cattle from dairy farms across three U","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.70167","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206467","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}
Yingcheng Wang, Mingjun Rui, Qiran Wei, Ting Fan Leung, Joyce H. S. You
Background
Nirsevimab, a long-acting monoclonal antibody, was shown to prevent respiratory syncytial virus (RSV) infections in newborns. We evaluated the cost-effectiveness of nirsevimab strategies for newborns from the societal perspective in Hong Kong.
Methods
A Markov model was developed to simulate outcomes of four nirsevimab strategies in newborns: (1) year-round, (2) seasonal, (3) catch-up, and (4) no nirsevimab. Primary outcomes included RSV lower respiratory tract infections (LRTI) related events, direct and indirect costs, quality-adjusted life year (QALY) loss, and incremental cost per QALY (ICER).
Results
In base-case analysis, all strategies with nirsevimab reduced RSV–LRTI-related events. The catch-up group had the lowest QALY loss per 100,000 infants (38.82), followed by year-round (45.71), seasonal (60.60), and no intervention groups (81.52). Three nirsevimab cost levels were examined: 10%, 25%, and 50% of the US cost. At 10% US cost (USD52), all strategies were cost-saving versus no intervention. At 25% US cost (USD130), the ICER of the catch-up group (vs. no intervention) was 141,925 USD/QALY. At 50% US cost (USD260), all nirsevimab strategies were not cost-effective versus no intervention at a willingness-to-pay of 162,401 USD/QALY. Influential factors with thresholds were identified for RSV-LRTI incidence, RSV-related hospitalization and mortality, and nirsevimab effectiveness at the 25% US cost level (USD130). In probabilistic sensitivity analysis, the catch-up and no intervention strategies were cost-effective 100% of the time at 10% (USD52) and 50% (USD260) US cost, respectively. At 25% US cost (USD130), the catch-up strategy was cost-effective 58.56% of the time.
Conclusions
The cost-effectiveness acceptance of nirsevimab was highly subject to drug cost and effectiveness of nirsevimab, RSV-LRTI incidence, and RSV–LRTI-related consequences.
{"title":"Cost-Effectiveness Analysis of Nirsevimab for Respiratory Syncytial Virus Disease Prevention in Newborns of Hong Kong","authors":"Yingcheng Wang, Mingjun Rui, Qiran Wei, Ting Fan Leung, Joyce H. S. You","doi":"10.1111/irv.70153","DOIUrl":"10.1111/irv.70153","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Nirsevimab, a long-acting monoclonal antibody, was shown to prevent respiratory syncytial virus (RSV) infections in newborns. We evaluated the cost-effectiveness of nirsevimab strategies for newborns from the societal perspective in Hong Kong.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A Markov model was developed to simulate outcomes of four nirsevimab strategies in newborns: (1) year-round, (2) seasonal, (3) catch-up, and (4) no nirsevimab. Primary outcomes included RSV lower respiratory tract infections (LRTI) related events, direct and indirect costs, quality-adjusted life year (QALY) loss, and incremental cost per QALY (ICER).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>In base-case analysis, all strategies with nirsevimab reduced RSV–LRTI-related events. The catch-up group had the lowest QALY loss per 100,000 infants (38.82), followed by year-round (45.71), seasonal (60.60), and no intervention groups (81.52). Three nirsevimab cost levels were examined: 10%, 25%, and 50% of the US cost. At 10% US cost (USD52), all strategies were cost-saving versus no intervention. At 25% US cost (USD130), the ICER of the catch-up group (vs. no intervention) was 141,925 USD/QALY. At 50% US cost (USD260), all nirsevimab strategies were not cost-effective versus no intervention at a willingness-to-pay of 162,401 USD/QALY. Influential factors with thresholds were identified for RSV-LRTI incidence, RSV-related hospitalization and mortality, and nirsevimab effectiveness at the 25% US cost level (USD130). In probabilistic sensitivity analysis, the catch-up and no intervention strategies were cost-effective 100% of the time at 10% (USD52) and 50% (USD260) US cost, respectively. At 25% US cost (USD130), the catch-up strategy was cost-effective 58.56% of the time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The cost-effectiveness acceptance of nirsevimab was highly subject to drug cost and effectiveness of nirsevimab, RSV-LRTI incidence, and RSV–LRTI-related consequences.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145199262","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}
Nicolas Banholzer, David Kronthaler, Pascal Bittel, Lavinia Furrer, James D Munday, Matthias Egger, Tina Hascher, Philipp Jent, Lukas Fenner
Background
Viral respiratory infections contribute to sick days in school children. We monitored respiratory infections, absences, and symptoms in a Swiss school.
