Background Influenza A viruses (IAVs) are significant pathogens of humans and other animals. Although endemic in humans and birds, novel IAV strains can emerge, jump species, and cause epidemics, like the latest variant of H5N1. Wastewater-based epidemiology (WBE) has been shown capable of detecting human IAVs. We aimed to assess whether whole-genome sequencing (WGS) of IAVs from wastewater is possible and can be used to discriminate between circulating strains of human and any non-human IAVs, such as those of avian origin. Methods Using a pan-IAV RT-quantitative PCR assay, six wastewater treatment works (WWTWs) across Northern Ireland were screened from Aug 1 to Dec 5, 2022. A nanopore WGS approach was used to sequence RT-qPCR-positive samples. Phylogenetic analysis of sequences relative to currently circulating human and non-human IAVs was performed. For comparative purposes, clinical data (PCR test results) were supplied by The Regional Virus Laboratory, Belfast Health and Social Care Trust (Belfast, Northern Ireland, UK). Findings We detected a dynamic IAV signal in wastewater from Sept 5, 2022, onwards across Northern Ireland, which did not show a clear positive relationship with the clinical data obtained for the region. Meta (mixed strain) whole-genome sequences were generated from wastewater samples displaying homology to only human and avian IAV strains. The relative proportion of IAV reads of human versus avian origin differed across time and sample site. A diversity in subtypes and lineages was detected (eg, H1N1, H3N2, and several avian). Avian segment 8 related to those found in recent H5N1 clade 2.3.4.4b was identified. Interpretation WBE affords a means to monitor circulating human and avian IAV strains and provide crucial genetic information. As such, WBE can provide rapid, cost-effective, year-round One Health surveillance to help control IAV epidemic and pandemic-related threats. However, optimisation of WBE protocols are necessary to ensure observed wastewater signals not only correlate with clinical case data, but yield information on the wider environmental pan-influenz-ome. Funding Department of Health for Northern Ireland.

Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics limit the public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric in determining prevalence of severe acute respiratory syndrome coronavirus 2 in the community, but its application to other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, applying reverse-transcription quantitative polymerase chain reaction and partial G-gene sequencing to track RSV levels and variants in the community. We report increasing detection of RSV in wastewater concomitant with increasing numbers of positive clinical cases. Analysis of wastewater-derived RSV sequences permitted identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance and aid the management of RSV by informing the timely deployment of pharmaceutical and nonpharmaceutical interventions. The genomic wastewater-based epidemiology platform has the potential to complement ongoing global surveillance efforts and aid the management of respiratory syncytial virus by informing the timely deployment of pharmaceutical and nonpharmaceutical interventions.

Background Influenza A viruses (IAV) are significant pathogens of humans and other animals. Although endemic in humans and birds, novel IAV strains can emerge, jump species, and cause epidemics, like the latest variant of H5N1. Wastewater-based epidemiology (WBE) has very recently been shown to detect human IAV but whether it can detect avian-origin IAV, and if whole genome sequencing (WGS) can be used to discriminate circulating strains of IAV in wastewater remains unknown. Methods Using a pan-IAV RT-qPCR assay, six wastewater treatment works (WWTWs) across Northern Ireland (NI), were screened from August to December 2022. A WGS approach using Oxford Nanopore technology was employed to sequence positive samples. Phylogenetic analysis of sequences relative to currently circulating human and avian IAVs was performed. Findings We detected a dynamic IAV signal in wastewater from September 2022 onwards across NI. “Meta” whole genome sequences were generated displaying homology to both human and avian IAV strains. The relative proportion of human versus avian-origin IAV reads differed across time and sample site. A diversity in subtypes and lineages was detected (e.g. H1N1, H3N2, and several avian). Avian segment 8 related to those found in recent H5N1 clade 2.3.4.4b was identified. Interpretation WBE affords a means to monitor circulating human and avian IAV strains and provide crucial genetic information. As such WBE can provide rapid, cost-effective, year-round “one-health” IAV surveillance to help control epidemic and pandemic threats. Funding This study was funded by the Department of Health for Northern Ireland as part of the Northern Ireland Wastewater Surveillance Programme. Highlights Author Summary Influenza A virus (IAV) is a major pathogen of humans and other animals and causes regular epidemics and devastating pandemics. Recently, a novel variant of highly-pathogenic H5N1 avian influenza has emerged spreading across the world killing millions of birds and infecting mammals, enhancing its pandemic potential. Strengthening global surveillance systems for human and animal IAV is thus a major priority. Wastewater-based epidemiology (WBE) has been applied to track SARS-CoV-2 and IAV in humans but whether this approach could work for avian IAV is not known. Here, we develop a “one-health” method to survey pan-IAV levels and genetically characterise the viruses. Through this we highlight co-detection of human and avian IAVs in wastewater, with homology to recent H5N1 isolates. Our work demonstrates the potential for WBE to help defend against not only human infections but emerging, zoonotic IAVs of pandemic potential. ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Department of Health for Northern Ireland as part of the Northern Ireland Wastewater Surveillance Programme. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. [1]: pending:yes

