#Influenza and Other Respiratory Viruses Research #References (by AMEDEO, June 14 '25)

 

Antiviral Res

1. MARTINEZ-GZEGOZEWSKA Y, Rasmussen L, Nebane NM, McKellip S, et al
   High-throughput screening for identification of Influenza A inhibitors using a cell-based immunofluorescence assay.
   Antiviral Res. 2025 Jun 6:106209. doi: 10.1016/j.antiviral.2025.106209.
   PubMed         Abstract available
   
   

   
   Arch Virol

2. LU Y, Ni J, Huang S, Guo Y, et al
   Epidemiological characteristics of human parainfluenza virus infections and phylogenetic analysis of human parainfluenza virus type 3 isolated from children with respiratory tract infections from 2020 to 2022 in Zhejiang, China.
   Arch Virol. 2025;170:157.
   PubMed         Abstract available
   
   
3. JIN H, Cho YR, Jung YT
   Single-particle quantification of SARS-CoV-2 virus-like particles using flow virometry.
   Arch Virol. 2025;170:149.
   PubMed         Abstract available
   
   

   
   Cell

4. STEVENS J, Culberson E, Kinder J, Ramiriqui A, et al
   Microbiota-derived inosine programs protective CD8(+) T cell responses against influenza in newborns.
   Cell. 2025 Jun 3:S0092-8674(25)00563-X. doi: 10.1016/j.cell.2025.
   PubMed         Abstract available
   
   

   
   Drug Saf

5. ROQUE-PEREIRA L, Sisay MM, Ogar CK, Duran CE, et al
   Comparison of Adverse Events in Pregnant Persons Receiving COVID-19 and Influenza Vaccines: A Disproportionality Analysis Using Combined Data from US VAERS and EudraVigilance Spontaneous Report Databases.
   Drug Saf. 2025 Jun 10. doi: 10.1007/s40264-025-01561.
   PubMed         Abstract available
   
   

   
   Epidemiol Infect

6. BARBER CA, Chien LC, Labus B, Crank K, et al
   Application of joinpoint regression to SARS-CoV-2 wastewater-based epidemiology in Las Vegas, Nevada, USA.
   Epidemiol Infect. 2025;153:e68.
   PubMed         Abstract available
   
   

   
   Eur J Epidemiol

7. LI Y, Li H, Adair T
   The impact of the pandemic on non-COVID-19 causes of death in the United States: a multiple cause of death analysis.
   Eur J Epidemiol. 2025;40:463-474.
   PubMed         Abstract available
   
   

   
   J Virol

8. JONES JE, Lakdawala SS
   Host origin is a determinant of coevolution between gene segments of avian H9 influenza viruses.
   J Virol. 2025 Jun 13:e0151824. doi: 10.1128/jvi.01518.
   PubMed         Abstract available
   
   
9. LV H, Teo QW, Lee C-CD, Liang W, et al
   Correction for Lv et al., "Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model".
   J Virol. 2025 Jun 12:e0078325. doi: 10.1128/jvi.00783.
   PubMed        
   
   
10. SULLIVAN OM, Nesbitt DJ, Schaack GA, Feltman EM, et al
    IFIT3 RNA-binding activity promotes influenza A virus infection and translation efficiency.
    J Virol. 2025 Jun 11:e0028625. doi: 10.1128/jvi.00286.
    PubMed         Abstract available
    
    

    
    J Virol Methods

11. COLOTTE M, Luis A, Coudy D, Tuffet S, et al
    Room temperature storage and shipping of encapsulated synthetic RNAs as quality control materials for SARS-CoV-2 molecular diagnostic assays.
    J Virol Methods. 2025;337:115169.
    PubMed         Abstract available
    
    
12. CHENTOUFI HA, Galipeau Y, Arnold C, Dewar-Darch D, et al
    Comparative performance of serum and plasma samples in SARS-CoV-2 serology and neutralization assays.
    J Virol Methods. 2025;337:115186.
    PubMed         Abstract available
    
    

    
    PLoS One

13. DAS B, Heath LS
    Variant evolution graph: Can we infer how SARS-CoV-2 variants are evolving?
    PLoS One. 2025;20:e0323970.
    PubMed         Abstract available
    
    
14. BURHAN E, Azzumar F, Sinuraya FAG, Prasetyo S, et al
    Vaccine effectiveness of inactivated and mRNA COVID-19 vaccine platform during Delta and Omicron wave in Jakarta, Indonesia: A test-negative case-control study.
    PLoS One. 2025;20:e0320779.
    PubMed         Abstract available
    
    
15. LOGANATHAN T, Zaini AZ, Majid HA
    Exploring the barriers and facilities migrants face in accessing COVID-19 vaccines in Malaysia: A qualitative study.
    PLoS One. 2025;20:e0326045.
    PubMed         Abstract available
    
    
16. KUATEWO M, Ebelin W, Doegah PT, Aberese-Ako M, et al
    Fake news, misinformation, vaccine hesitancy and the role of community engagement in COVID-19 vaccine acceptance in Southern Ghana.
    PLoS One. 2025;20:e0316969.
    PubMed         Abstract available
    
    
17. ATAC O, Peterson LE, Waters TM
    The impact of the COVID-19 pandemic on vaccinations in United States primary care practices.
    PLoS One. 2025;20:e0325934.
    PubMed         Abstract available
    
    
18. ANAND A, Shoele K
    Identifying the effectiveness of face mask in a large population with a network-based fluid model.
    PLoS One. 2025;20:e0324229.
    PubMed         Abstract available
    
