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Immune Priming and the Risk of COVID-19, Influenza, and Other Acute Respiratory Infections: Insights From an N3C Cohort. 免疫启动和COVID-19、流感和其他急性呼吸道感染的风险:来自N3C队列的见解
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-03-01 DOI: 10.1111/irv.70253
Tomás M León, Lyndsey M Muehling, Rachel Baccile, Olga Morozova

Background: The emergence of SARS-CoV-2 and introduction of COVID-19 vaccines into immunologically naïve populations may alter the dynamics of other acute viral respiratory infections (viral ARIs) and vice versa. Competing forces, including viral interference, cross-reactive immunity, shared susceptibility, and immune dysregulation, may affect the risk. The potential net impact of various immune-priming events and their timing on the risk of viral ARIs is largely unknown.

Methods: Using data from the National Clinical Cohort Collaborative (N3C) COVID-19 Enclave, this retrospective population-based cohort study investigated the relationship between immune-priming events (COVID-19 and influenza vaccinations, and SARS-CoV-2, influenza, other, and unspecified viral ARIs) between January 2018 and September 2021 and the risk of viral ARIs during October 2021-April 2022. The sample included N = 608,725 individuals from seven data partners with well-ascertained COVID-19 and influenza vaccination data.

Results: Early COVID-19 vaccination (December 2020-March 2021) and SARS-CoV-2 infection during the overlapping period (October 2020-March 2021) were associated with a lower risk of all outcomes, including non-SARS-CoV-2 infections. Off-season influenza vaccination (January-June 2021) was associated with a lower risk of SARS-CoV-2 and any viral ARI. Other priming events showed mixed associations, with a lack of evidence of stronger protection from more recent immune-priming events.

Conclusions: This exploratory analysis suggests potential crossprotection between viral ARIs that may inform vaccination strategies. While ascertainment and healthcare-seeking biases in electronic health records may inflate positive associations between infection outcomes and immune priming, negative (i.e., protective) associations are of potential public health significance and warrant further investigation.

背景:SARS-CoV-2的出现和COVID-19疫苗在免疫naïve人群中的引入可能改变其他急性病毒性呼吸道感染(病毒性呼吸道感染)的动态,反之亦然。相互竞争的力量,包括病毒干扰、交叉反应性免疫、共同易感性和免疫失调,都可能影响风险。各种免疫启动事件及其时间对病毒性急性呼吸道感染风险的潜在净影响在很大程度上是未知的。方法:利用国家临床队列协作(N3C) COVID-19 Enclave的数据,这项基于人群的回顾性队列研究调查了2018年1月至2021年9月期间免疫启动事件(COVID-19和流感疫苗,SARS-CoV-2,流感,其他和未指定的病毒性ARIs)与2021年10月至2022年4月期间病毒性ARIs风险之间的关系。样本包括来自7个数据合作伙伴的N = 608,725人,他们具有明确的COVID-19和流感疫苗接种数据。结果:早期接种COVID-19疫苗(2020年12月- 2021年3月)和重叠期(2020年10月- 2021年3月)的SARS-CoV-2感染与所有结局(包括非SARS-CoV-2感染)的风险较低相关。非季节流感疫苗接种(2021年1月至6月)与较低的SARS-CoV-2和任何病毒性ARI风险相关。其他启动事件显示出混合关联,缺乏证据表明对最近的免疫启动事件有更强的保护作用。结论:这一探索性分析表明,病毒性急性呼吸道感染之间潜在的交叉保护可能为疫苗接种策略提供信息。虽然电子健康记录中的确定和寻求医疗保健的偏见可能夸大感染结果与免疫启动之间的积极联系,但消极(即保护性)联系具有潜在的公共卫生意义,值得进一步调查。
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引用次数: 0
Survival bias and declining mortality risk in long-term COVID-19 studies. COVID-19长期研究中的生存偏差和死亡率风险下降
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-03-01 DOI: 10.1111/irv.70247
Wiessam Abu Ahmad, Ronen Arbel
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引用次数: 0
Evaluating the Health Economic Impacts of Baloxavir Marboxil and Oseltamivir for the Treatment of Influenza in Adult Outpatients in Hong Kong: A Cost-Effectiveness Analysis. 评估巴洛韦-马博西和奥司他韦治疗香港成人门诊病人流感的健康经济影响:成本-效果分析。
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-03-01 DOI: 10.1111/irv.70243
Ruohan Chen, Zengyang Shao, Kaiming Bi, Benjamin John Cowling, Zhanwei Du

