One year after the first autochthonous transmission of West Nile virus (WNV) to birds and horses in Germany, an epizootic emergence of WNV was again observed in 2019. The number of infected birds and horses was considerably higher compared to 2018 (12 birds, two horses), resulting in the observation of the first WNV epidemy in Germany: 76 cases in birds, 36 in horses and five confirmed mosquito-borne, autochthonous human cases. We demonstrated that Germany experienced several WNV introduction events and that strains of a distinct group (Eastern German WNV clade), which was introduced to Germany as a single introduction event, dominated mosquito, birds, horse and human-related virus variants in 2018 and 2019. Virus strains in this clade are characterized by a specific-Lys2114Arg mutation, which might lead to an increase in viral fitness. Extraordinary high temperatures in 2018/2019 allowed a low extrinsic incubation period (EIP), which drove the epizootic emergence and, in the end, most likely triggered the 2019 epidemic. Spatiotemporal EIP values correlated with the geographical WNV incidence. This study highlights the risk of a further spread in Germany in the next years with additional human WNV infections. Thus, surveillance of birds is essential to provide an early epidemic warning and thus, initiate targeted control measures.

The emergence of West Nile virus (WNV) and Usutu virus (USUV) in Europe resulted in significant outbreaks leading to avifauna mortality and human infections. Both viruses have overlapping geographical, host and vector ranges, and are often co‐circulating in Europe. In Germany, a nationwide bird surveillance network was established to monitor these zoonotic arthropod‐borne viruses in migratory and resident birds. In this framework, co‐infections with WNV and USUV were detected in six dead birds collected in 2018 and 2019. Genomic sequencing and phylogenetic analyses classified the detected WNV strains as lineage 2 and the USUV strains as lineages Africa 2 (n=2), Africa 3 (n=3), and Europe 2 (n=1). Preliminary attempts to co‐propagate both viruses in‐vitro failed. However, we successfully cultivated WNV from two animals. Further evidence for WNV‐USUV co‐infection was obtained by sampling live birds in four zoological gardens with confirmed WNV cases. Three snowy owls had high neutralizing antibody titers against both WNV and USUV, of which two were also positive for USUV‐RNA. In conclusion, further reports of co‐infections in animals as well as in humans are expected in the future, particularly in areas where both viruses are present in the vector population.

Borna disease virus 1 (BoDV-1) is the causative agent of Borna disease, a fatal neurologic disorder of domestic mammals and humans, resulting from spill-over infection from its natural reservoir host, the bicolored white-toothed shrew (Crocidura leucodon). The known BoDV-1-endemic area is remarkably restricted to parts of Germany, Austria, Switzerland and Liechtenstein. To gain comprehensive data on its occurrence, we analysed diagnostic material from suspected BoDV-1-induced encephalitis cases based on clinical and/or histopathological diagnosis. BoDV-1 infection was confirmed by RT-qPCR in 207 domestic mammals, 28 humans and seven wild shrews. Thereby, this study markedly raises the number of published laboratory-confirmed human BoDV-1 infections and provides a first comprehensive summary. Generation of 136 new BoDV-1 genome sequences from animals and humans facilitated an in-depth phylogeographic analysis, allowing for the definition of risk areas for zoonotic BoDV-1 transmission and facilitating the assessment of geographical infection sources. Consistent with the low mobility of its reservoir host, BoDV-1 sequences showed a remarkable geographic association, with individual phylogenetic clades occupying distinct areas. The closest genetic relatives of most human-derived BoDV-1 sequences were located at distances of less than 40 km, indicating that spill-over transmission from the natural reservoir usually occurs in the patient´s home region.

The first cluster of patients suffering from coronavirus disease 2019 (COVID-19) was identified on December 21, 2019, and as of July 29, 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been linked with 664,333 deaths and number at least 16,932,996 worldwide. Unprecedented in global societal impact, the COVID-19 pandemic has tested local, national, and international preparedness for viral outbreaks to the limits. Just as it will be vital to identify missed opportunities and improve contingency planning for future outbreaks, we must also highlight key successes and build on them. Concomitant to the emergence of a novel viral disease, there is a ‘research and development gap’ that poses a threat to the overall pace and quality of outbreak response during its most crucial early phase. Here, we outline key components of an adequate research response to novel viral outbreaks using the example of SARS-CoV-2. We highlight the exceptional recent progress made in fundamental science, resulting in the fastest scientific response to a major infectious disease outbreak or pandemic. We underline the vital role of the international research community, from the implementation of diagnostics and contact tracing procedures to the collective search for vaccines and antiviral therapies, sustained by unique information sharing efforts.

Background: Multiple reports have described neonatal SARS‐CoV‐2 infection, including likely in utero transmission and early postnatal infection, but published estimates of neonatal infection range by geography and design type.Objectives: To describe maternal, pregnancy and neonatal characteristics among neonates born to people with SARS‐CoV‐2 infection during pregnancy by neonatal SARS‐CoV‐2 testing results.Methods: Using aggregated data from the Surveillance for Emerging Threats to Mothers and Babies Network (SET‐NET) describing infections from 20 January 2020 to 31 December 2020, we identified neonates who were (1) born to people who were SARS‐CoV‐2 positive by RT‐PCR at any time during their pregnancy, and (2) tested for SARS‐CoV‐2 by RT‐PCR during the birth hospitalisation.Results: Among 28,771 neonates born to people with SARS‐CoV‐2 infection during pregnancy, 3816 (13%) underwent PCR testing and 138 neonates (3.6%) were PCR positive. Ninety‐four per cent of neonates testing positive were born to people with infection identified ≤14 days of delivery. Neonatal SARS‐CoV‐2 infection was more frequent among neonates born preterm (5.7%) compared to term (3.4%). Neonates testing positive were born to both symptomatic and asymptomatic pregnant people.Conclusions: Jurisdictions reported SARS‐CoV‐2 RT‐PCR results for only 13% of neonates known to be born to people with SARS‐CoV‐2 infection during pregnancy. These results provide evidence of neonatal infection identified through multi‐state systematic surveillance data collection and describe characteristics of neonates with SARS‐CoV‐2 infection. While perinatal SARS‐CoV‐2 infection was uncommon among tested neonates born to people with SARS‐CoV‐2 infection during pregnancy, nearly all cases of tested neonatal infection occurred in pregnant people infected around the time of delivery and was more frequent among neonates born preterm. These findings support the recommendation for neonatal SARS‐CoV‐2 RT‐PCR testing, especially for people with acute infection around the time of delivery.