The emergence of SARS‐CoV‐2 variants has exacerbated the COVID‐19 global health crisis. Thus far, all variants carry mutations in the spike glycoprotein, which is a critical determinant of viral transmission being responsible for attachment, receptor engagement and membrane fusion, and an important target of immunity. Variants frequently bear truncations of flexible loops in the N‐terminal domain (NTD) of spike; the functional importance of these modifications has remained poorly characterised. We demonstrate that NTD deletions are important for efficient entry by the Alpha and Omicron variants and that this correlates with spike stability. Phylogenetic analysis reveals extensive NTD loop length polymorphisms across the sarbecoviruses, setting an evolutionary precedent for loop remodelling. Guided by these analyses, we demonstrate that variations in NTD loop length, alone, are sufficient to modulate virus entry. We propose that variations in NTD loop length act to fine‐tune spike; this may provide a mechanism for SARS‐CoV‐2 to navigate a complex selection landscape encompassing optimisation of essential functionality, immune‐driven antigenic variation and ongoing adaptation to a new host.

A thin, 30 mu m, flexible, robust low-density polyethylene, LDPE, film, loaded with 30 wt% P25 TiO2, is extruded and subsequently rendered highly active photocatalytically by exposing it to UVA (352 nm, 1.5 mW cm(-2)) for 144 h. The film was tested for anti-viral activity using four different viruses, namely, two strains of Influenza A Virus (IAV), WSN, and a recombinant PR8, encephalomyocarditis virus (EMCV), and SARS-CoV-2 (SARS2). The film was irradiated with either UVA radiation (352 nm, 1.5 mW cm(-2); although only 0.25 mW cm-2 for SARS2) or with light from a cool white fluorescent lamp (UVA irradiance: 365 nm, 0.047 mW cm(-2)). In all cases the films exhibited an average virus inactivation rate of > 1.5log/h. In the case of SARS2, the rates were > 2log/h, with the rate determined using a dedicated, low intensity UVA source (0.25 mW cm(-2)) only 1.3 x's faster than that for a cool white lamp (UVA irradiance = 0.047 mW cm(-2)), which suggests that SARS2 is particularly prone to pho-tocatalytic inactivation even under low UV irradiation conditions, such as found in a room lit with just white fluorescent tubes. This is the first example of a flexible, very thin, photocatalytic plastic film, produced by a scalable process (extrusion), for virus inactivation. The potential of such a film for use as a disposable, self -sterilising thin plastic material alternative to the common, non-photocatalytic, inert equivalent used currently for curtains, aprons and table coverings in healthcare is discussed briefly.

Respiratory syncytial virus (RSV) infection is the leading cause of hospitalisation in children worldwide, but there is still no vaccine or anti-viral treatment available. RSV has been implicated in the development of respiratory diseases such as asthma. Toll like receptor 4 (TLR4) has been well characterised in the immune responses to RSV. However, the role of TLR4 in RSV infection remains unclear. To study RSV in the lung epithelium, where RSV preferentially infects ciliated cells, we used a well-differentiated primary airway epithelial cell (WD-PAEC) model: a pseudostratified epithelium that produces mucus and beating cilia. We demonstrate in this physiologically relevant model that TLR4 is a pro-viral factor. Inhibition of TLR4 using TAK-242 significantly reduces RSV titres in WD-PAECs in a dose-dependent manner but has no effect on RSV growth kinetics in a range of immortalised respiratory-derived cell lines. Specific inhibition of a range of downstream effectors of TLR4 signalling in the WD-PAEC model identified p38 MAPK as a pro-viral factor, whereas inhibition of MEK1/2 significantly increased RSV titres. Our data demonstrate a role for TLR4 in RSV infection and highlight the importance of biologically relevant models to study virus-host interactions. Author summary Respiratory Syncytial Virus (RSV) can cause severe respiratory infection in young children and is responsible for approximately 200,000 deaths worldwide every year. Despite decades of research since the identification of this virus in the 1950s there is still no vaccine or treatment available. Advances in research have led to the development of cell cultures that are very similar to the cells that line human airways. These cultures provide an opportunity to study how viruses interacts with airway cells in a representative model and may provide insights that traditional research models have not yet been able to answer. Using this experimental model we show that a drug, TAK-242 which targets a pathogen recognition receptor on the surface of cells, reduces growth of RSV and dampens the immune response to infection in these airway cells. Our data demonstrate potential targets for RSV treatments and also highlight the importance of using relevant experimental models.