Background: Baloxavir marboxil, an antiviral used only in private hospitals in Hong Kong since February 2019 for treating influenza, is recognized for its efficacy against strains resistant to standard antiviral agents, providing an alternative to neuraminidase inhibitors such as oseltamivir.

Methods: This study compares the cost-effectiveness of baloxavir and oseltamivir for influenza treatment in otherwise healthy (OwH) and high-risk (HR) adult outpatients in Hong Kong from the healthcare-payer's perspective. A decision tree was utilized to study the progression of influenza and estimate associated costs and quality-adjusted life-years (QALYs) over 14 days for each antiviral.

Findings: In the general population, the incremental cost-effectiveness ratio (ICER) for baloxavir is $89,921 per QALY. Compared to oseltamivir, baloxavir shows a QALY gain with an incremental cost of $13,626 per QALY, below the $152,667 willingness-to-pay (WTP) threshold. At this WTP level, there is a 92% chance the additional cost of baloxavir is accepted. As oseltamivir resistance rises, its economic benefit decreases, while baloxavir's improves. In the OwH population, baloxavir's ICER is $145,316 compared to baseline and $115,811 compared to oseltamivir, with a 49% probability of baloxavir being cost-effective. In the HR population, baloxavir dominates, with ICERs of $36,163 and $-15,072, and a 99% probability of cost-effectiveness.

Conclusion: As a result, baloxavir could potentially be considered as the influenza agent of choice over oseltamivir in Hong Kong, despite a higher acquisition cost. Therefore, we recommended that integrating baloxavir into the Hospital Authority Drug Formulary in Hong Kong could enhance healthcare resource allocation and improve patient outcomes.

背景:Baloxavir marboxil是一种自2019年2月以来仅在香港私立医院用于治疗流感的抗病毒药物,因其对标准抗病毒药物耐药的菌株有效而得到认可,为神经氨酸酶抑制剂(如奥司他韦)提供了替代方案。方法:本研究比较了巴洛韦和奥司他韦在香港健康(OwH)和高危(HR)成人门诊患者中治疗流感的成本-效果。采用决策树来研究流感的进展,并估计每种抗病毒药物的相关成本和超过14天的质量调整生命年(QALYs)。结果:在一般人群中,baloxavir的增量成本-效果比(ICER)为89,921美元/ QALY。与奥司他韦相比,巴洛昔韦显示出质量aly的增加,每个质量aly的增量成本为13,626美元,低于152,667美元的支付意愿(WTP)阈值。在这个WTP水平上,有92%的机会接受巴洛昔韦的额外费用。随着奥司他韦耐药性的上升,其经济效益下降,而巴洛韦的经济效益提高。在OwH人群中,巴洛昔韦的ICER与基线相比为145,316美元,与奥司他韦相比为115,811美元,巴洛昔韦具有成本效益的概率为49%。在人力资源人群中,巴洛昔韦占主导地位,ICERs分别为36163美元和- 15072美元,成本-效果概率为99%。结论:因此,尽管巴洛昔韦的获取成本较高,但在香港,巴洛昔韦可能被视为流感药物的首选,而不是奥司他韦。因此,我们建议将巴洛韦纳入香港医院管理局的药物处方集,以改善医疗资源的分配和患者的治疗效果。
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引用次数: 0
Populations at Risk for Severe or Complicated Rhinovirus Illness: A Systematic Review and Meta-Analysis. 严重或复杂鼻病毒疾病风险人群:系统回顾和荟萃分析
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-03-01 DOI: 10.1111/irv.70251
David Gou, Jessica Bartoszko, Laura Weiler, Asal Alavi Parsi, Ante Cuvalo, Sahith Rajkumar, Dominik Mertz, Mark Loeb

