Thursday, June 19, 2025

Discovery of a Novel #Parahenipavirus, Parahenipavirus_GH, in #Shrews in South #Korea, 2022

Abstract

Highly pathogenic henipaviruses (Nipah and Hendra viruses) and parahenipaviruses (Langya virus) have demonstrated significant zoonotic potential. We aimed to identify Henipavirus or Parahenipavirus species in rodents and shrews in South Korea to underline the potential zoonotic transmission risk. Kidney and lung tissues from 285 rodents and shrews were screened for Henipavirus and Parahenipavirus using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) targeting the Gamak virus and Daeryong virus (DARV) sequences. Based on the qRT-PCR results, 75 out of the 285 individuals tested positive, with the highest viral loads in the kidneys of Apodemus agrarius, Crocidura lasiura, and Crocidura shantungensis. A kidney sample from C. shantungensis that exhibited the lowest Ct value was further analyzed using PCR, Sanger sequencing, and metagenomic analysis, yielding a near-complete genome of a novel Parahenipavirus, designated Parahenipavirus_GH (PHNV-GH), which is phylogenetically related to DARV and Jingmen virus but exhibits distinct genomic features. Ixodes granulatus ticks were also identified on the host shrew. The identification of PHNV-GH in southern South Korea expands the known geographical distribution range of parahenipaviruses and highlights the ongoing risk of zoonotic transmission. Given the uncertain transmission dynamics and pathogenic potential of parahenipaviruses, comprehensive environmental surveillance and characterization of emerging parahenipaviruses are essential for preventing future outbreaks.

Source: Viruses, https://www.mdpi.com/1999-4915/17/6/867

____

#Inactivation of #Influenza A Viruses (#H1N1, #H5N1) During #Grana-Type Raw #Milk #Cheesemaking: Implications for Foodborne #Transmission Risk

Abstract

Background

The detection of H5N1 highly pathogenic avian influenza virus (HPAIV) in lactating dairy cattle in the United States, with high viral titers in raw milk, has raised concerns about potential zoonotic transmission through the consumption of unpasteurized milk and raw-milk dairy products. While inactivation studies exist for pasteurized milk, data on virus persistence during the manufacture of raw-milk cheeses remain scarce

Aim

To evaluate the survival and inactivation of avian influenza viruses (AIV), including both low pathogenic (LPAIV, H1N1) and highly pathogenic (HPAIV, H5N1) strains, during the production and ripening of Grana-type hard cheeses made from raw bovine milk. 

Methods

Experimental cheesemaking was conducted using raw milk artificially contaminated with A-Duck-Italy-281904-2-06 (H1N1; 10 7,75 EID50 per mL) or A-Duck-Italy-326224-2-22 (H5N1 clade 2.3.4.4b; 10 6,75 EID50 per mL). Cheeses were produced in accordance with Parmigiano Reggiano production standards and ripened for 30 days at 5 or 6 degrees Celsius. Viral presence was assessed in finished cheeses by inoculation on SPF embryonated chicken eggs (ECE), hemagglutination (HA) assay, and monoclonal antibody-based ELISA. 

Results

No infectious virus was detected in any cheese sample produced from contaminated milk following two blind passages in SPF-ECE. Both HA and ELISA tests yielded negative results, indicating complete inactivation of the virus. 

Conclusion

This study demonstrates that the traditional Grana-type cheese production process, including curd cooking, acidification, and ripening, effectively inactivates both LPAIV and HPAIV, even at high contamination levels. These findings support the microbiological safety of hard cheeses made from raw milk with regard to AIV, contributing to risk assessment and food safety policies during avian influenza outbreaks.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.06.18.660327v1

____

Wednesday, June 18, 2025

Mapping #Haemagglutinin #Residues Driving #Antigenic Diversity in #H5Nx Avian #Influenza Viruses

