Cyril Barbezange

Zoonotic infections caused by influenza A viruses (IAVs) of animal origin are a major public health concern, as they may represent the initial step toward the emergence of a pandemic strain. The host range of IAVs is shaped by species‐specific virus‐host interactions, and several host barriers have been identified that restrict the adaptation of avian viruses to humans. We used a comparative interaction screen by mammalian cell‐based Nanoluciferase two‐hybrid (mN2H) assay to investigate whether differences in the interaction networks between viral proteins from human, avian, and zoonotic IAVs and a curated panel of human innate immune factors could serve as indicators of the zoonotic potential of avian IAVs. The results revealed both conserved and strain‐specific interactions, while underscoring limitations in comparing interactions across independent screens. Complementary functional analyses by siRNA knockdowns identified cellular factors and pathways potentially involved in host restriction, as well as pro‐viral factors that could represent potential antiviral targets. The comparative interactomic mN2H approach holds promise for evaluating avian IAV zoonotic potential, but our findings highlighted the need for further studies using broader cellular libraries to fully validate its predictive value.

Previous research has demonstrated that influenza A virus (IAV) infection activates activating protein-1 (AP-1) transcription factors as part of the antiviral response. In this study, we identified cFos as the most upregulated AP-1 transcription factor during IAV infection in A549 human lung cells. Surprisingly, the knockdown of cFos resulted in impaired IAV replication. Fluorescence microscopy and functional analyses indicated that cFos is implicated in IAV infection through its nuclear function, rather than its cytoplasmic role as an activator of lipid synthesis. The investigation into the role of cFos in IAV infection revealed increased apoptosis and elevated interferon- β mRNA levels in cFos–knockdown A549 cells during IAV infection. This suggests that cFos may enhance cell survival and reduce interferon- β expression during infection, thereby facilitating IAV proliferation. Furthermore, the levels of viral NA mRNA and the expression of late viral proteins NA and M2 decreased upon cFos–knockdown. Overall, this study identifies cFos as a proviral factor for IAV, through the modulation of innate immunity and apoptosis during infection, and potentially by supporting the viral transcription.

Previous research has demonstrated that Influenza A virus (IAV) infection activates AP-1 transcription factors as part of the antiviral response. In this study, we identified cFos as the most upregulated AP-1 transcription factor during IAV infection in A549 human lung cells. Surprisingly, the knockdown of cFos resulted in impaired IAV replication. Fluorescence microscopy and functional analyses indicated that cFos is implicated in IAV infection through its nuclear function, rather than its cytoplasmic role as an activator of lipid synthesis. The investigation into the role of cFos in IAV infection revealed increased apoptosis and elevated interferon-β mRNA levels in cFos-knockdown A549 cells during IAV infection. This suggests that cFos may enhance cell survival and reduce interferon-β expression during infection, thereby facilitating IAV proliferation. Furthermore, the levels of viral NA mRNA and the expression of late viral proteins NA and M2 decreased upon cFos knockdown. Overall, this study identifies cFos as a proviral factor for IAV, through the modulation of innate immunity and apoptosis during infection, and potentially by supporting the viral transcription. Author Summary: Influenza A viruses pose a significant threat to global public health. Understanding the interaction between the virus and host is essential for the development of antiviral therapies. We identified cFos, a cellular Activating Protein-1, as a pro-viral factor for influenza A viruses. cFos was found to enhance cell survival and regulate the expression of certain cytokines during viral infection. Our findings also suggested a potential role for cFos in the viral transcription, especially of the viral proteins expressed late in the viral cycle.

Reliable large-scale testing for respiratory viruses, including influenza viruses, coronaviruses, such as SARS-CoV-2, and respiratory syncytial virus (RSV) is essential for both endemic surveillance and pandemic response. While RT-qPCR remains the current gold standard, the COVID-19 pandemic highlighted the need for alternative, scalable detection platforms. Although alternative approaches like liquid chromatography coupled with mass spectrometry (LC-MS) are well-suited for viral multiplexing, they have yet to undergo clinical validation. Here, we present a quantitative immuno-multiple reaction monitoring (iMRM) assay, called Winterplex, for the simultaneous detection of influenza A, influenza B, RSV, and SARS-CoV-2, each targeted via two proteotypic peptides per virus. The method was validated according to ISO standards for in vitro diagnostics and benchmarked against RT-qPCR. To enhance future pandemic preparedness, urgent investment is needed to translate and expand multiplexed MS-based diagnostic methodologies, which offer the flexibility to incorporate a wide range of targets, making them ideally suited for rapid and adaptable responses to emerging viral threats.

The performance of Oracol collection device (Oracol) for oral fluid sampling for SARS-CoV-2 molecular detection was compared to nasopharyngeal swabs (NPS). Samples (n = 128) were collected from symptomatic and asymptomatic adults after PCR confirmed COVID-19 on NPS. All samples were tested by 3 real-time PCRs (RT-qPCR) for E, N and RdPR genes. Accuracy of Oracol compared to NPS was 38.28 % for E-gene, 47.66 % for RdRp-gene and 83.59 % for N-gene. A clear correlation between the N-gene Ct values on NPS and on Oracols was observed (p < 0.001). The sensitivity of the Oracol compared to the NPS increased in participants with an N-gene Ct value <30 on NPS (89.08%) reaching 93.2 % with a N-gene Ct value <25. Oracol can be considered an alternative to NPS to detect SARS-CoV-2, especially in populations where NPS is not well tolerated.