Background: Although most rhinovirus infections are mild and subside quickly, vulnerable populations may experience severe illness. Identifying populations at risk for severe or complicated rhinovirus illness can strengthen the ongoing search for preventative and therapeutic treatments. This systematic review and meta-analysis aimed to summarize the populations at risk for the development of severe or complicated rhinovirus illness.

Methods: We searched CENTRAL, EMBASE, and MEDLINE in April 2024 for studies reporting risk factors for severe rhinovirus infection, defined as lower respiratory tract infection (LRTI), hospitalization, critical care unit (CCU) admission, mechanical ventilation, or death. We pooled odds ratios using random-effects meta-analysis, assessed risk of bias using the Newcastle-Ottawa Scale, and rated the certainty of evidence using the GRADE framework.

Results: From 29 observational studies (n = 13,185 participants), we analyzed 13 risk factor-outcome combinations. With high certainty, age < 1 year and premature birth are not associated with the risk of LRTI, and diabetes mellitus is not associated with mortality. With moderate certainty, any comorbidity and pulmonary comorbidity are probably associated with increased risk of LRTI, age > 18 years and malignancy are probably associated with increased risk of mortality, and malignancy is probably associated with an increased risk of CCU admission. Many risk factors lacked sufficient evidence for meta-analysis.

Conclusions: Individuals with comorbidities are at greater risk of severe rhinovirus illness. Our findings can inform clinical risk stratification and guide the development and targeted use of emerging therapies. Further comprehensive research is required to elucidate additional risk factors and strengthen the evidence.

背景:虽然大多数鼻病毒感染是轻微的,并且会迅速消退,但脆弱人群可能会出现严重的疾病。确定有严重或复杂鼻病毒疾病风险的人群可以加强正在进行的预防性和治疗性治疗的研究。本系统综述和荟萃分析旨在总结发生严重或复杂鼻病毒疾病的高危人群。方法:我们检索了2024年4月CENTRAL、EMBASE和MEDLINE中报告严重鼻病毒感染危险因素的研究,定义为下呼吸道感染(LRTI)、住院、重症监护病房(CCU)住院、机械通气或死亡。我们使用随机效应荟萃分析合并优势比,使用纽卡斯尔-渥太华量表评估偏倚风险,并使用GRADE框架对证据的确定性进行评级。结果:从29项观察性研究(n = 13,185名参与者)中,我们分析了13种危险因素-结局组合。可以肯定的是,18岁和恶性肿瘤可能与死亡风险增加有关,恶性肿瘤可能与CCU入院风险增加有关。许多危险因素缺乏足够的证据进行meta分析。结论:有合并症的个体发生严重鼻病毒疾病的风险更大。我们的发现可以为临床风险分层提供信息,并指导新兴疗法的发展和有针对性的使用。需要进一步的全面研究来阐明其他危险因素并加强证据。
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引用次数: 0
A Monoclonal Antibody ELISA-Based Assay for Measuring the Potency of Candidate H5 Clade 2.3.4.4b Pandemic Influenza Vaccines. 基于单克隆抗体elisa的H5分支2.3.4.4b大流行性流感候选疫苗效价测定方法
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-03-01 DOI: 10.1111/irv.70206
Marcus Odin, Falko Schmeisser, Jackeline Soto, Jerry P Weir

Background: The single radial immunodiffusion (SRID) assay is used to determine the potency of inactivated influenza vaccines. Nevertheless, development of alternative influenza vaccine potency assays with greater sensitivity and less reliance on large quantities of reference reagents is needed. Many candidate alternative potency assays use monoclonal antibodies (mAbs) to quantify the relevant immunogenic form of HA in vaccines. Although the feasibility of such assays has been demonstrated, concerns remain as to whether the necessary antibody reagents can be generated in the timeframes of vaccine manufacture, particularly for pandemic vaccines.