Abstract

Since its emergence in 1996, the H5 avian influenza virus (AIV) A/Goose/Guangdong/1/1996 (Gs/GD) haemagglutinin (HA) has evolved into over 30 genetically and antigenically distinct clades, including the widespread clade 2.3.4.4b. Vaccination is widely used in endemic regions to reduce poultry losses and zoonotic risk. However, the evolving antigenic diversity and global co-circulation of multiple clades challenges protective efficacy of poultry vaccines with poor antigenic matching to field strains, resulting in immune escape and vaccine failure. This study aimed to improve vaccine seed selection by identifying HA epitopes contributing to inter-clade antigenic differences. Recombinant clade-representative viruses were generated using HA genes from circulating H5 AIVs via reverse genetics with A/Puerto Rico/8/1934 (PR8) internal and neuraminidase genes. Antigenic relationships were assessed using haemagglutination inhibition (HI) assays with homologous and heterologous chicken antisera. Antigenic cartography revealed a clear distinction of clade 2.3.4.4 from others and notable intra-clade diversity. Pairwise antigenic and genetic comparisons identified 48 putative antigenic residues. These were individually introduced into a candidate HA by site-directed mutagenesis, and antigenic influence assessed by HI using sera raised against the non-mutated HA. Four residues R82K, A83T, T204I, and F229Y had significant antigenic effects, with three (R82K, T204I, F229Y) being novel. These findings demonstrate that combining serology and in silico residue analysis can identify key antigenic determinants. This work highlights the need for precise antigenic matching in vaccine design and highlights the value of combining molecular and immunological tools to optimise vaccine seed selection against diverse and evolving H5 AIV strains.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.06.18.660338v1

____

qRTPCR #Detection of Inactivated #H5 Avian #Influenza Virus in Raw #Milk Samples by Miniaturized Instruments Designed for On-Site Testing

Abstract

Highly pathogenic avian influenza virus (HPAIV) of H5 and H7 subtypes has emerged as one of the most important zoonotic pathogens in the 21st century with significant economic consequences. The recent outbreak of H5N1 avian influenza (AI) in dairy cattle highlighted the importance of early detection in managing and mitigating HPAIV outbreaks. A successful high-speed diagnostic response requires rapid site and specimen access, minimal time for test protocols, and prompt communication of the diagnostic results to government officials. A new diagnostic paradigm that consists of miniaturized extractor and qPCR instruments (EZextractor and EZcycler MiniQ), designed for mobile, on-site testing has been compared with a platform of benchtop instruments (QIAGEN RNeasy and QuantStudio 5) for detecting inactivated H5 avian influenza virus (AIV) spiked in raw milk samples. Two sets of experiments were performed: 1) 15 raw milk samples, obtained from 15 different farms, diluted with phosphate-buffered saline and spiked with the virus to reach approximately 10 copies/mcL virus concentration, and 2) raw milk samples from two farms, each spiked with the inactivated AIV H5 followed by 5 series of dilution to reach AIV concentrations of 1000, 100, 10, 1 and 0.1 copies/mcL. Results show that despite the inhibitors in raw milk, AIV in all samples can be detected by both platforms. The MT platform showed higher sensitivity than the benchtop platform: the Ct values from the MT were ~2 units lower than the benchtop Ct values. Our findings demonstrate the robustness of the MT platform for diagnosing AIV H5 in raw milk samples and support its use as an on-site diagnostic for rapid surveillance and response.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.06.02.657307v2

____

Low #Prevalence of #MERS #Coronavirus #Infection in #Camel-Exposed #Patients Presenting with Respiratory Symptoms in Northern #Kenya

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus that causes acute respiratory disease after transmission via close contact with camels. In contrast to the incidence of MERS-CoV human infections in the Middle East, MERS-CoV infections in the Horn of Africa have been rarely reported despite the high number of camels and common camel–human interactions in the area. Whether passive cross-sectional sampling misses active human cases is a significant gap in our understanding of MERS-CoV epidemiology and its impact in the Horn of Africa. To address this gap, we conducted a prospective cross-sectional study at Laisamis Catholic Hospital in northern Kenya’s camel pastoralist community. A total of 942 patients with acute respiratory symptoms were enrolled over 18 months (August 2022–February 2024); 54% of these individuals reported frequent contact with camels and consumption of camel products. Testing via reverse transcriptase – polymerase chain reaction (RT-PCR) revealed that all patients (N = 942) had negative results for MERS-CoV RNA on either nasopharyngeal or oropharyngeal swabs at the time of presentation. Because polymerase chain reaction testing may only detect active cases with higher levels of viral shedding, serology was also performed on a randomly selected subset of 297 individuals from the total sample pool to detect IgG antibodies. Only eight individuals (2.7%) exhibited positive results by serology; accounting for the test specificity of 99.8%, the 95% CI for true MERS-CoV seropositivity was 0.72–4.27%. Despite frequent camel interactions, MERS-CoV seroprevalence was low, suggesting limited zoonotic transmission in this setting and highlighting the need for more comprehensive diagnostics to identify prevalent causes of acute respiratory illness in pastoralist communities.