Methods
Serial saliva sampling (three per week) and daily recording of absences and symptoms over 6 weeks during the winter of 2023/24 in four Swiss school classes (age 14–15).
Results
We analyzed 1047 samples of 67/84 (80%) participants, identifying 87 infection episodes across eight viruses: 28 (32%) human rhinovirus, 18 (21%) influenza A/B, 11 (13%) respiratory syncytial virus, 14 (16%) human coronaviruses, 6 (7%) parainfluenza virus, and 5 (6%) influenza B; SARS-CoV-2 was not detected. Spatiotemporal trends revealed seasonal epidemic trends and evidence of transmission within classes. Viral loads (interquartile range 29.5–36.9 Ct) and duration of detection (modeled range 3.2–5.3 days) were similar for all viruses. School absences were more likely temporally associated with influenza B infections than with other respiratory viral infections (> 99% vs. 38%, p = 0.005), and the absences tended to be longer (average 4.2 vs. 2.2 days). Symptoms varied depending on the pathogen detected, with absences temporally associated with human rhinovirus and parainfluenza virus infections commonly involving runny nose and sore throat, while absences associated with influenza infections often involved fever.
Conclusions
Class-specific distribution patterns suggest a major contribution of within-class to overall respiratory virus transmission. Respiratory viruses showed certain distinct profiles in relation to school absences and symptoms. This highlights the importance of infection control measures, including vaccination, and virus-specific monitoring to better understand transmission dynamics in schools.
背景：病毒性呼吸道感染导致学龄儿童请病假。我们监测了瑞士一所学校的呼吸道感染、缺勤和症状。方法在瑞士4个班级（14-15岁），于2023/24年冬季连续6周进行唾液取样（每周3次）和每日缺勤和症状记录。结果：我们分析了67/84（80%）名参与者的1047份样本，确定了8种病毒的87次感染：28例（32%）人鼻病毒，18例（21%）流感A/B病毒，11例（13%）呼吸道合胞病毒，14例（16%）人冠状病毒，6例（7%）副流感病毒，5例（6%）流感B病毒；未检测到SARS-CoV-2。时空趋势揭示了季节性流行趋势和班级内传播的证据。所有病毒的病毒载量（四分位数范围29.5-36.9 Ct）和检测持续时间（模型范围3.2-5.3天）相似。与其他呼吸道病毒感染相比，乙型流感感染更可能与缺课时间有关（> 99% vs. 38%, p = 0.005），缺课时间往往更长（平均4.2 vs. 2.2天）。症状因检测到的病原体而异，暂时缺席与人鼻病毒和副流感病毒感染有关，通常涉及流鼻涕和喉咙痛，而与流感感染相关的缺席通常涉及发烧。结论班级特异性分布模式提示班级内对呼吸道病毒传播的主要贡献。呼吸道病毒在缺课和症状方面表现出某些不同的特征。这突出了感染控制措施的重要性，包括疫苗接种和病毒特异性监测，以更好地了解学校中的传播动态。
{"title":"Absences, Symptoms and Respiratory Viruses in a Swiss School: Longitudinal Study With Serial Saliva Sampling","authors":"Nicolas Banholzer, David Kronthaler, Pascal Bittel, Lavinia Furrer, James D Munday, Matthias Egger, Tina Hascher, Philipp Jent, Lukas Fenner","doi":"10.1111/irv.70143","DOIUrl":"https://doi.org/10.1111/irv.70143","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Viral respiratory infections contribute to sick days in school children. We monitored respiratory infections, absences, and symptoms in a Swiss school.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Serial saliva sampling (three per week) and daily recording of absences and symptoms over 6 weeks during the winter of 2023/24 in four Swiss school classes (age 14–15).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We analyzed 1047 samples of 67/84 (80%) participants, identifying 87 infection episodes across eight viruses: 28 (32%) human rhinovirus, 18 (21%) influenza A/B, 11 (13%) respiratory syncytial virus, 14 (16%) human coronaviruses, 6 (7%) parainfluenza virus, and 5 (6%) influenza B; SARS-CoV-2 was not detected. Spatiotemporal trends revealed seasonal epidemic trends and evidence of transmission within classes. Viral loads (interquartile range 29.5–36.9 Ct) and duration of detection (modeled range 3.2–5.3 days) were similar for all viruses. School absences were more likely temporally associated with influenza B infections than with other respiratory viral infections (> 99% vs. 38%, <i>p</i> = 0.005), and the absences tended to be longer (average 4.2 vs. 2.2 days). Symptoms varied depending on the pathogen detected, with absences temporally associated with human rhinovirus and parainfluenza virus infections commonly involving runny nose and sore throat, while absences associated with influenza infections often involved fever.