    
19. ALJOHANI A
    A novel spectral transformation technique based on special functions for improved chest X-ray image classification.
    PLoS One. 2025;20:e0325058.
    PubMed         Abstract available
    
    
20. WEIGL N, Pleimelding C, Gilberg L, Huynh D, et al
    Detectable SARS-CoV-2 specific immune responses in recovered unvaccinated individuals 250 days post wild type infection.
    PLoS One. 2025;20:e0325923.
    PubMed         Abstract available
    
    
21. TANG L, Tang C, Luo H
    How regulatory orders and public fear affect vehicle mobility under COVID-19: A global perspective from urban overall vehicles using multi-source data.
    PLoS One. 2025;20:e0325118.
    PubMed         Abstract available
    
    
22. CONNOLLY SP, Garcia Leon A, Green S, McGee D, et al
    Longitudinal SARS-CoV-2 antibody response in a healthcare worker cohort utilising the Abbott Alinity(R) anti-nucleocapsid assay.
    PLoS One. 2025;20:e0325544.
    PubMed         Abstract available
    
    
23. CAHN P, Barreto L, Figueroa MI, Fink V, et al
    Immune response induced by the recombinant novel coronavirus vaccine (Adenovirus type 5 vector) (Ad5-nCoV) in persons living with HIV (PLWH).
    PLoS One. 2025;20:e0312893.
    PubMed         Abstract available
    
    
24. PERROY B, Velasco PF, Gurchani U, Casati R, et al
    Three forms of temporal disorientation: A thematic analysis of subjective reports about Covid-19 restriction periods.
    PLoS One. 2025;20:e0324476.
    PubMed         Abstract available
    
    
25. GERBECKS J, Yzermans CJ, Duckers MLA, Bosmans M, et al
    Health symptoms and post-COVID-19: Comparing symptomatic groups based on self-reported and primary care data.
    PLoS One. 2025;20:e0323960.
    PubMed         Abstract available
    
    
26. LAM CN, Kumar N, Herzig SE, Unger JB, et al
    Associations between COVID-19 infection, symptom severity, perceived susceptibility, and long-term adherence to protective behaviors: The Los Angeles pandemic surveillance cohort study.
    PLoS One. 2025;20:e0326097.
    PubMed         Abstract available
    
    
27. KHAMMAWAN P, Thongprachum A, Intawong K, Chariyalertsak S, et al
    Severity, mortality, long COVID-19, and quality of life: Insights from a cohort study of hospitalized COVID-19 patients during the delta variant predominance period in Thailand.
    PLoS One. 2025;20:e0324061.
    PubMed         Abstract available
    
    
28. HASHMI E, Altaf A, Anwar MW, Jamal MH, et al
    BI-SENT: bilingual aspect-based sentiment analysis of COVID-19 Tweets in Urdu language.
    PLoS One. 2025;20:e0317562.
    PubMed         Abstract available
    
    
29. LAIL AJ, Vuyk WC, Machkovech H, Minor NR, et al
    Amplicon sequencing of pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle.
    PLoS One. 2025;20:e0325203.
    PubMed         Abstract available
    
    

    
    Proc Natl Acad Sci U S A

30. HUOT M, Wang D, Liu J, Shakhnovich EI, et al
    Predicting high-fitness viral protein variants with Bayesian active learning and biophysics.
    Proc Natl Acad Sci U S A. 2025;122:e2503742122.
    PubMed         Abstract available
    
    
31. GOZZI N, Perra N, Vespignani A
    Comparative evaluation of behavioral epidemic models using COVID-19 data.
    Proc Natl Acad Sci U S A. 2025;122:e2421993122.
    PubMed         Abstract available
    
    
32. CAOBI A, Su CM, Beusch CM, Kenney D, et al
    SARS-CoV-2 nsp15 enhances viral virulence by subverting host antiviral defenses.
    Proc Natl Acad Sci U S A. 2025;122:e2426528122.
    PubMed         Abstract available
    
    

    
    Virus Res

33. ZHOU X, Feng L
    The Association Between Influenza Infection and Acute Myocardial Infarction: A Comprehensive Systematic Review and Meta-Analysis.
    Virus Res. 2025 Jun 9:199594. doi: 10.1016/j.virusres.2025.199594.
    PubMed         Abstract available

#IAEA DG Grossi’s #Statement to #UNSC on #Situation in #Iran (June 14 '25)

Early this morning, the International Atomic Energy Agency (IAEA) was informed of the military operation launched by Israel which includes attacks on nuclear facilities in the Islamic Republic of Iran.

As I reported this morning to the IAEA Board of Governors, we have been in permanent contact with the Iran Nuclear Regulatory Authority, to ascertain the status of relevant nuclear facilities and to assess any wider impacts on nuclear safety and security.

Iran has confirmed that at present, only the Natanz Fuel Enrichment Plant site has been attacked in today’s strikes. This facility contains the Fuel Enrichment Plant and the Pilot Fuel Enrichment Plant.

At Natanz, the above-ground part of the Pilot Fuel Enrichment Plant, where Iran was producing uranium enriched up to 60% U-235, has been destroyed.

Electricity infrastructure at the facility (electrical sub-station, main electric power supply building, emergency power supply and back-up generators) has been destroyed.

There is no indication of a physical attack on the underground cascade hall containing part of the Pilot Fuel Enrichment Plant and the main Fuel Enrichment Plant. However, the loss of power to the cascade hall may have damaged the centrifuges there.

The level of radioactivity outside the Natanz site has remained unchanged and at normal levels indicating no external radiological impact to the population or the environment from this event.