Source: American Journal of Tropical Medicine and Hygiene, https://www.ajtmh.org/view/journals/tpmd/aop/article-10.4269-ajtmh.25-0098/article-10.4269-ajtmh.25-0098.xml

____

Tuesday, June 17, 2025

In vitro and in vivo characterization of a #bat #merbecovirus with #ACE2- and #DPP4-independent cell entry

ABSTRACT

Betacoronaviruses, which have caused three human outbreaks within the last two decades, are thought to originate from bats, raising the concern that bat coronaviruses could cause a novel human outbreak in the future. To determine whether the bat merbecovirus EjCoV-3 strain, previously detected in Eptesicus japonensis in Japan, has the potential to infect humans, we analyzed its cellular entry mechanism. Cellular entry of EjCoV-3 via the spike protein requires protease treatment and is mediated by an unknown receptor, other than DPP4 or ACE2. We generated cultivable recombinant EjCoV-3 using bacterial artificial chromosome-based reverse genetics and found that it efficiently replicated in human respiratory and intestinal cell cultures as well as nasal ciliated epithelium in hamsters. These findings suggest that bat merbecovirus with ACE2- and DPP4-independent cell entry has the potential to cause human infections, highlighting the importance of extensive bat surveillance for pandemic preparedness.


IMPORTANCE

Betacoronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2, have caused three significant outbreaks in the past two decades and are believed to have originated from bats. To investigate the potential for future outbreaks, we generated a Japanese bat-derived MERS-related coronavirus, designated EjCoV-3, using reverse genetics. Our results showed that EjCoV-3 does not utilize ACE2 and DPP4, cell entry receptors for SARS-CoV and MERS-CoV, as a means of infection. However, we found that EjCoV-3 is the first bat merbecovirus capable of efficiently replicating in human respiratory cells and the respiratory tract of hamsters. These findings provide new insight into the potential for MERS-related coronaviruses that do not use ACE2 and DPP4 to infect the human respiratory tract, highlighting the importance of preparedness for outbreaks caused by these viruses.

Source: Journal of Virology, https://journals.asm.org/doi/full/10.1128/jvi.00727-25?af=R

____

Incidence of #healthcare-associated #infections in long-term #care #facilities in nine #European countries: a 12-month, prospective, longitudinal cohort study

Summary

Background

The number of older people in need of long-term care is increasing, and health-care-associated infections (HAIs) are a major cause of morbidity and mortality for residents of long-term care facilities (LTCFs). This study, organised by the European Centre for Disease Prevention and Control (ECDC), provided data on the incidence of HAIs and related adverse outcomes in LTCFs in European countries, supplementing the available estimates from repeated point prevalence surveys conducted by the ECDC.

Methods

In this longitudinal, prospective cohort study, we analysed all HAIs collected in a convenience sample of residents from 65 LTCFs (including general nursing homes, residential homes, and mixed facilities) in nine EU or European Economic Area (EEA) countries (Belgium, Finland, France, Italy, Lithuania, Luxembourg, the Netherlands, Poland, and Spain) over 12 months. Eligible residents were those expected to stay in the LTCF for at least the entire study period. Data were collected with three questionnaires: an institutional questionnaire, a residents' questionnaire, and an HAI questionnaire. HAIs were defined according to standard ECDC criteria. The primary outcome was HAI incidence. Incidence measures, estimated using generalised estimating equation models to account for sample heterogeneity, were percentages of each type of HAI, numbers of HAIs per 100 LTCF residents (ratio), and numbers of HAIs per 1000 resident-days (incidence rate).