Methods: We describe the development and evaluation of a mAb-based ELISA assay to measure the potency of several candidate H5 clade 2.3.4.4b A/Astrakhan/3212/2020 influenza vaccines prepared recently in response to the ongoing H5N1 outbreak in the United States. The assay uses H5 mAbs that were generated and characterized several years prior to the emergence of these H5N1 viruses.

Results: Correlation of the ELISA potency results with traditional SRID potency values was excellent for a cell-based vaccine and one egg-based vaccine. The ELISA and SRID potency values for the second egg-based vaccine were not as well aligned initially, but alignment was improved by use of an internal standard.

Conclusions: The results demonstrated that the ELISA potency assay is suitable for determining the potency of inactivated H5 A/Astrakhan/3212/2020 influenza vaccines. Moreover, the results demonstrate the importance of preparing libraries of antibody reagents for influenza subtypes with pandemic potential so that suitable mAbs are available for development of alternative mAb vaccine potency assays when needed.

背景:单径向免疫扩散(SRID)试验用于确定灭活流感疫苗的效力。然而,需要开发具有更高灵敏度和较少依赖大量参考试剂的替代流感疫苗效力测定法。许多候选的替代效力测定使用单克隆抗体(mab)来量化疫苗中相关的HA免疫原性形式。虽然这种检测方法的可行性已得到证明,但在疫苗生产的时限内,特别是在大流行性流感疫苗生产的时限内,是否能够生产出必要的抗体试剂,仍然令人关切。方法:我们描述了一种基于单克隆抗体(mab)的ELISA检测方法的开发和评估,用于测量最近为应对美国正在进行的H5N1疫情而制备的几种候选H5进化支2.3.4.4b a /Astrakhan/3212/2020流感疫苗的效力。该检测使用的H5单克隆抗体是在这些H5N1病毒出现前几年产生和鉴定的。结果:一种细胞疫苗和一种蛋疫苗的ELISA效价结果与传统的SRID效价值具有良好的相关性。第二种蛋基疫苗的ELISA效价和SRID效价最初没有很好地一致,但通过使用内标提高了一致性。结论:ELISA效价法适用于h5a /阿斯特拉罕/3212/2020流感灭活疫苗的效价测定。此外,研究结果表明,为具有大流行潜力的流感亚型准备抗体试剂库的重要性,以便在需要时为开发替代单抗疫苗效力测定提供合适的单抗。
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引用次数: 0
Symptoms Associated With Detection of Viral Versus Bacterial Pathogens in Outpatients With Lower Respiratory Infections. 下呼吸道感染门诊患者病毒与细菌病原体检测的相关症状
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-03-01 DOI: 10.1111/irv.70229
Mark Ebell, Dan J Merenstein, Bruce Barrett, Cassie Hulme, Sarah Walters, Caroline Hamer, Michelle Buhr

Purpose: This study aims to identify symptoms that predict a high likelihood of viral infection, so these patients could be triaged for home care to avoid antibiotics.

Methods: We recruited adults presenting to US primary or urgent care sites with a chief complaint of cough and symptoms consistent with LRTI. Data collected included demographics, comorbidities, symptoms, and 46 viral and bacterial respiratory pathogens by PCR. Chi-square tests were done to evaluate the association between individual symptoms and viral versus bacterial infections. Symptoms with a p < 0.10 for the association were retained for logistic regression. We created four regression models using stepwise backward elimination at p < 0.20, with viral infection, bacterial infection, and mixed infection as the dependent variables. A simple risk score was created assigning positive and negative points for viral and bacterial symptoms.