However, due to the impacts, there is radiological and chemical contamination inside the facilities in Natanz. The type of radiation present inside the facility, primarily alpha particles, is manageable with appropriate radiation protection measures.

At present, the Iranian authorities are informing us of attacks on the other facilities, the Fordow Fuel Enrichment Plant; and Esfahan site, where a fuel plate fabrication plant, a fuel manufacturing plant, a uranium conversion facility and an enriched UO2 powder plant are located. However I have to inform that at this moment we do not have enough information beyond indicating that military activity has been taking place around these facilities as well which initially had not been part of military operation.

All these developments are deeply concerning. I have repeatedly stated that nuclear facilities must never be attacked, regardless of the context or circumstances, as it could harm both people and the environment.  Such attacks have serious implications for nuclear safety, security and safeguards, as well as regional and international peace and security.

In this regard, the IAEA recalls the numerous General Conference resolutions on the topic of military attacks against nuclear facilities, in particular, GC(XXIX)/RES/444 and GC(XXXIV)/RES/533, which provide, inter alia, that “any armed attack on and threat against nuclear facilities devoted to peaceful purposes constitutes a violation of the principles of the United Nations Charter, international law and the Statute of the Agency”. 

Furthermore, the IAEA has consistently underlined that “armed attacks on nuclear facilities could result in radioactive releases with grave consequences within and beyond the boundaries of the State which has been attacked”, as was stated in GC(XXXIV)/RES/533.

As Director General of the International Atomic Energy Agency, and consistent with the objectives of the IAEA under the IAEA Statute, I call on all parties to exercise maximum restraint to avoid further escalation. I reiterate that any military action that jeopardizes the safety and security of nuclear facilities risks grave consequences for the people of Iran, the region, and beyond.

Madame Under Secretary General evoked that yesterday, the Board of Governors of the IAEA adopted an important resolution on Iran’s safeguards obligations. In addition to this, the Board resolution stressed its support for a diplomatic solution to the problems posed by the Iranian nuclear programme.

The IAEA continues to monitor the situation closely.  Our Incident and Emergency Center (IEC) has maintained continuous contact with Iranian authorities from the onset of the attack, regularly confirming the status of the facilities and will continue to do so in the coming days. Additionally, we have established a task force comprising several senior staff members to monitor the situation closely over the next few days, and they will be available 24/7at the disposal of the UNSC.

The IAEA stands ready to provide technical assistance, and remains committed to its nuclear safety, security and safeguards mandate in all circumstances. I stand ready to engage with all relevant parties to help ensure the protection of nuclear facilities and the continued peaceful use of nuclear technology in accordance with the Agency mandate, including, deploying Agency nuclear security and safety experts (in addition to our safeguards inspectors in Iran) wherever necessary to ensure that nuclear installations are fully protected and continue to be used exclusively for peaceful purposes.

As I informed today the IAEA Board of Governors, I have indicated to the respective authorities my readiness to travel at the earliest to assess the situation and ensure safety, security and non-proliferation in Iran.

I have also been in contact with our inspectors in Iran and Israel. The safety of our staff is of paramount importance. All necessary actions are being taken to ensure they are not harmed.

Despite the current military actions and heightened tensions, it is clear that the only sustainable path forward—for Iran, for Israel, the entire region, and the international community—is one grounded in dialogue and diplomacy to ensure peace, stability, and cooperation. 

The International Atomic Energy Agency, as the International technical institution entrusted with overseeing the peaceful use of nuclear energy, remains a unique and vital forum for dialogue, especially now. 

In accordance with its Statute and longstanding mandate, the IAEA provides the framework and natural platform where facts prevail over rhetoric and where engagement can replace escalation. 

I reaffirm the Agency’s readiness to facilitate technical discussions and support efforts that promote transparency, safety, security and the peaceful resolution of nuclear-related issues in Iran.

Source: IAEA, https://www.iaea.org/newscenter/statements/director-general-grossis-statement-to-unsc-on-situation-in-iran

____

Amplicon #sequencing of pasteurized retail #dairy enables genomic #surveillance of #H5N1 avian #influenza virus in #USA #cattle

Abstract

Highly pathogenic avian influenza (HPAI) viruses with H5 hemagglutinin (HA) genes (clade 2.3.4.4b) are causing an ongoing panzootic in wild birds. Circulation of these viruses is associated with spillover infections in multiple species of mammals, including a large, unprecedented outbreak in American dairy cattle. Before widespread on-farm testing, there was an unmet need for genomic surveillance. Infected cattle can shed high amounts of HPAI H5N1 viruses in milk, allowing detection in pasteurized retail dairy samples. Over a 2-month sampling period in one Midwestern city, we obtained dairy products processed in 20 different states. Here we demonstrate that a tiled-amplicon sequencing approach produced over 90% genome coverage at greater than 20x depth from 5 of 13 viral RNA positive samples, with higher viral copies corresponding to better sequencing success. The sequences clustered phylogenetically within the rest of the cattle outbreak sequences reported. A combination of RT-qPCR testing and sequencing from retail dairy products can be a useful component of a One Health framework for responding to the avian influenza outbreak in cattle.

Source: PLoS One, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0325203

____

Role of Nonpharmaceutical #Interventions during 1918–1920 #Influenza #Pandemic, #Alaska, #USA

Abstract

Previous studies investigating the 1918–1920 influenza pandemic have provided a comprehensive overview of the spread of the pandemic and possible explanations for high mortality rates in Alaska, USA. Our understanding of the role of nonpharmaceutical interventions (NPIs) is limited, however. To gain an overview of various agencies’ efforts to protect communities during the pandemic, we conducted a mixed-method assessment of a large pool of digitized historical newspapers and archival materials covering Alaska’s local and territorial responses to the pandemic. The study encompassed 14 local units of Alaska that implemented NPIs during October 1918–January 1919. Analyses indicated that 8 local units avoided the outbreak by implementing NPIs and that the other 6 units controlled the spread of influenza by implementing NPIs after the virus was introduced. In addition, some Indigenous communities escaped the pandemic by implementing mandatory and voluntary restrictions. Information on NPI effects of could guide future influenza pandemic preparedness and response.