Findings

HAIs were analysed in 3029 residents of LTCFs between Jan 1–May 4, 2022, and Jan 1–May 12, 2023. The mean age of study participants was 80·9 years (SD 14·6), including 960 (31·7%) men and 2069 (68·3%) women. 3763 HAIs were recorded, with at least one HAI identified in 1717 (57%) of 3029 residents. There were 124·2 HAIs (95% CI 118·6–129·9) per 100 residents and 1·8 HAIs (0·9–3·3) per 1000 resident-days. 160 (4·3% [95% CI 3·9–5·4]) HAIs led to hospitalisation, and 154 (4·5% [2·5–4·8]) were associated with death. Respiratory tract infections (RTIs) were the most frequent type of infection (n=1080, 28·9% [95% CI 27·3–30·5]), including pneumonia (n=279, 7·3% [6·4–8·3]) and other lower RTIs (n=394, 10·7% [9·6–11·8]), followed by urinary tract infections (UTIs; n=743, 18·7% [17·2–20·3]). RTIs showed the highest incidence of mortality (n=85, 2·3% [95% CI 1·8–2·8] of all HAIs). Severe cases of COVID-19 (n=72, 1·9% [95% CI 1·5–2·4] of all HAIs) were less frequent than mild or moderate cases (n=615, 16·0% [14·9–17·1] of all HAIs).

Interpretation

This study shows the high incidence of HAIs among LTCF residents in EU or EEA countries, with more than one in two residents experiencing at least one HAI, and with RTIs and UTIs accounting for almost half of all observed HAIs.

Source: Lancet Infectious Diseases, https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(25)00217-8/fulltext?rss=yes#fig1

____

#Cambodia confirmed one additional #human #infection with #influenza A #H5N1 (Min. Health, June 17 '25)



{Automatic translation}

The Ministry of Health of Cambodia notified a case of avian influenza A(H5N1): the patient is a 65-years-old woman from Kraing Ampil, Takeo Province. The patient is now hospitalized in Intensive Care Unit. She developed fever, cough, shortness of breath, did not report contact with diseased birds. A Response Team is investigating actively, adopting prevention and control measures.

The case has been confirmed by Pasteur Institute of Cambodia. (...) Despite investigations so far excluded direct contact with diseases or dead poultry, the patient's relatives own birds and more analysis are being conducted.

The Rapid Response Team continues to investigate the outbreak with the cooperation of local health authorities to find possible source of infection among poultry and humans.

Close contacts of the patient are being searched and will be offered the antiviral oseltamivir for post-exposure prophylaxis.

(...)

Source: Cambodia Ministry of Health, https://moh.gov.kh/kh/notice/detail/161

____

Monday, June 16, 2025

#Assessment of public #health #risk of novel #reassortant #H3N3 avian #influenza viruses that emerged in #chickens

ABSTRACT

Influenza A (H3N2) viruses are historically responsible for the 1968 Hong Kong flu pandemic. Since then, H3N2 has continued to circulate as a seasonal influenza virus in humans. Public health concerns were raised in 2022 when human infections with novel reassortant H3N8 influenza viruses originating from chickens were first reported in China. Here, we conducted a systematic surveillance of H3 avian influenza viruses (AIVs) circulating in poultry and assessed the public health risk of emergent H3 reassortants. We found that H3 AIVs were prevalent in both ducks and chickens. Notably, in December 2022, a novel chicken-derived H3N3 subtype virus was identified, which gradually replaced the previously predominant H3N8 virus and became prevalent in chickens. Genetic analysis demonstrated that the novel H3N3 virus is a triple-reassortment strain with the H3 gene segment from chicken H3N8 virus, the N3 gene segment from the H10N3 virus, and internal gene segments derived from H9N2 viruses. Compared with chicken H3N8 and duck H3N3 viruses, the novel chicken H3N3 viruses produced higher yields and induced greater pathogenicity in human respiratory epithelial cells and mammalian models (mouse and ferret). Importantly, the chicken H3N3 viruses could be transmitted efficiently between ferrets through direct contact. The polymerase activity of the chicken H3N3 viruses in mammalian cells was markedly increased by the PA gene originating from the H9N2 virus. Our findings indicate that the circulation of novel chicken H3N3 viruses poses a threat to both the poultry industry and human public health.