Results: We enrolled 718 adults with acute cough and obtained valid PCR specimens for 618. Four symptoms were significantly more likely with viral infections and less common in bacterial: coryza, confusion, fever, and chest congestion. Three symptoms were more likely with bacterial infections and less likely with viral infections: presence of sputum, sputum that is colored, and double-sickening (feeling better but then worsening). A simple risk score identified patients with a low (29%), moderate (56%), or high (79%) likelihood of having only viral pathogens detected.

Conclusions: Seven symptoms were identified that could help primary care clinicians distinguish between viral and bacterial LRTI. A simple risk score is proposed but requires prospective validation.

目的:本研究旨在确定预测病毒感染可能性高的症状,以便对这些患者进行分类,进行家庭护理,避免使用抗生素。方法:我们招募了以咳嗽和与下呼吸道感染症状一致的主诉到美国初级或紧急护理机构就诊的成年人。收集的数据包括人口统计学、合并症、症状和46种病毒性和细菌性呼吸道病原体。卡方检验评估个体症状与病毒感染和细菌感染之间的关系。结果:我们招募了718名患有急性咳嗽的成年人,其中618人获得了有效的PCR标本。有四种症状明显更可能与病毒感染有关,而在细菌感染中较不常见:鼻炎、精神错乱、发烧和胸闷。有三种症状更可能是细菌感染,更不可能是病毒感染:有痰、痰是有色的、双重恶心(感觉好些了,但后来又加重了)。简单的风险评分将患者分为低(29%)、中(56%)或高(79%)可能只检测到病毒病原体。结论:确定了七种症状,可以帮助初级保健临床医生区分病毒性和细菌性下呼吸道感染。提出了一个简单的风险评分,但需要前瞻性验证。
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引用次数: 0
Impact of First SARS-CoV-2 Infection Variant on Serological Responses Against Omicron: Findings From the SIREN Study 首个SARS-CoV-2感染变体对抗组粒血清学反应的影响:来自SIREN研究的发现
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-22 DOI: 10.1111/irv.70204
Ferdinando Insalata, Ana Atti, Edward J. Carr, Ashley D. Otter, SIREN study group, Sarah Foulkes, Giulia Dowgier, Agnieszka Hobbs, Mary Y. Wu, Susan Hopkins, Andre Charlett, Rupert Beale, Victoria Hall

Introduction

Despite the existing hybrid immunity, a sharp increase in SARS-CoV-2 reinfections was observed worldwide following Omicron variant emergence. We investigated whether the first infecting variant indelibly shapes serological responses against Omicron (BA.1 and BA.2) reinfection.

Methods

Participants with a sequence-confirmed Alpha (n = 23) or Delta (n = 10) first infection before third vaccine dose (V3) that subsequently had a BA.1 or BA.2 reinfection were selected. Sera were tested for anti-SARS-CoV-2 spike (anti-S) and live virus microneutralisation (LV-N) against Ancestral, Alpha, Delta, Omicron BA.1 and BA.2. Antibody responses and waning post-V3 were compared by first infection variant using mixed-effect models, as well as inferred titres days before reinfections. Individual's neutralisation responses were compared 12 weeks post-V3, among those with Alpha and Delta primary infection.

Results

After V3, those with Delta first infection had higher LV-N Omicron BA.1 titres (fold difference (FD) = 2.7, p = 0.05) compared to Alpha primary infection. Participants with Delta first infection presented higher LV-N BA.1 (FD = 1.89, p = 0.004) and LV-N BA.2 (FD = 2.06, p = 0.001) titres pre-Omicron reinfections. Individuals' neutralisation responses against Ancestral were higher than any other subsequent variants, regardless of first infection variant.

Conclusions

A previous Delta SARS-CoV-2 infection induced a higher serological response against a subsequent Omicron infection when compared to Alpha first infections.