Source: US Centers for Disease Control and Prevention, https://wwwnc.cdc.gov/eid/article/31/7/24-1048_article

____

Host #origin is a determinant of #coevolution between gene segments of avian #H9 #influenza viruses

ABSTRACT

Several emerging influenza viruses, including H7N9 and H5N6 viruses, trace their origins to reassortment with H9N2 viruses that contributed internal gene segments. However, the evolutionary constraints governing the reassortment of H9N2 viruses remain unknown. In seasonal human influenza A viruses, gene segments coevolve at both the nucleotide and amino acid levels. Here, we demonstrate that evolutionary relationships between gene segments, including polymerase subunits in human H3N2 viruses, differ from avian H9 viruses. Avian H9 viruses were characterized by little coevolution between gene segments or between polymerase subunits. Strikingly, protein trees built from avian H9 polymerase subunits diverge despite known functional constraints on polymerase evolution. The evolutionary divergence observed between gene segments of avian H9 viruses was consistent across isolates from different continents, suggesting that coevolution between H9 gene segments is not dependent on regionally defined avian lineages. Instead, coevolution between gene segments was only found in H9 viruses that crossed the species barrier into humans. Our study reveals the role of the host in the coevolution of influenza gene segments and suggests that high reassortment potential in avian species may be a consequence of evolutionary flexibility between gene segments.

Source: Journal of Virology, https://journals.asm.org/doi/full/10.1128/jvi.01518-24?af=R

____

#USA, Monitoring for Avian #Influenza A(#H5) Virus In #Wastewater (#CDC, June 13 '25)

 

{Excerpt}

Time Period: June 01, 2025 - June 07, 2025

- H5 Detection: 4 sites (1.1%)

- No Detection: 370 sites (98.9%)

- No samples in last week: 73 sites

(...)

Source: US Centers for Disease Control and Prevention, https://www.cdc.gov/bird-flu/h5-monitoring/index.html

____

#Japan - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification [FINAL]

 Sea Otters in Hokkaido Region.

Source: WOAH, https://wahis.woah.org/#/in-review/6551

____

Re-Emergence of #Usutu Virus and Spreading of #WestNile Virus #Neuroinvasive Infections During the 2024 Transmission Season in #Croatia

Abstract

Neuroinvasive arboviruses such as tick-borne encephalitis virus (TBEV), West Nile virus (WNV), Usutu virus (USUV), and Toscana virus (TOSV) have (re-)emerged with increasing incidence and geographic range. We analyzed the epidemiology of arboviral infections in Croatia during the 2024 transmission season. A total of 154 patients with neuroinvasive diseases (NID), 1596 horses, 69 dead birds, and 7726 mosquitoes were tested. Viral RNA was detected using RT-qPCR. IgM/IgG-specific antibodies were detected using commercial ELISA or IFA, with confirmation of cross-reactive samples by virus neutralization test. RT-qPCR-positive samples were Sanger sequenced. Arboviral etiology was confirmed in 33/21.42% of patients with NID. WNV was most frequently detected (17/11.03%), followed by TBEV (10/6.49%), USUV (5/3.24%), and TOSV (1/0.64%). WNV infections were reported in regions previously known as endemic, while in one continental county, WNV was recorded for the first time. USUV infections re-emerged after a six-year absence. In addition to human cases, acute WNV infections were recorded in 11/395 (2.78%) of horses and two dead crows. WNV IgG seropositivity was detected in 276/1168 (23.63%) and TBEV IgG seropositivity in 68/428 (15.88%) horses. None of the tested mosquito pools were positive for WNV and USUV RNA. Phylogenetic analysis showed the circulation of WNV lineage 2 and Usutu Europe 2 lineage. Climate conditions in 2024 in Croatia were classified as extremely warm, which could, at least in part, impact the quite intense arboviral season. The spreading of flaviviruses in Croatia highlights the need for continuous surveillance in humans, animals, and vectors (“One Health”).

Source: Viruses, https://www.mdpi.com/1999-4915/17/6/846

____

Broad geographical #circulation of a novel #vesiculovirus in #bats in the #Mediterranean region