Source: mBio, https://journals.asm.org/doi/10.1128/mbio.00677-25

____

Virological characterization of a new isolated strain of #Andes virus involved in recent person-to-person #transmission #outbreak reported in #Argentina

Abstract

On November 2, 2018, a person-to-person transmission outbreak of Andes virus (Orthohantavirus andesense) began in the small town of Epuyén, Argentina. The strain demonstrated a high capacity for sustained transmission among the human population requiring the implementation of quarantine measures, rigorous contact tracing, isolation of close contacts, and active clinical monitoring to prevent further spread. In this study, we report the isolation of this strain, which we name the ARG-Epuyén strain, directly from a clinical sample after just three passages in cell culture. Complete sequencing revealed only a single amino acid change post-isolation, suggesting that this strain can be considered a non-adapted wild-type Andes virus, marking a critical step toward the development of medical countermeasures against this emerging pathogen. The pathogenicity and transmissibility potential of ARG-Epuyén were evaluated in hamsters, the only animal model for Hantavirus Pulmonary Syndrome. Additionally, this strain was compared with Andes/ARG, an ANDV strain previously isolated from the same geographical area in the Argentinian Patagonia, from a rodent specimen. Our findings revealed high infectiousness and efficient hamster-to-hamster transmission through direct contact experiments, although ARG-Epuyén appeared to be less pathogenic than Andes/ARG.

Source: PLoS Neglected Tropical Diseases, https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0013205

____

#Persistence and Active #Replication Status of #Oropouche Virus in Different Body Sites: Longitudinal Analysis of a #Traveler Infected with a Strain Spreading in Latin America

Abstract

An unprecedented outbreak of Oropouche virus (OROV) is occurring in the Americas, characterized by thousands of confirmed cases and a wide geographical spread, including areas outside the Amazon Basin. Little is known about this neglected arbovirus regarding its pathophysiological aspects and potentially different transmission modes. This study describes the clinical course of a man who returned from a trip to Cuba and presented to our hospital 4 days after the onset of febrile symptoms. The patient was diagnosed with Oropouche fever and was followed for 177 days after the onset of symptoms. We performed a longitudinal investigation of the samples collected from several body sites (whole blood, serum, urine, and semen) with the aim of providing further insights into OROV infection dynamics, using the detection of antigenomic RNA as a marker of active viral replication. Clinical samples that were longitudinally collected over the course of OROV infection showed consistently higher amounts of antigenomic RNA compared to genomic RNA, even after viral clearance from serum. Moreover, our case study showed the persistence of OROV RNA in serum of less than 15 days from the onset of symptoms, as compared to up to one month in urine, three months in semen, and four months in whole blood. Our study suggests that Oropouche virus may persist in an actively replicating state in different body sites for long periods of time, with important implications for transmission dynamics. Furthermore, our results provide a diagnostic indication, suggesting that serum is inferior to both urine and whole blood as preferred diagnostic samples. Further studies are needed to determine the pathogenetic implications of these findings, as they have been derived from a single case and must be confirmed using a larger number of cases.

Source: Viruses, https://www.mdpi.com/1999-4915/17/6/852

____

The #Seroprevalence of #Influenza A Virus #Infections in Polish #Cats During a Feline #H5N1 Influenza #Outbreak in 2023