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Class-specific distribution patterns suggest a major contribution of within-class to overall respiratory virus transmission. Respiratory viruses showed certain distinct profiles in relation to school absences and symptoms. This highlights the importance of infection control measures, including vaccination, and virus-specific monitoring to better understand transmission dynamics in schools.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.70143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181648","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}
Judith U. Oguzie, Gustavo Hernandez-Vidal, Gustavo Moreno-Degollado, Gregory C. Gray
<p>Boosepivirus (BooV), a recently proposed genus within the family <i>Picornaviridae</i>, includes species A, B, and C, each with distinct genotypic subdivisions (e.g., B1 and B2) [<span>1</span>]. To date, BooV has been detected exclusively in fecal samples from cattle in several geographic locations with no prior reports of its presence in respiratory specimens [<span>2-5</span>]. Here, we describe the first detection of the BooV B1 genotype in a nasal swab collected from a beef yearling exhibiting respiratory symptoms in Mexico.</p><p>As part of a One Health surveillance for novel respiratory viruses on US and Mexican beef cattle farms in 2024, farm workers collected deep nasal swabs from 40 sick beef cattle and 12 bioaerosol samples from a farm in Nuevo León, Mexico. RNA was extracted from nasal swab specimens using the QIAamp Viral RNA Mini Kit on the QIAcube Connect automated system (QIAGEN Inc., Valencia, CA). Sequencing libraries were prepared with the Illumina Nextera XT Library Prep Kit (San Diego), following established protocols [<span>6</span>]. Libraries were sequenced on the Illumina NovaSeq X platform, generating 75-bp paired-end reads.</p><p>Raw metagenomic sequencing (mNGS) reads were processed using the Chan Zuckerberg ID (CZ ID) platform (https://czid.org). Subsequently, BooV genomes were aligned with published BooV sequences from the NCBI database using MAFFT [<span>7</span>], and a maximum likelihood phylogenetic tree was generated with IQ-TREE [<span>8</span>]. The resulting tree was visualized and annotated in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).</p><p>One of the 40 sick cow samples from the farm was chosen for mNGS based on pan-coronavirus assay positivity, which yielded evidence for a rodent coronavirus [<span>9</span>]. The specimen was collected from a 17-month-old beef yearling with fever and nasal discharge. The specimen had no molecular evidence of influenza A or D.</p><p>We assembled a contig of 7512 nt in length. BLASTn analysis demonstrated 87.63% nucleotide identity with strain 21-0305 (GenBank accession no. MZ052226.1). At the protein level, BLASTp analysis of the amino acid sequence revealed 98.33% identity with strain Bo-12-11/2009/JPN (GenBank accession no. LC036581.1) and 98.29% identity with strain 21-0305 (GenBank accession no. MZ052226.1). Phylogenetic analysis further showed that our sequence formed a monophyletic cluster with MZ052226.1, which was previously isolated from a diarrheic calf in the United States (Figure 1).</p><p>Notably, this is the first report of BooV detection in a nasal specimen. The BooV sequence has been submitted to the GenBank database under accession number PX262393. Although we cannot rule out fecal contamination of the yearling's airway, as the yearling had marked respiratory signs, our finding suggests the possibility of BooV's association with respiratory illness in cattle. This detection highlights the value of employing broad-range diagnostics when