Abstract

Bats are the natural reservoirs for a variety of emerging and re-emerging viruses. Among them, rabies virus (genus Lyssavirus, family Rhabdoviridae) is one of the first and most emblematic described in these animals. Since its first description, several new bat lyssaviruses have been regularly identified. In addition to lyssaviruses, other bat rhabdoviruses have also been discovered, including members of the genera Vesiculovirus, Ledantevirus and, more recently, Alphanemrhavirus and Tupavirus. However, the family Rhabdoviridae is one of the most abundant and diverse viral families, with 434 officially recognized species, divided into 5 subfamilies and 56 different genera. The number of rhabdoviruses associated with bats is therefore probably higher than that currently available. In this study, we first developed and validated a combined nested RT-qPCR technique (pan-rhabdo RT-nqPCR) dedicated to the broad detection of animal rhabdoviruses. After validation, this technique was used for a large retrospective screening of archival bat samples (n = 1962), including blood (n = 816), brain (n = 723) and oral swab (n = 423). These samples were collected from various bat species over a 12-year period (2007–2019) in 9 different countries in Europe and Africa. A total of 23 samples (1.2%) from bat species Miniopterus schreibersii, Rhinolophus euryale and Rhinolophus ferrumequinum tested positive for rhabdovirus infection, including 17 (2.1%) blood and 6 (1.4%) oral swab samples, all collected from bats originating from the Mediterranean region. Complete virus genome sequences were obtained by next-generation sequencing for most of the positive samples. Molecular and phylogenetic analysis of these sequences demonstrated that these virus isolates, named Mediterranean bat virus (MBV), were closely related and represented a new species, Mediterranean vesiculovirus, within the Vesiculovirus genus. MBV was more specifically related to other bat vesiculoviruses previously described from China and North America, together clustering into a distinct group of bat viruses within this genus. Interestingly, our results suggest that MBV is widespread, at least in the western part of the Mediterranean region, where it circulates in the blood of several bat species. These results expand the host range and viral diversity of bat vesiculoviruses, and pave the way for further studies to determine the transmission route and dissemination dynamics of these viruses in bat colonies, as well as to assess their potential threat to public health.

Author summary

Bats are the natural hosts for a wide variety of viruses, particularly those belonging to the family Rhabdoviridae, which include the lyssaviruses, the etiological agents of rabies. This viral family is one of the most abundant and diverse, with 434 officially recognized species. However, the current diversity of these viruses in bats remains poorly understood. To address this, we developed a new method for detecting rhabdoviruses in bat samples collected over a period of 12 years in several European and African countries. From nearly 2,000 samples, we discovered a new rhabdovirus, which was named Mediterranean bat virus (MBV). MBV has been detected in the blood and oral swabs of specific bat species (Rhinolophus sp. and Miniopterus schreibersii) living on both sides of the Mediterranean region. Based on phylogenetic analysis, we determined that MBV represented a unique group within the genus Vesiculovirus, but still related to other bat vesiculoviruses discovered in China and North America. These results expand the host range and viral diversity of bat rhabdoviruses, and pave the way for further studies to determine the transmission route and dissemination dynamics of these viruses in bat colonies, as well as to assess their potential threat to public health.

Source: PLoS Neglected Tropical Diseases, https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0013172

____

#Management and #outcomes of #children hospitalised with #COVID19 including Incidental and Nosocomial infections in #Australia 2020-2023: a national surveillance study

Highlights

• Acute COVID-19 usually causes mild illness even in young and immunosuppressed children

• Nosocomial SARS-CoV-2 infection is associated with more severe disease

• Concurrent serious bacterial infection is rare in children admitted with acute COVID-19.

ABSTRACT

Background

Management and outcomes of children hospitalised with acute SARS-CoV-2 infection may differ throughout the pandemic or with admission type (clinical COVID-19, incidental COVID-19 or nosocomial infection).

Objectives

Describe the severity, management and outcomes of hospitalised children with acute SARS-CoV-2 infection in Australia across the first 4 years of the pandemic and compare between admission types, SARS-CoV-2 variants, age groups and immune status.

Study design

A multi-centre prospective cohort study of 6,009 children aged 0-16 years between January 2020 to June 2023.

Results

Most children (84.3%) did not receive respiratory support, 33.4% received antibiotics and 8% were admitted to intensive care unit (ICU). Infants <6 months old were more likely to be admitted with clinical COVID than older children (12-16 years). Older children were more likely to receive antibiotics (27.8% vs 43.9%), corticosteroids (11.3% vs 34.1) or ICU admission (5.2% vs 13.5%). Compared to immunocompetent children, the immunosuppressed (7.7%) were more likely to have nosocomial infection (9.5% v 3.9%), receive antibiotics (57% vs 25%) or antivirals (18% vs 4.4%), but less likely to require respiratory support (93.4% vs 83.8%) or ICU admission (3.5% vs 8%). Children with nosocomial SARS-CoV-2 infection had higher rates of invasive ventilation (8%) and ICU admission (21%) compared to those with clinical (2.1% and 7.1% respectively) or incidental COVID-19 (4.8% and 9.1% respectively).

Conclusions

Acute COVID-19 generally caused mild disease in hospitalised children, with management and outcomes differing by age and admission type. Similar outcomes were observed across the pandemic. Nosocomial SARS-CoV-2 infection was associated with more severe disease.

Source: Journal of Clinical Virology, https://www.sciencedirect.com/science/article/abs/pii/S1386653225000666?dgcid=rss_sd_all

____

#Mpox in #Africa: What we know and what is still lacking

Abstract

Emerging as a major global health threat, Mpox previously known as Monkeypox has drawn attention due to a worrying surge in cases. This zoonotic disease, native to Central and West Africa, is marked by fever, rash, and lymphadenopathy and is primarily spread through direct contact with infected animals or people and indirectly through contaminated objects. Recent studies have indicated possible sexual transmission, underscoring how human behavior and environmental changes are increasing its prevalence, even though human-to-human transmission is less efficient than that of smallpox. Mpox is endemic in several African countries, and currently, the infection has spread in non-endemic countries, including Rwanda, Uganda, and Kenya. Democratic Republic of Congo is the epicenter of the current Mpox outbreak. From January 1, 2022, to August 6, 2024, sixteen African countries reported Mpox outbreak. Several factors, including population immunity deficiencies and changes to the environment and ecology, have led to the widespread of Mpox in Africa. Challenges such as the fragile healthcare system, limited vaccine availability and access, weak surveillance, and low public awareness poses difficulty in containing the infection in affected countries. Given the potential of Mpox to disrupt several sectors including health systems, which may ultimately reverse progress in achieving the sustainable development goals by 2030. It is imperative for countries, both within and outside Africa, to extend financial aid and human resources to combat the infection effectively.