Abstract

Recently, cats have emerged as potential incidental hosts for avian and human influenza A viruses (IAVs), including the highly pathogenic avian influenza (HPAI) H5N1 virus. Following an unprecedented outbreak of H5N1 HPAI in cats in Poland in June 2023, we conducted a cross-sectional epidemiological study to assess the seroprevalence of IAV, especially H5Nx, infections in domestic cats. Eight hundred thirty-five serum samples collected in June 2023 were tested using a competitive ELISA for antibodies to IAV nucleoprotein. Positive or doubtful samples were further screened for H5-specific antibodies. The overall seropositivity for IAV was 8.5% (CI 95%: 6.8%, 10.6%; 71/835 cats), and 23/68 IAV-seropositive cats (33.8%) were also seropositive for H5 antigen. Multivariable analysis identified young age (≤8 years) and male sex as significant risk factors for H5 seropositivity, while non-H5-IAV seropositivity was more common in cats aged ≥12 years. These findings suggest different exposure pathways and host risk profiles for H5 and non-H5 IAVs and underscore the importance of enhanced surveillance in cats, particularly in regions affected by HPAI outbreaks. Given the susceptibility of cats to both avian and human IAVs, including subclinical infections, there is a theoretical risk for viral reassortment. Preventive measures, including vaccinating humans and restricting outdoor access for cats, should be considered in endemic areas.

Source: Viruses, https://www.mdpi.com/1999-4915/17/6/855

____

Sunday, June 15, 2025

The Annunciation, Dante Gabriel Rossetti (1849 - 1850)

 


Public Domain.

Source: WikiArt, https://www.wikiart.org/en/dante-gabriel-rossetti/the-annunciation

____

#SARS-CoV-2 #antibody #immunity across three #continents: the West #Africa, West #Indies, West #London Consortium

Abstract

Background

The experience of the COVID-19 pandemic has differed across continents. We hypothesized that regional differences in SARS-CoV-2 immunity might explain this observation. We therefore established the WWW Consortium in Ghana, W Africa; Jamaica, W Indies; and W London. Here, we describe the extent to which antibody immunity differs between these geographic locations. 

Methods

The WWW Consortium harmonises across the HERITAGE (Accra, Ghana), WINDFall (Kingston, Jamaica) and Legacy (London, UK) studies, establishing sharing frameworks for samples, metadata, and data; related permissions and oversight; and associated physical and cloud infrastructure. With centralised testing, we performed serological assessments across all three locations at two snapshots in 2024 (April 1st - August 18th; August 19th - December 31st) using high-throughput live virus neutralization and anti-nucleocapsid IgG, including n=763 individuals. 

Findings

We found that across all sites most participants had detectable neutralising antibody titres against JN.1 and XEC - the predominant variants in 2024. There were site-related differences in immunity: vaccine-included SARS-CoV-2 strains were better neutralised by participants from the Legacy study - Ancestral, BA.5, XBB.1.5 initially, and JN.1 after a homologous booster in autumn 2024. For HERITAGE, neutralisation of both alpha- (HCoV-229E) and beta-coronaviruses (HCoV-OC43) was higher than WINDFall suggesting a cross-coronavirus serological response in West Africa. Finally, antigenic cartography identified two distinct antibody landscapes, with JN.1 and XEC antigenically distant in Legacy, but not in HERITAGE and WINDFall. 

Interpretation

There is international heterogeneity in SARS-CoV-2 antibody immunity. Global recommendations for vaccine strain selection should incorporate data from diverse populations to ensure accurate, equitable recommendations. 

Funding: The Wellcome Trust.

Source: MedRxIV, https://www.medrxiv.org/content/10.1101/2025.06.13.25329588v1

____

Campus-based #genomic #surveillance uncovers early emergence of a future dominant A(#H3N2) #influenza clade

