SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event.

The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T ('Basel cluster'), including 157 identical sequences at the root of the 'Basel cluster', some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions. Trial Registration: ClinicalTrials.gov NCT04351503.

Natural history study of an understudied sea catfish species from Panama (Siluriformes: Ariidae)

The semi-anadromous sea catfish species Cathorops tuyra (Ariidae, Besudo sea catfish) from the Tropical Eastern Pacific has been found reproductively active in the freshwater rivers and lakes of the Panama Canal. Despite growing concerns for biodiversity, reports on natural history are lacking for many Neotropical sea catfishes. We aimed to provide data on the diet and seasonal timing of spawning of C. tuyra for an autochthonous, semi-anadromous, brackish water population from Rio Santa Maria and an allochthonous freshwater non-migrating population from Rio Chagres, an affluent to the Panama Canal, to understand how changing from semi-anadromous to residential lifestyle affects the natural history of a species. Fish from both sampling sites were dissected and information on stomach content, size, weight, parasitic load, sex, maturity, and number of eggs were recorded. In Rio Chagres, there was a female bias and individuals were larger and in pre-spawning mode compared to Rio Santa Maria. Parasite prevalence was low in Rio Chagres and zero in Rio Santa Maria. The diets were very similar between populations: gastropods, bivalves, and insects were the most important prey items in both rivers representing a diverse omnivorous diet that is similar to that of other catfishes.(AU)

El bagre de mar semi-anádromo Cathorops tuyra (Ariidae, Bagre besudo) del Pacífico Oriental Tropical se encuentra reproductivamente activa en los ríos y lagos del Canal de Panamá. A pesar de la creciente preocupación por la biodiversidad, faltan informes sobre la historia natural de muchos de los bagres Neotropicales. Nuestro objetivo es proporcionar datos básicos sobre la dieta y el momento del desove estacional de C. tuyra para una población autóctona semi-anádroma de agua salobre de Río Santa María y una población alóctona residente de agua dulce de Río Chagres para comprender cómo el cambio de un estilo de vida semi-anádromo a residencial afecta la historia natural de una especie. Se disecaron peces de ambos sitios de muestreo y se registró la información de contenido del estómago, tamaño, peso, carga parasitaria, sexo, madurez y número de huevos. En Río Chagres hubo un sesgo femenino y los individuos eran más grandes y estaban en modo pre-desove que en Río Santa María. La prevalencia de parásitos fue baja en el Río Chagres y cero en Río Santa María. Las dietas fueron muy similares entre poblaciones: gasterópodos, bivalvos e insectos fueron las presas más importantes en ambos ríos, lo que representa una dieta omnívora diversa, que es similar a la de otros bagres.(AU)

Strong genome-wide divergence between sympatric European river and brook lampreys.

Lampreys, together with hagfishes, are the only extant representatives of jawless vertebrates and thus of prime interest for the study of vertebrate evolution [1]. Most lamprey genera occur in two forms with divergent life histories: a parasitic, anadromous and a non-parasitic, freshwater resident form [2-8]. The taxonomic status of such 'paired species' is disputed, however. While indistinguishable at larval stages, but clearly distinct as adults, they cannot be differentiated with available genetic data [6,7], which has fuelled speculations that the two forms may in fact represent products of phenotypic plasticity within a single species. Here, we use restriction site-associated DNA sequencing (RADseq) to examine the genetic population structure of sympatric European river (Lampetra fluviatilis L., 1758) and brook (Lampetra planeri Bloch, 1784) lampreys. We find strong genetic differentiation and identify numerous fixed and diagnostic single nucleotide polymorphisms (SNPs) between the two species, 12 of which can be unequivocally assigned to specific genes.