Molecular epidemiology and disease severity of influenza virus infection in patients with haematological disorders

nfluenza virus infection is a common cause of self‐limiting respiratory tract infection(RTI), however immunocompromised patients are at an increased risk for a severecourse of disease or fatal outcome. We therefore aimed to gain a betterunderstanding of the molecular epidemiology of influenza viruses from patientswith haematological disorders and their impact on the clinical course of disease.Molecular analysis using polymerase chain reaction (PCR) of nasopharyngeal swabswas performed for influenza virus in haematological patients at the HeidelbergUniversity Hospital. Clinical data was evaluated to identify associated risk factors.For phylogenetic analysis, the hemagglutinin (HA) gene was sequenced. Out of 159influenza positive patients, 117 patients developed upper RTI (influenza A:n= 73;influenza B:n= 44). Lower RTI was observed inn= 42 patients (26%),n= 22/42patients developed severe disease andn= 16/159 (10.1%) patients died. Risk factorsfor lower RTI were nosocomial infection (p= 0.02), viral shedding for≥14 days(p= 0.018), IgG levels <6 g/dL (p= 0.046), bacterial/fungal co‐infections (p< 0.001).Risk factors for fatal outcome were age≥65 years (p= 0.032), bacterial/fungal(p≤0.001) co‐infections and high viral load (p= 0.026). Sequencing of the HA gene(n= 115) revealed subtype A(H3N2) (n= 46), A(H1N1)pdm09 (n= 24), B/Victoria(n= 34), B/Yamagata (n= 11). There was no correlation between influenza (sub)typeand lower RTI. Influenza infection in haematological patients is associated withsignificant morbidity and mortality, the risk for aggravating co‐infections, prolongedviral shedding and nosocomial transmission emphasizing the need for infectioncontrol.Peer Reviewe

Novel ressortant swine H3N2 influenza A viruses in Germany

Analysis of 228 H3N2 swine influenza A virus isolates collected between 2003 and 2015 in Germany revealed important changes in molecular epidemiology. The data indicate that a novel reassortant, Rietberg/2014-like swine H3N2, emerged in February 2014 in Northern Germany. It is comprised of a hemagglutinin gene of seasonal H3N2 (A/Denmark/129/2005-like), a neuraminidase gene of Emmelsbuell/2009-like swine H1N2 and the internal gene cassette of pandemic H1N1 viruses. Together with Danish swine H3N2 strains of 2013–2015 with identical genome layout, the Rietberg/2014-like viruses represent a second swine H3N2 lineage which cocirculates with a variant of the Gent/1984-like swine H3N2 lineage. This variant, named Gent1984/Diepholz-like swine H3N2, has a Gent/1984-like HA and a Diepholz/2008-like NA; the origin of the internal gene cassette likely derived from avian-like swine H1N1. The first isolate of the Gent1984/Diepholz reassortant emerged in Northern Germany in September 2011 whereas the last German Gent/1984-like isolate was collected in October 2011.Peer Reviewe

Virological Surveillance and Molecular Characterization of Human Parainfluenzavirus Infection in Children with Acute Respiratory Illness: Germany, 2015–2019

Human parainfluenza viruses (HPIVs) are important causes of respiratory illness, especially in young children. However, surveillance for HPIV is rarely performed continuously, and national-level epidemiologic and genetic data are scarce. Within the German sentinel system, to monitor acute respiratory infections (ARI), 4463 respiratory specimens collected from outpatients < 5 years of age between October 2015 and September 2019 were retrospectively screened for HPIV 1–4 using real-time PCR. HPIV was identified in 459 (10%) samples. HPIV-3 was the most common HPIV-type, with 234 detections, followed by HPIV-1 (113), HPIV-4 (61), and HPIV-2 (49). HPIV-3 was more frequently associated with age < 2 years, and HPIV-4 was more frequently associated with pneumonia compared to other HPIV types. HPIV circulation displayed distinct seasonal patterns, which appeared to vary by type. Phylogenetic characterization clustered HPIV-1 in Clades 2 and 3. Reclassification was performed for HPIV-2, provisionally assigning two distinct HPIV-2 groups and six clades, with German HPIV-2s clustering in Clade 2.4. HPIV-3 clustered in C1, C3, C5, and, interestingly, in A. HPIV-4 clustered in Clades 2.1 and 2.2. The results of this study may serve to inform future approaches to diagnose and prevent HPIV infections, which contribute substantially to ARI in young children in Germany.Peer Reviewe

Vaccination against Borna Disease: Overview, Vaccine Virus Characterization and Investigation of Live and Inactivated Vaccines

