Active faulting offshore the Maltese Islands revealed by geophysical and geochemical observations

<p>The Maltese Islands (central Mediterranean Sea) are intersected by two normal fault systems associated with continental rifting to the south. Because of a lack of evidence for offshore displacement and insignificant historical seismicity, the systems have been considered to be inactive. Here we integrate aerial and marine geological, geophysical and geochemical data to demonstrate that: (i) the majority of faults offshore the Maltese Islands underwent extensional to transtensional deformation during the last 20 ka, (ii) active degassing of CH<sub>4</sub> and CO<sub>2 </sub>occurs via these faults. The gases migrate through Miocene carbonate bedrock and the overlying Plio-Pleistocene sedimentary layers to generate pockmarks at the muddy seafloor and rise through the water column into the atmosphere. We infer that the offshore faults systems are permeable and that they were active recently and simultaneously. The latter can be explained by a transtensional system involving two right-stepping, right-lateral NW-SE trending faults, either binding a pull-apart basin between the islands of Malta and Gozo or associated with minor connecting antitethic structures. Such a configuration may be responsible for the generation or reactivation of faults onshore and offshore the Maltese Islands, and fits into the modern divergent strain-stress regime inferred from geodetic data.</p>

Novel Mammalian orthorubulavirus 5 Discovered as Accidental Cell Culture Contaminant

A distinct Russian Mammalian orthorubulavirus 5 (PIV5) was detected in cell culture exhibiting cytopathic effect and hypothesized to be contaminated by a scientist with respiratory symptoms. The identification of the divergent strain indicated a lack of knowledge on the diversity of PIV5 strains and calls for surveillance of global PIV5 strains.

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

BackgroundAccurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained.This study evaluates the performance of 41 SNP calling pipelines using simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella.ResultsWe evaluated the performance of 41 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli, but less dominant for clonal species such as Mycobacterium tuberculosis.ConclusionsThe accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. However, across the full range of (divergent) genomes, among the consistently highest-performing pipelines was Snippy.