We conducted a multicentre hospital‐based test‐negative case–control study to measure vaccine effectiveness (VE) against PCR‐confirmed influenza in adult patients with severe acute respiratory infection (SARI) during the 2022/2023 influenza season in Europe. Among 5547 SARI patients ≥18 years, 2963 (53%) were vaccinated against influenza. Overall VE against influenza A(H1N1)pdm09 was 11% (95% CI: −23–36); 20% (95% CI: −4–39) against A(H3N2) and 56% (95% CI: 22–75) against B. During the 2022/2023 season, while VE against hospitalisation with influenza B was >55%, it was ≤20% for influenza A subtypes. While influenza vaccination should be a priority for future seasons, improved vaccines against influenza are needed.

Introduction: The I-MOVE-COVID-19 and VEBIS hospital networks have been measuring COVID-19 vaccine effectiveness (VE) in participating European countries since early 2021. Aim: We aimed to measure VE against PCR-confirmed SARS-CoV-2 in patients ≥ 20 years hospitalised with severe acute respiratory infection (SARI) from December 2021 to July 2022 (Omicron-dominant period). Methods: In both networks, 46 hospitals (13 countries) follow a similar test-negative case–control protocol. We defined complete primary series vaccination (PSV) and first booster dose vaccination as last dose of either vaccine received ≥ 14 days before symptom onset (stratifying first booster into received < 150 and ≥ 150 days after last PSV dose). We measured VE overall, by vaccine category/product, age group and time since first mRNA booster dose, adjusting by site as a fixed effect, and by swab date, age, sex, and presence/absence of at least one commonly collected chronic condition. Results: We included 2,779 cases and 2,362 controls. The VE of all vaccine products combined against hospitalisation for laboratory-confirmed SARS-CoV-2 was 43% (95% CI: 29–54) for complete PSV (with last dose received ≥ 150 days before onset), while it was 59% (95% CI: 51–66) after addition of one booster dose. The VE was 85% (95% CI: 78–89), 70% (95% CI: 61–77) and 36% (95% CI: 17–51) for those with onset 14–59 days, 60–119 days and 120–179 days after booster vaccination, respectively. Conclusions: Our results suggest that, during the Omicron period, observed VE against SARI hospitalisation improved with first mRNA booster dose, particularly for those having symptom onset < 120 days after first booster dose.

Introduction Two large multicentre European hospital networks have estimated vaccine effectiveness (VE) against COVID-19 since 2021. Aim We aimed to measure VE against PCR-confirmed SARS-CoV-2 in hospitalised severe acute respiratory illness (SARI) patients ≥ 20 years, combining data from these networks during Alpha (March–June)- and Delta (June–December)-dominant periods, 2021. Methods Forty-six participating hospitals across 14 countries follow a similar generic protocol using the test-negative case–control design. We defined complete primary series vaccination (PSV) as two doses of a two-dose or one of a single-dose vaccine ≥ 14 days before onset. Results We included 1,087 cases (538 controls) and 1,669 cases (1,442 controls) in the Alpha- and Delta-dominant periods, respectively. During the Alpha period, VE against hospitalisation with SARS-CoV2 for complete Comirnaty PSV was 85% (95% CI: 69–92) overall and 75% (95% CI: 42–90) in those aged ≥ 80 years. During the Delta period, among SARI patients ≥ 20 years with symptom onset ≥ 150 days from last PSV dose, VE for complete Comirnaty PSV was 54% (95% CI: 18–74). Among those receiving Comirnaty PSV and mRNA booster (any product) ≥ 150 days after last PSV dose, VE was 91% (95% CI: 57–98). In time-since-vaccination analysis, complete all-product PSV VE was > 90% in those with their last dose < 90 days before onset; ≥ 70% in those 90–179 days before onset. Conclusions Our results from this EU multi-country hospital setting showed that VE for complete PSV alone was higher in the Alpha- than the Delta-dominant period, and addition of a first booster dose during the latter period increased VE to over 90%.

Background: To support the COVID‐19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS‐CoV‐2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with severe acute respiratory infections (SARI) and integrated SARS‐CoV‐2 detection within a broader range of respiratory pathogens. We evaluate the ability of the SARI surveillance to monitor general trends and early signals of viral genetic evolution of SARS‐CoV‐2 and compare it with the BGS as a reference model.Methods: Nine‐hundred twenty‐five SARS‐CoV‐2 positive samples from patients fulfilling the Belgian SARI definition between January 2020 and December 2022 were sequenced using the ARTIC Network amplicon tiling approach on a MinION platform. Weekly variant of concern (VOC) proportions and types were compared to those that were circulating between 2021 and 2022, using 96,251 sequences of the BGS.Results: SARI surveillance allowed timely detection of the Omicron (BA.1, BA.2, BA.4, and BA.5) and Delta (B.1.617.2) VOCs, with no to 2 weeks delay according to the start of their epidemic growth in the Belgian population. First detection of VOCs B.1.351 and P.1 took longer, but these remained minor in Belgium. Omicron BA.3 was never detected in SARI surveillance. Timeliness could not be evaluated for B.1.1.7, being already major at the start of the study period.Conclusions: Genomic surveillance of SARS‐CoV‐2 using SARI sentinel surveillance has proven to accurately reflect VOCs detected in the population and provides a cost‐effective solution for long‐term genomic monitoring of circulating respiratory viruses.

We conducted a multicentre hospital-based test-negative case–control study to measure vaccine effectiveness (VE) against PCR-confirmed influenza in adult patients with severe acute respiratory infection (SARI) during the 2022/23 influenza season in Europe. Among 5547 SARI patients ≥18 years, 2963 (53%) were vaccinated against influenza. Overall VE against influenza A(H1N1)pdm09 was 11% (95%CI: -23–36); 20% (95%CI: -4–39) against A(H3N2) and 56% (95%CI: 22–75) against B. During the 2022/23 season, while VE against hospitalisation with influenza B was >55%, it was ≤20% for influenza A subtypes. While influenza vaccination should be a priority for the upcoming season, improved vaccines against influenza are needed.