导语:尽管存在混合免疫,但在Omicron变体出现后,在全球范围内观察到SARS-CoV-2再感染急剧增加。我们研究了第一种感染变异体是否不可磨灭地影响对欧米克隆(BA.1和BA.2)再感染的血清学反应。方法:选择在第三次疫苗接种(V3)前首次感染序列确认为α型(n = 23)或δ型(n = 10),随后发生BA.1或BA.2再感染的参与者。检测血清抗sars - cov -2刺突(anti-S)和活病毒微量中和(LV-N)对祖传、α、Delta、欧米克隆BA.1和BA.2的抑制作用。使用混合效应模型比较首次感染变异的抗体反应和v3后的减弱,以及再次感染前几天的推断滴度。在Alpha和Delta原发感染的患者中,比较v3后12周的个体中和反应。结果:V3期后,Delta型首次感染患者的LV-N Omicron BA.1滴度较Alpha型首次感染患者高(FD = 2.7, p = 0.05)。Delta首次感染的受试者出现较高的LV-N BA.1 (FD = 1.89, p = 0.004)和LV-N BA.2 (FD = 2.06, p = 0.001)滴度。个体对祖传病毒的中和反应高于其他任何后续变异,与首次感染变异无关。结论:与Alpha首次感染相比,先前的Delta型SARS-CoV-2感染对随后的Omicron感染诱导了更高的血清学反应。
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引用次数: 0
Pathogenesis and Transmission of a Reassorted H1 Influenza A Virus Detected in North American Swine 在北美猪中检测到的重组H1型甲型流感病毒的发病机制和传播。
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-19 DOI: 10.1111/irv.70228
Débora B. Goulart, Carine K. Souza, Giovana C. Zanella, Celeste A. Snyder, Janice C. Zanella, Alexey Markin, Bailey Arruda, Tavis K. Anderson, Amy L. Baker

Background

The USDA influenza A virus in swine national surveillance plan identified an increase in the detection frequency of a group of swine 1A.1.1.3 hemagglutinin (HA) clade viruses. This change was associated with reassortment events that resulted in new neuraminidase (NA) gene pairings. We hypothesized that the new N1 genes improved the transmission efficiency of the virus.

Methods

We assessed the pathogenesis and transmission of four H1 1A.1.1.3 swine strains paired with different NA subtypes and lineages, all of which shared similar internal gene constellations.

Results

There was little variation in the titers of viral nasal shedding across the groups, and the different surface protein pairings had no effect on transmission efficiency. All IAV strains, reflecting both pre- and post-reassortment genetic patterns, were transmitted to naïve indirect contact pigs.

Conclusions

These data indicate that the combinations of 1A.1.1.3 HA with NA subtypes had little impact on transmission. These findings suggest that the increased detection of the H1 1A.1.1.3 clade in the United States was unlikely directly due to altered replication, transmission, or antigenic drift, but perhaps due to changes in population immunity resulting from differential vaccine use or prior exposure, variations in production practices, or ecological conditions.

背景:美国农业部猪流感病毒国家监测计划确定了一组猪A.1.1.3血凝素(HA)进化枝病毒的检测频率增加。这种变化与导致新的神经氨酸酶(NA)基因配对的重组事件有关。我们假设新的N1基因提高了病毒的传播效率。方法:对具有相似内部基因群的4种不同NA亚型和谱系的猪H1 1A.1.1.3毒株的发病机制和传播进行了研究。结果:病毒滴度在各组间差异不大,不同表面蛋白配对对传播效率无影响。所有IAV毒株,反映了重组前和重组后的遗传模式,都传播给naïve间接接触猪。结论:这些数据表明a .1.1.3 HA与NA亚型的组合对传播影响不大。这些研究结果表明,在美国,H1 a .1.1.3分支的检测增加不太可能直接归因于复制、传播或抗原漂移的改变,而可能是由于不同疫苗使用或先前暴露、生产实践的变化或生态条件导致的人群免疫力的变化。
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引用次数: 0
Strengthening Respiratory Virus Surveillance in Sub-Saharan Africa: Integrated Epidemiological and Genomic Monitoring in Côte d'Ivoire 加强撒哈拉以南非洲的呼吸道病毒监测:Côte科特迪瓦的综合流行病学和基因组监测。
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-18 DOI: 10.1111/irv.70239
Hervé A. Kadjo, Daouda Coulibaly, Yakoura Karidja Ouattara, Sylla Aboubacar, Diané Maxime, Nguessan Konan, Kouakou Luc-Venance, Kouassi Helene, Mboua Jean Marc, Kouakou Bertin, Adagba Marius, Edgard Adjogoua, Ekra Daniel, Meite Syndou