Source: PLoS Neglected Tropical Diseases, https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0013148

____

#UK - High pathogenicity avian #influenza #H5N1 viruses (#poultry) (Inf. with) - Immediate notification

A small commercial flock of 69 chickens, 23 ducks and 5 geese. Increased mortality reported in chickens as well as a drop in egg production in the ducks. Samples were taken and tested positive for HPAI H5N1. Location: Kirklees, West Yorkshire, England.

Source: WOAH, https://wahis.woah.org/#/in-review/6552

____

Ten Previously Unassigned #Human #Cosavirus #Genotypes Detected in Feces of #Children with Non-Polio #AFP in #Nigeria in 2020

Abstract

Since its discovery via metagenomics in 2008, human cosavirus (HCoSV) has been detected in the cerebrospinal fluid (CSF) and feces of humans with meningitis, acute flaccid paralysis (AFP), and acute gastroenteritis. To date, 34 HCoSV genotypes have been documented by the Picornaviridae study group. However, the documented genetic diversity of HCoSV in Nigeria is limited. Here we describe the genetic diversity of HCoSV in Nigeria using a metagenomics approach. Archived and anonymized fecal specimens from children (under 15 years old) diagnosed with non-polio AFP from five states in Nigeria were analyzed. Virus-like particles were purified from 55 pools (made from 254 samples) using the NetoVIR protocol. Pools were subjected to nucleic acid extraction and metagenomic sequencing. Reads were trimmed and assembled, and contigs classified as HCoSV were subjected to phylogenetic, pairwise identity, recombination analysis, and, when necessary, immuno-informatics and capsid structure prediction. Fifteen pools yielded 23 genomes of HCoSV. Phylogenetic and pairwise identity analysis showed that all belonged to four species (eleven, three, three, and six members of Cosavirus asiani, Cosavirus bepakis, Cosavirus depakis, and Cosavirus eaustrali, respectively) and seventeen genotypes. Ten genomes belong to seven (HCoSV-A3/A10, A15, A17, A19, A24, D3, and E1) previously assigned genotypes, while the remaining thirteen genomes belonged to ten newly proposed genotypes across the four HCoSV species, based on the near-complete VP1 region (VP1*) of the cosavirus genome. Our analysis suggests the existence of at least seven and eight Cosavirus bepakis and Cosavirus eaustrali genotypes, respectively (including those described here). We report the first near-complete genomes of Cosavirus bepakis and Cosavirus depakis from Nigeria, which contributes to the increasing knowledge of the diversity of HCoSV, raising the number of tentative genotypes from 34 to over 40. Our findings suggest that the genetic diversity of HCoSV might be broader than is currently documented, highlighting the need for enhanced surveillance.

Source: Viruses, https://www.mdpi.com/1999-4915/17/6/844

____

Impact of #serum versus #anticoagulant-containing #plasma on #influenza virus #neuraminidase-based serological assays

Abstract

The influenza virus neuraminidase (NA) is a promising target for next-generation influenza vaccines but standardized protocols for NA-based serological assays are lacking. Previous studies have demonstrated discordant results from haemagglutination inhibition and live virus microneutralization assays when comparing matched serum and plasma samples. It is therefore important to consider is the choice of serum or plasma samples in assays measuring influenza virus NA-specific antibodies. Here, we compared antibody titres against influenza A and B virus NAs in matched serum and different types of plasma using an enzyme-linked lectin assay (ELLA) and an enzyme-linked immunosorbent assay (ELISA). We observed good correlations between titres determined in serum and different types of plasma. However, there was variable and often poor agreement in the nominal titre values obtained from serum and different kinds of plasma in both ELLA and ELISA, with plasma samples often resulting in lower titres compared to serum samples. We also found differences in NA-specific responses to seasonal influenza vaccination assessed in serum versus plasma. Overall, our data demonstrate discrepancies between NA-specific antibody measurements in serum and plasma. We recommend the consistent use of serum as an important part of standardising NA-based serological assays.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.06.07.658460v1

____

#Lanka virus, a #Mus booduga-borne #orthohantavirus #infection-associated febrile illness in #SriLanka

Abstract

Background

In Sri Lanka, a high seroprevalence of antibodies against hantaviruses was reported in communities affected by chronic kidney disease of unknown etiology (CKDu). Recently, two rodent-borne hantaviruses, Lanka virus and Anjozorobe virus, were identified in these areas. However, it is unclear which virus is the source of infection in humans, and its pathogenicity is unknown.

Methodology/principal findings

A total of 181 sera from febrile patients from two CKDu-endemic regions, Girandurukotte and Polonnaruwa, were examined and Lanka virus genome was detected in two IgM-positive febrile patients. Of 76 serum samples from patients with fever of unknown etiology collected during 2016 examined to identify hantavirus genomes, antibodies, and serotypes, 10 were IgG-positive with five of them having IgM also. They were all without clinical features of hemorrhagic fever with renal syndrome, but three patients required treatment in the intensive care unit. A serotyping strategy was established based on the antigenic difference of the glycoprotein Gn of Lanka and Anjozorobe viruses. Using this method, febrile patients were found to be infected with the Lanka virus and none of the patient sera showed Anjozorobe virus infection pattern. Additionally, a total of 373 previously diagnosed seropositive serum samples from CKDu patients and healthy residents were serotyped to categorize 87% of seropositives as Lanka virus infection.

