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.

Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. We confirmed the performance of the approach using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework.

Eukaryotic microbial life at abyssal depths remains “uncharted territory” in eukaryotic microbiology. No phylogenetic surveys have focused on the largest benthic environment on this planet, the abyssal plains. Moreover, knowledge of the spatial patterns of deep-sea community structure is scanty, and what little is known originates primarily from morphology-based studies of foraminiferans. Here we report on the great phylogenetic diversity of microbial eukaryotic communities of all 3 abyssal plains of the southeastern Atlantic Ocean---the Angola, Cape, and Guinea Abyssal Plains---from depths of 5,000 m. A high percentage of retrieved clones had no close representatives in genetic databases. Many clones were affiliated with parasitic species. Furthermore, differences between the communities of the Cape Abyssal Plain and the other 2 abyssal plains point to environmental gradients apparently shaping community structure at the landscape level. On a regional scale, local species diversity showed much less variation. Our study provides insight into the community composition of microbial eukaryotes on larger scales from the wide abyssal sea floor realm and marks a direction for more detailed future studies aimed at improving our understanding of deep-sea microbes at the community and ecosystem levels, as well as the ecological principles at play.

Emerging variants of concern (VOCs) are driving the COVID-19 pandemic^1,2. Experimental assessments of replication and transmission of major VOCs and progenitors are needed to understand the mechanisms of replication and transmission of VOCs³. Here we show that the spike protein (S) from Alpha (also known as B.1.1.7) and Beta (B.1.351) VOCs had a greater affinity towards the human angiotensin-converting enzyme 2 (ACE2) receptor than that of the progenitor variant S(D614G) in vitro. Progenitor variant virus expressing S(D614G) (wt-S^614G) and the Alpha variant showed similar replication kinetics in human nasal airway epithelial cultures, whereas the Beta variant was outcompeted by both. In vivo, competition experiments showed a clear fitness advantage of Alpha over wt-S^614G in ferrets and two mouse models—the substitutions in S were major drivers of the fitness advantage. In hamsters, which support high viral replication levels, Alpha and wt-S^614G showed similar fitness. By contrast, Beta was outcompeted by Alpha and wt-S^614G in hamsters and in mice expressing human ACE2. Our study highlights the importance of using multiple models to characterize fitness of VOCs and demonstrates that Alpha is adapted for replication in the upper respiratory tract and shows enhanced transmission in vivo in restrictive models, whereas Beta does not overcome Alpha or wt-S^614G in naive animals.