{"title":"First Detection of Boosepivirus B1 in a Sick Yearling's Nasal Swab, Mexico","authors":"Judith U. Oguzie, Gustavo Hernandez-Vidal, Gustavo Moreno-Degollado, Gregory C. Gray","doi":"10.1111/irv.70165","DOIUrl":"https://doi.org/10.1111/irv.70165","url":null,"abstract":"<p>Boosepivirus (BooV), a recently proposed genus within the family <i>Picornaviridae</i>, includes species A, B, and C, each with distinct genotypic subdivisions (e.g., B1 and B2) [<span>1</span>]. To date, BooV has been detected exclusively in fecal samples from cattle in several geographic locations with no prior reports of its presence in respiratory specimens [<span>2-5</span>]. Here, we describe the first detection of the BooV B1 genotype in a nasal swab collected from a beef yearling exhibiting respiratory symptoms in Mexico.</p><p>As part of a One Health surveillance for novel respiratory viruses on US and Mexican beef cattle farms in 2024, farm workers collected deep nasal swabs from 40 sick beef cattle and 12 bioaerosol samples from a farm in Nuevo León, Mexico. RNA was extracted from nasal swab specimens using the QIAamp Viral RNA Mini Kit on the QIAcube Connect automated system (QIAGEN Inc., Valencia, CA). Sequencing libraries were prepared with the Illumina Nextera XT Library Prep Kit (San Diego), following established protocols [<span>6</span>]. Libraries were sequenced on the Illumina NovaSeq X platform, generating 75-bp paired-end reads.</p><p>Raw metagenomic sequencing (mNGS) reads were processed using the Chan Zuckerberg ID (CZ ID) platform (https://czid.org). Subsequently, BooV genomes were aligned with published BooV sequences from the NCBI database using MAFFT [<span>7</span>], and a maximum likelihood phylogenetic tree was generated with IQ-TREE [<span>8</span>]. The resulting tree was visualized and annotated in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).</p><p>One of the 40 sick cow samples from the farm was chosen for mNGS based on pan-coronavirus assay positivity, which yielded evidence for a rodent coronavirus [<span>9</span>]. The specimen was collected from a 17-month-old beef yearling with fever and nasal discharge. The specimen had no molecular evidence of influenza A or D.</p><p>We assembled a contig of 7512 nt in length. BLASTn analysis demonstrated 87.63% nucleotide identity with strain 21-0305 (GenBank accession no. MZ052226.1). At the protein level, BLASTp analysis of the amino acid sequence revealed 98.33% identity with strain Bo-12-11/2009/JPN (GenBank accession no. LC036581.1) and 98.29% identity with strain 21-0305 (GenBank accession no. MZ052226.1). Phylogenetic analysis further showed that our sequence formed a monophyletic cluster with MZ052226.1, which was previously isolated from a diarrheic calf in the United States (Figure 1).</p><p>Notably, this is the first report of BooV detection in a nasal specimen. The BooV sequence has been submitted to the GenBank database under accession number PX262393. Although we cannot rule out fecal contamination of the yearling's airway, as the yearling had marked respiratory signs, our finding suggests the possibility of BooV's association with respiratory illness in cattle. This detection highlights the value of employing broad-range diagnostics when","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 10","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.70165","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181584","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}
Ana María Puerto, José Eugenio Lozano, Marcos Lozano, Luca Basile, Gael Naveira-Barbeito, Inés Guiu Cañete, Juan Antonio Linares Dópido, Ana Fernández Ibáñez, Ana Carmen Ibáñez Pérez, Daniel Castrillejo, Eva Rivas Wagner, María Ángel Valcárcel de la Iglesia, Esteban Pérez Morilla, Isabel Martínez-Pino, Tomás Vega, Susana Monge, SiVIRA-MEM collaborators
Objectives
We estimated acute respiratory infections (ARIs) and influenza-like illness (ILI) thresholds for SiVIRA, a new integrated surveillance system set up in Spain in 2020.