Conclusions/significance

Lanka virus carried by little Indian field mouse (Mus booduga) is transmitted to humans, likely causing febrile illness occasionally while leading to severe disease in some of the febrile patients.

Author summary

Hantaviruses are known to be transmitted by rodents and cause severe diseases such as hemorrhagic fever with renal syndrome (HFRS) in humans. Although there have been few reports of typical HFRS in Sri Lanka, there are many antibody-positive individuals. The antibody positivity rate is particularly high in patients with chronic kidney disease by unknown etiology (CKDu), and the relationship between hantavirus infection and CKDu is being discussed. Meanwhile, rodent surveys have identified Lanka virus in little Indian field mouse (Mus booduga) and Anjozorobe virus in black rat (Rattus rattus) in Sri Lanka. However, it was unclear which virus was infecting the humans and its pathogenicity. This study showed that hantavirus infections in Sri Lanka could be asymptomatic or cause common fever-like symptoms and rarely require treatment in an ICU. It was also shown that the main source of infection is Lanka virus. This study leads us to the starting line of clarifying the Lanka virus-related health risks, such as its association with CKDu.

Source: PLoS Neglected Tropical Diseases, https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0013169

____

Evaluation of #country #preparedness for #Nipah and avian #influenza #zoonotic viral #threats in #Bangladesh

Highlights

• Systematic and routine monitoring antigenic drift and shift of AIV in wild birds and poultry is needed.

• Community-based surveillance is key for improving NiV case detection.

• Integrated surveillance across One Health sectors is required.

• Lab upgrades to BSL-3 are needed for enhanced biosafety and diagnostics.

Abstract

Nipah and avian influenza viruses (NiV and AIV) are priority zoonotic pathogens in Bangladesh and are also important globally because of their pandemic potential. To understand current strengths, areas for improvement, and opportunities to enhance preparedness for NiV and AIV in Bangladesh, as part of the USAID STOP Spillover program, 47 relevant stakeholders were surveyed, and two country leads of the primary surveillance systems were interviewed. Data was collected focusing on four different areas: research projects, surveillance systems, laboratories, and outbreak risk management systems. Despite progress in recent years, our study reveals significant gaps in preparedness, detection, and response capacities across sectors and highlights the importance of prioritizing extended and targeted surveillance, biosafety solutions for laboratories, and early event detection for resilient defenses against these viruses using a One Health framework.

Source: One Health, https://www.sciencedirect.com/science/article/pii/S2352771425001119?via%3Dihub

____

Promising Effects of #Duck #Vaccination against Highly Pathogenic Avian #Influenza, #France 2023–2024

Abstract

Highly pathogenic avian influenza causes substantial poultry losses and zoonotic concerns globally. Duck vaccination against highly pathogenic avian influenza began in France in October 2023. Our assessment predicted that 314–756 outbreaks were averted in 2023–2024, representing a 96%–99% reduction in epizootic size, likely attributable to vaccination.

Source: US Centers for Disease Control and Prevention, https://wwwnc.cdc.gov/eid/article/31/7/24-1445_article

____

Anti #Matrix Protein 1 Monoclonal #Antibody Neutralizes #Influenza A Virus Subtypes

Abstract

Background: 

Research on monoclonal antibodies (mAb) targeting conserved internal proteins of influenza is limited.The matrix protein 1 (M1), the most abundant and conserved internal protein, serves as an endoskeleton bridging cytoplasmic tails of envelope glycoproteins haemagglutinin (HA), neuraminidase (NA) and matrix protein 2 (M2) with viral ribonucleoprotein particles (vRNPs). Clinical studies reveal significant M1 antibody responses post-infection and vaccination, with demonstrated B and T cell recognition. Our study examines 2B-B10-G9, our lab-synthesized mAb targeting conserved linear epitope of M1 at the C-terminal domain (CTD). 

Methods: 

Binding of 2B-B10-G9 to the purified influenza A viruses (IAV) and influenza B viruses (IBV) were assessed using SDS-PAGE and Western blotting with Image J analysis. Purified viruses included IAV (H1N1, Pandemic (H1N1) 2009 (H1N1pdm09), and H3N2 subtypes) and IBV which was first isolated in 1940 (B/Lee/40), and B/Victoria lineage. Cytotoxicity of 2B-B10-G9 on the Madin-Darby canine kidney (MDCK) cells was studied by MTT (3-(4, 5-dimethylthiazol-2)-2, 5-diphenyltetrazolium bromide) cell proliferation assay to establish in vitro and in ovo treatment doses. In ovo studies involved injecting 2B-B10-G9 into the allantoic cavity of specific pathogen free (SPF) 10-day-old embryonated chicken eggs (ECE) immediately post-infection with influenza A/Puerto Rico/8/1934 (H1N1) followed by RT-qPCR analysis of the virulence genes HA, NA, and PB1 expressions in the allantoic fluid (AF) 48 hours post-infection. 

Results: 

mAb 2B-B10-G9 shows significantly stronger binding to the M1 protein of H1N1 subtype of IAV with respect to H3N2 subtype of IAV (p < 0.001), and it has significantly stronger binding to the M1 protein of H1N1 subtype of IAV with respect to H1N1pdm09 subtype, IBV including B/Lee/40, B/Victoria lineage. (p< 0.0001) mAb 2B-B10-G9 at dose of 40 ug/ml which was determined as an optimal dose according to the MTT assay, significantly reduced plaque-forming units (PFU)/ml of IAV H1N1 and H3N2 subtypes in vitro (p< 0.0001). In ovo treatment of IAV H1N1 subtype at the same dose 40 ug/ml, significantly suppressed the virulence genes HA, NA, and PB1 expressions compared to the untreated group (p< 0.0001, p< 0.001, p< 0.0001, respectively) and mouse isotype IgG1 mAb treated groups (p< 0.01). 