(1) Background: Vaccination of horses and sheep against Borna disease (BD) was common in endemic areas of Germany in the 20th century but was abandoned in the early 1990s. The recent occurrence of fatal cases of human encephalitis due to Borna disease virus 1 (BoDV-1) has rekindled the interest in vaccination. (2) Methods: The full genomes of the BD live vaccine viruses “Dessau” and “Giessen” were sequenced and analyzed for the first time. All vaccination experiments followed a proof-of-concept approach. Dose-titration infection experiments were performed in rabbits, based on both cell culture- and brain-derived viruses at various doses. Inactivated vaccines against BD were produced from concentrated cell culture supernatants and investigated in rabbits and horses. The BoDV-1 live vaccine “Dessau” was administered to horses and antibody profiles were determined. (3) Results: The BD live vaccine viruses “Dessau” and “Giessen” belong to clusters 3 and 4 of BoDV-1. Whereas the “Giessen” virus does not differ substantially from field viruses, the “Dessau” virus shows striking differences in the M gene and the N-terminal part of the G gene. Rabbits infected with high doses of cell-cultured virus developed neutralizing antibodies and were protected from disease, whereas rabbits infected with low doses of cell-cultured virus, or with brain-derived virus did not. Inactivated vaccines were administered to rabbits and horses, following pre-defined vaccination schemes consisting of three vaccine doses of either adjuvanted or nonadjuvanted inactivated virus. Their immunogenicity and protective efficacy were compared to the BD live vaccine “Dessau”. Seventy per cent of horses vaccinated with the BD live vaccine “Dessau” developed neutralizing antibodies after vaccination. (4) Conclusion: Despite a complex evasion of immunological responses by bornaviruses, some vaccination approaches can protect against clinical disease. For optimal effectiveness, vaccines should be administered at high doses, following vaccination schemes consisting of three vaccine doses as basic immunization. Further investigations are necessary in order to investigate and improve protection against infection and to avoid side effects

Late regulation of immune genes and microRNAs in circulating leukocytes in a pig model of influenza A (H1N2) infection

MicroRNAs (miRNAs) are a class of short regulatory RNA molecules which are implicated in modulating gene expression. Levels of circulating, cell-associated miRNAs in response to influenza A virus (IAV) infection has received limited attention so far. To further understand the temporal dynamics and biological implications of miRNA regulation in circulating leukocytes, we collected blood samples before and after (1, 3, and 14 days) IAV challenge of pigs. Differential expression of miRNAs and innate immune factor mRNA transcripts was analysed using RT-qPCR. A total of 20 miRNAs were regulated after IAV challenge, with the highest number of regulated miRNAs seen on day 14 after infection at which time the infection was cleared. Targets of the regulated miRNAs included genes involved in apoptosis and cell cycle regulation. Significant regulation of both miRNAs and mRNA transcripts at 14 days after challenge points to a protracted effect of IAV infection, potentially affecting the host’s ability to respond to secondary infections. In conclusion, experimental IAV infection of pigs demonstrated the dynamic nature of miRNA and mRNA regulation in circulating leukocytes during and after infection, and revealed the need for further investigation of the potential immunosuppressing effect of miRNA and innate immune signaling after IAV infection

Cross-protection between antigenically distinct H1N1 swine influenza viruses from Europe and North America

Background An avian-like H1N1 swine influenza virus (SIV) is enzootic in swine populations of Western Europe. The virus is antigenically distinct from H1N1 SIVs in North America that have a classical swine virus-lineage H1 hemagglutinin, as does the pandemic (H1N1) 2009 virus. However, the significance of this antigenic difference for cross-protection among pigs remains unknown. Objectives We examined protection against infection with a North American triple reassortant H1N1 SIV [A/swine/Iowa/H04YS2/04 (sw/IA/04)] in pigs infected with a European avian-like SIV [A/swine/Belgium/1/98 (sw/B/98)] 4 weeks earlier. We also examined the genetic relationships and serologic cross-reactivity between both SIVs and with a pandemic (H1N1) 2009 virus [A/California/04/09 (Calif/09)]. Results After intranasal inoculation with sw/IA/04, all previously uninfected control pigs showed nasal virus excretion, high virus titers in the entire respiratory tract at 4 days post-challenge (DPCh) and macroscopic lung lesions. Most pigs previously infected with sw/B/98 tested negative for sw/IA/04 in nasal swabs and respiratory tissues, and none had lung lesions. At challenge, these pigs had low levels of cross-reactive virus neutralizing and neuraminidase inhibiting (NI) antibodies to sw/IA/04, but no hemagglutination-inhibiting antibodies. They showed similar antibody profiles when tested against Calif/09, but NI antibody titers were higher against Calif/09 than sw/IA/04, reflecting the higher genetic homology of the sw/B/98 neuraminidase with Calif/09. Conclusions Our data indicate that immunity induced by infection with European avian-like H1N1 SIV affords protection for pigs against North American H1N1 SIVs with a classical H1, and they suggest cross-protection against the pandemic (H1N1) 2009 virus

Respiratory infections in children and adolescents in Germany during the COVID-19 pandemic

Background: Before the COVID-19 pandemic, acute respiratory infections (ARIs) in children were mainly characterised by three pathogens: respiratory syncytial viruses (RSV), influenza viruses and rhinoviruses. The impact of the COVID-19 pandemic and the measures taken in Germany (especially until the end of 2021) on the incidence of ARI in children and adolescents aged 0 to 14 years and the pathogens causing them has not yet been comprehensively analysed. Methods: The evaluation is based on data from population-based, virological and hospital-based surveillance instruments up to the end of 2022. Results: After the onset of the COVID-19 pandemic in early 2020, ARI rates remained almost consistently below pre-pandemic levels until autumn 2021, with only rhinoviruses continuously continuing to cause ARI. Only when the Omicron variant became predominant in 2022, there were measurable COVID-19 rates at population level in children, although COVID-19 hospitalisation rates remained comparatively low. RSV and influenza waves were initially absent and then occurred ‘out of season’, but were more severe than usual. Conclusions: While the measures taken were effective in inhibiting the number of respiratory infections for almost 1.5 years, moderately frequent but rather mild COVID-19 cases occurred when measures were lifted. When Omicron emerged in 2022 COVID-19 became moderately frequent but led predominantly to mild illnesses. For RSV and influenza, the measures resulted in changes in their annual timing and intensity