Interferon lambdas (IFNλ) (also known as type III IFNs) are critical cytokines that combat infection predominantly at barrier tissues, such as the lung, liver, and gastrointestinal tract. Humans have four IFNλs (1–4), where IFNλ1–3 show ~80%–95% homology, and IFNλ4 is the most divergent displaying only ~30% sequence identity. Variants in IFNλ4 in humans are associated with the outcome of infection, such as with hepatitis C virus. However, how IFNλ4 variants impact cytokine signalling in other tissues and how well this is conserved is largely unknown. In this study, we address whether differences in antiviral signalling exist between IFNλ4 variants in human hepatocyte and intestinal cells, comparing them to IFNλ3. We demonstrate that compared to IFNλ3, wild-type human IFNλ4 induces a signalling response with distinct magnitudes and kinetics, which is modified by naturally occurring variants P70S and K154E in both cell types. IFNλ4’s distinct antiviral response was more rapid yet transient compared to IFNλ1 and 3. Additionally, divergent antiviral kinetics were also observed using non-human primate IFNλs and cell lines. Furthermore, an IFNλ4-like receptor-interacting interface failed to alter IFNλ1’s kinetics. Together, our data provide further evidence that major functional differences exist within the IFNλ gene family. These results highlight the possible tissue specialisation of IFNλs and encourage further investigation of the divergent, non-redundant activities of IFNλ4 and other IFNλs.

Respiratory syncytial virus (RSV) infection is the leading cause of severe lower respiratory tract infections (LRTI) in infants worldwide. The immune responses to RSV infection are implicated in RSV pathogenesis but RSV immunopathogenesis in humans remains poorly understood. We previously demonstrated that IFN-λ1 is the principle interferon induced following RSV infection of infants and well-differentiated primary pediatric bronchial epithelial cells (WD-PBECs). Interestingly, RSV F interacts with the TLR4/CD14/MD2 complex to initiate secretion of pro-inflammatory cytokines, while TLR4 stimulation with house dust mite induces IFN-λ1 production. However, the role of TLR4 in RSV infection and concomitant IFN-λ1 induction remains unclear. Using our RSV/WD-PBEC infection model, we found that CLI-095 inhibition of TLR4 resulted in significantly reduced viral growth kinetics, and secretion of IFN-λ1 and pro-inflammatory chemokines. To elucidate specific TLR4 signalling intermediates implicated in virus replication and innate immune responses we selected 4 inhibitors, including LY294002, U0126, SB203580 and JSH-23. SB203580, a p38 MAPK inhibitor, reduced both viral growth kinetics and IFN-λ1 secretion, while JSH-23, an NF-κB inhibitor, reduced IFN-λ1 secretion without affecting virus growth kinetics. Our data indicate that TLR4 plays a role in RSV entry and/or replication and IFN-λ1 induction following RSV infection is mediated, in part, by TLR4 signalling through NF- κB and/or p38 MAPK. Therefore, targeting TLR4 or downstream effector proteins could present novel treatment strategies against RSV. Importance The role of TLR4 in RSV infection and IFN-λ1 induction is controversial. Using our WD-PBEC model, which replicates many hallmarks of RSV infection in vivo , we demonstrated that the TLR4 pathway is involved in both RSV infection and/or replication and the concomitant induction of IFN-λ1 and other pro-inflammatory cytokines. Increasing our understanding of the role of TLR4 in RSV immunopathogenesis may lead to the development of novel RSV therapeutics.