Background

Following WHO recommendations issued in 2019 and 2022, the National Influenza Center (NIC) of Côte d'Ivoire initiated the integration of Respiratory Syncytial Virus (RSV) and SARS-CoV-2 surveillance into its existing sentinel influenza surveillance to strengthen the monitoring of respiratory viruses.

Methods

The national influenza sentinel surveillance protocol was revised to include specific requirement of RSV and SARS-CoV-2. Nasopharyngeal swabs were collected between January 2022 and December 2023 for all three viruses and were tested by real time RT-PCR. Only PCR-positive samples with Ct value < 28 and adequate sample volume were selected for sequencing. CDC Flu SC2 multiplex rRT-PCR assay and Oxford Nanopore MinION Mk1C were used; influenza sequencing was performed at CDC Atlanta. Phylogenetic analyses were conducted to identify genotypes, lineages, and assess genetic relatedness to global strains.

Results

Between January 2022 and December 2023, 8316 samples were tested; 12.6% (n = 1044) were positive for at least one of the three viruses. RSV (5.63%) detection in severe acute respiratory infection (SARI) cases increased significantly from 3.4% in 2022 to 8.4% in 2023 (p < 0.0001). Similarly, influenza (3.71%) detection in SARI cases rose from 1.3% to 2.6% (p = 0.0057). SARS-CoV-2 (3.22%) detection was significantly associated with age (p = 0.002). All three viruses circulated year-round with distinct seasonal peaks. Genomic analysis showed that A(H3N2) viruses belonged to clade 3C.2a1b.2a.2, A(H1N1) pdm09 to clade 6B.1A.5a.2 and B/Victoria to clade V1A.3a.2, all aligning with global trends. Among SARS-CoV-2 cases, BA.2 and BA.5 sublineages of Omicron predominated in 2022 while XBB and XBB.1.5 sublineages emerged in 2023. Whole genome sequencing revealed RSV A strains as genotype A.D.5.1 and RSV B as genotype B.D.E.1.

Conclusion

Integration of RSV and SARS-CoV-2 into influenza sentinel surveillance has enabled continuous detection and genomic characterization, reinforcing the critical role of integrated sentinel surveillance for timely response to respiratory virus threats.

背景:根据世卫组织2019年和2022年发布的建议,Côte科特迪瓦国家流感中心(NIC)开始将呼吸道合胞病毒(RSV)和SARS-CoV-2监测纳入其现有的流感哨点监测,以加强对呼吸道病毒的监测。方法:修订国家流感哨点监测方案,纳入RSV和SARS-CoV-2的具体要求。在2022年1月至2023年12月期间收集了所有三种病毒的鼻咽拭子,并通过实时RT-PCR进行了检测。结果:2022年1月至2023年12月共检测样品8316份;12.6% (n = 1044)至少对三种病毒中的一种呈阳性。RSV(5.63%)在严重急性呼吸道感染(SARI)病例中的检出率从2022年的3.4%显著增加到2023年的8.4%。(p)结论:将RSV和SARS-CoV-2整合到流感哨点监测中,可以实现连续检测和基因组鉴定,加强了综合哨点监测对及时应对呼吸道病毒威胁的关键作用。
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引用次数: 0
Nomenclature for Tracking of Genetic Variation of Seasonal Influenza Viruses 季节性流感病毒遗传变异追踪的命名法。
IF 4.2 4区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-13 DOI: 10.1111/irv.70230
Richard A. Neher, John Huddleston, Trevor Bedford, Nicola S. Lewis, Ruth Harvey, Monica Galiano, Alexander M. P. Byrne, Sarah James, Derek Smith, Marta Łuksza, Denis Ruchnewitz, Michael Laessig, Seiichiro Fujisaki, Shinji Watanabe, Hideki Hasegawa, Norman Hassell, David E. Wentworth, Rebecca Kondor, Yi Mo Deng, Clyde Dapat, Kanta Subbarao, Ian Barr