Methods
We retrospectively extracted diagnostic codes from primary healthcare databases between Weeks 30/2010 and 39/2021, using methods similar to SiVIRA. Epidemic and intensity thresholds were estimated using the moving epidemic method (MEM).
Results
The epidemic threshold for the 2024–2025 season was 400 cases per 100,000 persons for ARI and 36 for ILI, and medium, high, and very high intensity thresholds were 953, 1079, and 1139 for ARI and 167, 218, and 246 for ILI, estimating low intensity.
Conclusions
Reconstructing the historical series using electronic health records was possible and allowed the estimation of thresholds. Experience gained will guide the choice of MEM parameters in the future.
{"title":"Establishing Epidemic and Intensity Thresholds After a Major Change in Respiratory Virus Surveillance in Spain in 2020","authors":"Ana María Puerto, José Eugenio Lozano, Marcos Lozano, Luca Basile, Gael Naveira-Barbeito, Inés Guiu Cañete, Juan Antonio Linares Dópido, Ana Fernández Ibáñez, Ana Carmen Ibáñez Pérez, Daniel Castrillejo, Eva Rivas Wagner, María Ángel Valcárcel de la Iglesia, Esteban Pérez Morilla, Isabel Martínez-Pino, Tomás Vega, Susana Monge, SiVIRA-MEM collaborators","doi":"10.1111/irv.70136","DOIUrl":"https://doi.org/10.1111/irv.70136","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Objectives</h3>\u0000 \u0000 <p>We estimated acute respiratory infections (ARIs) and influenza-like illness (ILI) thresholds for SiVIRA, a new integrated surveillance system set up in Spain in 2020.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We retrospectively extracted diagnostic codes from primary healthcare databases between Weeks 30/2010 and 39/2021, using methods similar to SiVIRA. Epidemic and intensity thresholds were estimated using the moving epidemic method (MEM).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The epidemic threshold for the 2024–2025 season was 400 cases per 100,000 persons for ARI and 36 for ILI, and medium, high, and very high intensity thresholds were 953, 1079, and 1139 for ARI and 167, 218, and 246 for ILI, estimating low intensity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Reconstructing the historical series using electronic health records was possible and allowed the estimation of thresholds. Experience gained will guide the choice of MEM parameters in the future.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.70136","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145110726","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}
Adamou Lagare, William W. Davis, Neha N. Patel, Goumbi Kadade, Jean Testa, Saidou Mamadou, Julia Fitzner, Stefano Tempia, A. Danielle Iuliano
<div> <section> <h3> Background</h3> <p>Influenza contributes substantially to severe acute respiratory infection (SARI) morbidity and mortality worldwide. However, few countries have estimated influenza disease burden, especially middle and low-income countries. Burden data are important to understand the impacts of illness on the population and to inform interventions. Currently, Niger has no recommendations for seasonal influenza vaccination or antiviral use. We estimated the national number and rates of SARI and influenza-associated SARI hospitalizations, mild/moderate illness, and death among children aged < 5 years in Niger.</p> </section> <section> <h3> Methods</h3> <p>We utilized influenza surveillance data among children aged < 5 years hospitalized with SARI at three sentinel hospitals located in Niamey during 2015–2018 along with estimated catchment area population data to calculate the influenza-associated SARI hospitalization rates per 100,000 population. Rates were calculated for age groups < 1, 1–4, and < 5 years using the World Health Organization (WHO) methods and a hospital admission survey; then, we extrapolated the estimates nationally. We also used the influenza burden pyramid tool developed by WHO and the John Hopkins Center for Health Security to estimate influenza-associated mild/moderate illnesses and influenza-associated deaths for Niger.