Abstract

We conducted genomic surveillance of seasonal influenza during the 2022-2023 northern hemisphere flu season on a large university setting in Southwest Arizona USA to understand the diversity, evolution, and spread within a local environment and how it relates to national data. Through high-throughput sequencing and bioinformatics, we identified 100 positive samples (19%) from 516 clinical swabs collected at the student health clinic. We observed a dominance of subtype A(H3N2) which was consistent nationally for the 2022-2023 season. However, we found stark differences when examining subtype-specific H3 clades, which included an early dominance of clade 2a.3a.1 variants contrasting from country-level data in which 2b variants were most abundant. These variants might have contributed to the early seasonal peak on campus which lagged national trends by one month. We used phylodynamics to understand the timing, source, and impact of clade-specific introductions on campus and observed introductions of 2b variants from North America, Europe, and Asia in early 2022 which possibly contributed to its later-season dominance on campus towards the end of 2022. We also observed the impact of 2b variants in our Bayesian epidemiological model, as its its emergence and rapid rise coincided with the peak of infection on campus. We found several highly prevalent H3 mutations in known epitope sites that have been observed in multiple 3c.2a clades. In particular, we note the presence of N96S (N=57, 63%) which is a defining mutation of 2a.3 and 2a.3a.1 variants and has been shown to create a new potential N-glycosylation site in the globular head. We estimated vaccine effectiveness via an H3 epitope model with a range of 0.13-0.48 which overlaps with estimates for that year. Taken together, the abundance of antigenic drift mutations, in addition to our identification of numerous sequons found within HA1 (globular head) with high glycosylation potential likely contributed to moderate vaccine effectiveness on campus for that season. As 2a.3a.1 variants became nearly the exclusive H3 clade nationally in 2023-2024 as well as 2024-2025, our identification of their dominance on campus highlights the importance of monitoring local settings as potential early examples for national and influenza trajectories. By using high-throughput sequencing and multiple bioinformatics methods, we show the importance of genomic epidemiology in semi-closed, highly-dense university settings and its potential for early insight of seasonal influenza diversity at a national scale.

Source: MedRxIV, https://www.medrxiv.org/content/10.1101/2025.06.13.25329559v1

____

Saturday, June 14, 2025

History of Mass Transportation: The FS E554 Three-Phase Electric Locomotive

 


Di EmmeBi Photos - https://www.flickr.com/photos/mauboi/6258052858/, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=108173035

Source: Wikipedia, https://it.wikipedia.org/wiki/Locomotiva_FS_E.554

____

#Coronavirus Disease Research #References (by AMEDEO, June 14 '25)

 


    Antiviral Res

  1. CHANG CW, Oswal N, Murugan M, Goldgirsh K, et al
    A novel cellular tool for screening human pan-coronavirus antivirals.
    Antiviral Res. 2025 Jun 10:106212. doi: 10.1016/j.antiviral.2025.106212.
    PubMed         Abstract available


    Clin Infect Dis

  2. LEE R, Kim N, Kim WB, Im KI, et al
    Effectiveness and safety of Autologous Virus-Specific T Cell Therapy for Persistent COVID-19 in People with Immunocompromise: A Clinical Trial Study.
    Clin Infect Dis. 2025 Jun 10:ciaf302. doi: 10.1093.
    PubMed         Abstract available

  3. SUDNIK P, Walsh EE, Branche AR, Islam M, et al
    Comprehensive Analysis of Cardiovascular Events and Risk Factors in Patients Hospitalized with RSV.
    Clin Infect Dis. 2025 Jun 12:ciaf310. doi: 10.1093.
    PubMed         Abstract available


    Int J Infect Dis

  4. WEE LE, Ho RWL, Lim JT, Chiew CJ, et al
    Long-term multi-systemic sequelae post-hospitalization for Omicron COVID-19 versus influenza: a retrospective cohort study.
    Int J Infect Dis. 2025 Jun 9:107946. doi: 10.1016/j.ijid.2025.107946.
    PubMed         Abstract available


    J Infect

  5. BUTLER CC, Hobbs FDR, Little P, Richards D, et al
    Ivermectin and COVID-19.
    J Infect. 2025 Jun 8:106530. doi: 10.1016/j.jinf.2025.106530.
    PubMed        


    J Med Virol

  6. PEREZ-COZAR F, Cal-Sabater P, Rybakowska P, Arribas-Rodriguez E, et al
    High-Dimensional Immunophenotyping of Post-COVID-19 and Post-Influenza Patients Reveals Persistent and Specific Immune Signatures After Acute Respiratory Infection.
    J Med Virol. 2025;97:e70435.
    PubMed         Abstract available

  7. FERNANDEZ-DE-LAS-PENAS C, Arendt-Nielsen L, Gil-Crujera A, Gomez-Sanchez SM, et al
    ACE1 rs1799752 Polymorphism Is not Associated With the Presence of Post-COVID-19 Condition.
    J Med Virol. 2025;97:e70438.
    PubMed        