Conclusions: 

These findings highlight that anti-M1 mAb 2B-B10-G9, targeting conserved linear epitope at the CTD of M1 protein, might be considered as a possible therapeutic option for IAV H1N1 and H3N2 subtypes related to its significant recognition and binding, viral neutralization and suppression of expression of virulence genes including HA, NA and PB1.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.06.09.658662v1

____

#Oseltamivir #Treatment vs Supportive Care for Seasonal #Influenza Requiring #Hospitalization

Key Points

-- Question:  In adults with influenza requiring admission to hospital, is oseltamivir treatment within the first 2 days of admission, when compared with supportive care without oseltamivir, associated with a decreased risk of death in hospital?

-- Findings: In this cohort study of 11 073 patients hospitalized with influenza, oseltamivir treatment was associated with an adjusted risk reduction of 1.8% for in-hospital mortality when compared with supportive care.

-- Meaning: The findings of this study support current guidelines that recommend oseltamivir treatment for patients admitted to hospital with influenza; clinical trials should be conducted to generate better quality evidence.

Abstract

Importance  

Current guidelines recommend oseltamivir treatment for all patients hospitalized with influenza, but this guidance is based on suboptimal evidence.

Objective  

To evaluate outcomes associated with oseltamivir treatment when compared with supportive care for severe seasonal influenza requiring hospitalization.

Design, Setting, and Participants  

This retrospective cohort study using target trial emulation included adult patients admitted to hospital with influenza from 30 hospitals in Ontario, Canada, from January 2015 to June 2023. Data were analyzed from November 2024 to March 2025.

Exposure  

Oseltamivir treatment on hospital day 0 or 1 vs supportive care without oseltamivir.

Main Outcome and Measures  

The primary outcome was in-hospital mortality. Secondary outcomes included time to being discharged alive and readmission within 30 days. Overlap weighting of propensity scores was used to balance covariates, and a competing risk model was used to compare time to being discharged alive.

Results  

Of 11 073 patients (mean [SD] age, 72.6 [16.8] years; 5793 female [52.3%]), there were 7632 patients (68.9%) and 3441 patients (31.1%) in the oseltamivir and supportive care groups, respectively. In hospital, 268 patients (3.5%) and 168 patients (4.9%) in the oseltamivir and supportive care groups died, respectively, with an adjusted risk difference of −1.8% (95% CI, −2.8% to −0.9%; P < .001). The oseltamivir treatment group was more likely to be discharged alive (adjusted subdistribution hazard ratio, 1.20; 95% CI, 1.15 to 1.25; P < .001). After discharge, 645 patients (8.5%) and 336 patients (9.8%) were readmitted in the oseltamivir and supportive care groups, respectively, with an adjusted risk difference of −1.5% (95% CI, −2.8% to −0.2%; P = .02).

Conclusions and Relevance  

In this cohort study of patients hospitalized with influenza, oseltamivir treatment was associated with a lower in-hospital mortality risk, earlier discharge, and lower readmission rate, supporting evidence for the current guideline recommendation of oseltamivir treatment for severe influenza. Clinical trials are needed to definitively answer this question.

Source: JAMA Network Open, https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2835158

____

Monotherapy with #antibody 1C3 partially protects #Ebola virus-exposed #macaques

ABSTRACT

A cocktail of human monoclonal antibodies 1C3 and 1C11 previously protected macaques from a lethal exposure to either Ebola virus (EBOV) or Sudan virus (SUDV). 1C3 is of particular interest because its paratope strongly binds with unique stoichiometry to the glycoprotein head of several orthoebolaviruses, resulting in neutralization of EBOV and SUDV. Therefore, we evaluated the protective activity of 1C3 as a standalone therapeutic in macaques exposed to either EBOV or SUDV. Two doses of 1C3 monotherapy, administered 4 and 7 days post-exposure, did not protect SUDV-exposed macaques and partially protected EBOV-exposed macaques. Notably, in a macaque that succumbed to EBOV infection, we identified two mutually exclusive escape mutations that emerged immediately after the first dose and resulted in two amino acid changes at the 1C3 binding site. We also detected a subconsensus treatment-emergent mutation likely affecting the 1C3 binding site in all three deceased SUDV-exposed macaques. Our findings highlight combination treatment with 1C11 as critical for protection, particularly against SUDV, and in vivo activity of unpartnered 1C3 as susceptible to rapid EBOV and SUDV escape under therapeutic pressure.

IMPORTANCE

A cocktail of human monoclonal antibodies 1C3 and 1C11 previously protected macaques exposed to a lethal dose of either Ebola virus (EBOV) or Sudan virus (SUDV). Since the unique binding characteristics of 1C3 are of particular interest, we evaluated its protective activity as monotherapy in macaques exposed to either EBOV or SUDV. Two doses of 1C3 alone did not protect SUDV-exposed macaques and only partially protected EBOV-exposed macaques. Importantly, failure to protect was associated with the rapid emergence of previously in vitro-identified escape mutations at the 1C3 binding site, highlighting the importance of its use in combination with 1C11 for protection against fatal disease outcome and avoiding rapid EBOV and SUDV escape. Findings have broader implications for the wise use of combination-based monoclonal antibody therapeutics to improve outcomes and prevent resistance in filovirid diseases.

Source: Journal of Virology, https://journals.asm.org/doi/full/10.1128/jvi.00296-25?af=R

____