Background

Genomic surveillance of human seasonal influenza viruses is an essential component of the Global Influenza Surveillance and Response system (GISRS) and informs the recommendations for the seasonal influenza vaccine composition. Phylogenetic analysis of viral genome sequences is used to identify groups of viruses sharing potential antigenic change, and computational models are used to predict which viral variants are likely to circulate at high levels in upcoming seasons. To facilitate discussion and reporting of genetic diversity, as well as to communicate antigen recommendations, up-to-date and sufficiently granular definitions of genetic clades are important.

Methods

We implemented a nomenclature system for Segments 4 (haemagglutinin) and 6 (neuraminidase) of human Influenza A(H3N2), A(H1N1)pdm09, and Influenza B that dynamically adapts to the diversity of circulating viruses. New subclades were proposed by a clade suggestion algorithm based on criteria including (i) the number of sequences in the group, (ii) the distance from the direct parent clade, and (iii) the weighted number of amino acid substitutions on the branch leading to the common ancestor of the subclade.

Results

Algorithmic clade proposals were reviewed and assigned a systematic hierarchical label consisting of a leading letter, followed by numbers (e.g., G.1.3). Names are kept short by aliasing that is collapsing prefixes into unique letters. Subclade definitions are shared openly to promote adoption and tool development. Nextclade is supporting this new nomenclature, and it is being used routinely by the GISRS network.

Conclusions

With increasing genomic surveillance, the need for up-to-date classification schemes is growing and we hope that the current dynamic proposal will adapt to growing data volumes and aid in simplifying the interpretation of these data.

背景:人类季节性流感病毒的基因组监测是全球流感监测和应对系统(GISRS)的一个重要组成部分,并为季节性流感疫苗组合的建议提供信息。病毒基因组序列的系统发育分析用于识别共享潜在抗原变化的病毒组,并使用计算模型来预测哪些病毒变体可能在即将到来的季节中大量传播。为了促进对遗传多样性的讨论和报告,以及交流抗原建议,重要的是对遗传支系进行最新和足够细化的定义。方法:对甲型流感(H3N2)、甲型H1N1 pdm09和乙型流感病毒的第4段(血凝素)和第6段(神经氨酸酶)实施命名系统,该系统可动态适应流行病毒的多样性。新的亚支系是由一种基于标准的进化枝建议算法提出的,该标准包括(i)组中的序列数,(ii)与直系亲本进化枝的距离,以及(iii)分支上导致亚支系共同祖先的氨基酸取代的加权数。结果:对算法进化提案进行了审查,并分配了一个系统的分层标签,该标签由首字母和数字组成(例如,G.1.3)。名称通过别名保持简短,别名将前缀折叠成唯一的字母。子分支定义是公开共享的,以促进采用和工具开发。Nextclade支持这种新的命名法,并且它正在被GISRS网络常规使用。结论:随着基因组监测的增加,对最新分类方案的需求正在增长,我们希望当前的动态建议将适应不断增长的数据量,并有助于简化这些数据的解释。
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引用次数: 0
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Influenza and Other Respiratory Viruses
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