    J Virol

  8. COTTIGNIES-CALAMARTE A, Marteau F, He F, Belouzard S, et al
    Direct pharmacological AMPK activation inhibits mucosal SARS-CoV-2 infection by reducing lipid metabolism, restoring autophagy flux and the type I IFN response.
    J Virol. 2025 Jun 12:e0039425. doi: 10.1128/jvi.00394.
    PubMed         Abstract available

  9. LIU M, Aryal B, Niu X, Wang Q, et al
    Engineering a recombination-resistant live attenuated vaccine candidate with suppressed interferon antagonists for PEDV.
    J Virol. 2025 Jun 12:e0045125. doi: 10.1128/jvi.00451.
    PubMed         Abstract available

  10. MORGAN AL, Vu MN, Zhou Y, Lokugamage KG, et al
    The furin cleavage site is required for pathogenesis, but not transmission, of SARS-CoV-2.
    J Virol. 2025 Jun 10:e0046725. doi: 10.1128/jvi.00467.
    PubMed         Abstract available

  11. FOSTER CSP, Walker GJ, Jean T, Wong M, et al
    Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution.
    J Virol. 2025 Jun 9:e0036325. doi: 10.1128/jvi.00363.
    PubMed         Abstract available

  12. LOKUGAMAGE KG, Zhou Y, Alvarado RE, Plante JA, et al
    Convergent evolution in nucleocapsid facilitated SARS-CoV-2 adaptation for human infection.
    J Virol. 2025 Jun 12:e0209124. doi: 10.1128/jvi.02091.
    PubMed         Abstract available

  13. LI C, Shi Y, Xie C, Duan K, et al
    GSDMD and GSDME exhibit distinct roles in enteric coronavirus PDCoV-induced pyroptosis and inflammatory responses.
    J Virol. 2025 Jun 12:e0187624. doi: 10.1128/jvi.01876.
    PubMed         Abstract available

  14. HARRIS C, Kapingidza AB, San JE, Christopher J, et al
    Design of SARS-CoV-2 RBD immunogens to focus immune responses toward conserved coronavirus epitopes.
    J Virol. 2025 Jun 13:e0046525. doi: 10.1128/jvi.00465.
    PubMed         Abstract available


    JAMA

  15. GOSTIN LO, Reiss D, Offit PA
    Changed Recommendations for COVID-19 Vaccines for Children and Pregnant Women: A Failure of Process, Policy, and Science.
    JAMA. 2025 Jun 13. doi: 10.1001/jama.2025.10658.
    PubMed        

  16. ZETTLER PJ, Cha S, Despres S, Lurie P, et al
    FDA Review of Novavax's COVID-19 Vaccine-Regulatory Integrity and Deviations From Standard Practice.
    JAMA. 2025 Jun 9. doi: 10.1001/jama.2025.9898.
    PubMed        


    Lancet Infect Dis

  17. URIU K, Okumura K, Uwamino Y, Chen L, et al
    Virological characteristics of the SARS-CoV-2 NB.1.8.1 variant.
    Lancet Infect Dis. 2025 Jun 6:S1473-3099(25)00356.
    PubMed        

  18. GUO C, Yu Y, Liu J, Jian F, et al
    Antigenic and virological characteristics of SARS-CoV-2 variants BA.3.2, XFG, and NB.1.8.1.
    Lancet Infect Dis. 2025 Jun 5:S1473-3099(25)00308.
    PubMed        


    N Engl J Med

  19. MCINTYRE L, Fergusson D, McArdle T, English S, et al
    A Crossover Trial of Hospital-Wide Lactated Ringer's Solution versus Normal Saline.
    N Engl J Med. 2025 Jun 12. doi: 10.1056/NEJMoa2416761.
    PubMed         Abstract available


    Zhonghua Jie He He Hu Xi Za Zhi

  20. CHEN T, Xu ZJ
    [Recomment of the correctly understand and standardize the use of terms and concepts related to interstitial lung disease].
    Zhonghua Jie He He Hu Xi Za Zhi. 2025;48:589-591.
    PubMed         Abstract available

#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

____

My New Space

Most Popular Posts