</p> </section> <section> <h3> Results</h3> <p>Influenza viruses were detected in 175/1796 (9.7%) specimens collected and tested during the study period from children aged < 5 years at the three SARI sentinel surveillance sites. The influenza percentage positive was 7.7% (58/754) among infants aged < 1 year and 11.3% (117/1038) among children aged 1–4 years. The estimated mean annual national number of SARI hospitalizations among children aged < 5 years was 16,406 (95% CI: 15,117–17,779) and the estimated SARI hospitalization rate per 100,000 population was 405.3 (95% CI: 373.5–439.2). The estimated mean annual national number of influenza-associated SARI hospitalizations among children aged < 5 years was 1484 (95% CI: 1162–1813; rate: 36.7; 95% CI: 28.7–44.8). The estimated mean annual national number of influenza-associated mild illnesses, hospitalized patients, and deaths among children aged < 5 years in Niger was 218,030 (95% CI: 43,303–527,236), 1261 (95% CI: 38–3271), 223 (95% CI: 22–614), and 15 (95% CI: 6–373) respectively.</p> </section> <section> <h3> Conclusions</h3> <p>’This study estimated a substantial influenza disease burden among children aged < 5 years in Niger, highlighting, for decision makers, the importance of resource al
{"title":"The National Burden of Influenza-Associated Respiratory Illness Among Children Aged <5 Years in Niger, 2015–2018","authors":"Adamou Lagare, William W. Davis, Neha N. Patel, Goumbi Kadade, Jean Testa, Saidou Mamadou, Julia Fitzner, Stefano Tempia, A. Danielle Iuliano","doi":"10.1111/irv.70160","DOIUrl":"10.1111/irv.70160","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Influenza contributes substantially to severe acute respiratory infection (SARI) morbidity and mortality worldwide. However, few countries have estimated influenza disease burden, especially middle and low-income countries. Burden data are important to understand the impacts of illness on the population and to inform interventions. Currently, Niger has no recommendations for seasonal influenza vaccination or antiviral use. We estimated the national number and rates of SARI and influenza-associated SARI hospitalizations, mild/moderate illness, and death among children aged < 5 years in Niger.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We utilized influenza surveillance data among children aged < 5 years hospitalized with SARI at three sentinel hospitals located in Niamey during 2015–2018 along with estimated catchment area population data to calculate the influenza-associated SARI hospitalization rates per 100,000 population. Rates were calculated for age groups < 1, 1–4, and < 5 years using the World Health Organization (WHO) methods and a hospital admission survey; then, we extrapolated the estimates nationally. We also used the influenza burden pyramid tool developed by WHO and the John Hopkins Center for Health Security to estimate influenza-associated mild/moderate illnesses and influenza-associated deaths for Niger.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Influenza viruses were detected in 175/1796 (9.7%) specimens collected and tested during the study period from children aged < 5 years at the three SARI sentinel surveillance sites. The influenza percentage positive was 7.7% (58/754) among infants aged < 1 year and 11.3% (117/1038) among children aged 1–4 years. The estimated mean annual national number of SARI hospitalizations among children aged < 5 years was 16,406 (95% CI: 15,117–17,779) and the estimated SARI hospitalization rate per 100,000 population was 405.3 (95% CI: 373.5–439.2). The estimated mean annual national number of influenza-associated SARI hospitalizations among children aged < 5 years was 1484 (95% CI: 1162–1813; rate: 36.7; 95% CI: 28.7–44.8). The estimated mean annual national number of influenza-associated mild illnesses, hospitalized patients, and deaths among children aged < 5 years in Niger was 218,030 (95% CI: 43,303–527,236), 1261 (95% CI: 38–3271), 223 (95% CI: 22–614), and 15 (95% CI: 6–373) respectively.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>’This study estimated a substantial influenza disease burden among children aged < 5 years in Niger, highlighting, for decision makers, the importance of resource al","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145080601","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}
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