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ABSTRACT Municipal wastewater harbors diverse RNA viruses, which are responsible for many emerging and reemerging diseases in humans, animals, and plants. Although genomic sequencing can be a high-throughput approach for profiling the RNA virome in wastewater, wastewater processing methods often influence sequencing outcomes. Here, we systematically evaluated two wastewater processing methods, tangential-flow ultrafiltration (TFF) and Nanotrap Microbiome A Particles, for detecting the target RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via amplicon sequencing and characterizing the RNA virome using whole-transcriptome shotgun sequencing. Our results from paired comparison tests showed that the TFF and Nanotrap methods recovered similar SARS-CoV-2 variants at the lineage level (analysis of similarity [ANOSIM]R= −0.012,P= 0.874). Optimizing automated procedures for the Nanotrap method and concentration factors for the TFF method was critical for achieving high-depth and high-breadth coverage of the target virus genome. Notably, the two methods enriched distinct RNA viromes from the same wastewater samples (ANOSIMR= 0.260,P= 0.002), with TFF samples showing 22-fold and 7-fold higher relative abundances ofReoviridaeandCoronaviridae, respectively. These differences are likely due to the distinct virus concentration mechanisms employed by each method, which are influenced by liquid-solid partitioning of virus particles and interactions of viral surface proteins with ligands. Our findings underscore the importance of optimizing wastewater processing methods for genomic monitoring and have implications for broader environmental applications.IMPORTANCEWastewater genomic sequencing is an emerging technology for tracking viral infections within communities. However, different methods for concentrating viruses and extracting nucleic acids can influence the recoveries of RNA virome from wastewater. An in-depth understanding of virus concentration mechanisms and their impact on sequencing data quality and bioinformatic output would be critical to guide method selection and optimization. Specifically, this study systematically evaluated tangential-flow ultrafiltration and Nanotrap microbiome particles for their application to sequence SARS-CoV-2 and whole RNA virome from wastewater. Both methods yielded high-quality sequencing data for amplicon sequencing of SARS-CoV-2, but their outcomes diverged in the recovered RNA virome. We identified RNA viruses that are preferentially recovered by each of these two methods and proposed considerations of method selection for future studies of wastewater RNA virome. 

The COVID-19 pandemic has prompted an unprecedented global effort to understand and mitigate the spread of the SARS-CoV-2 virus. In this study, we present a comprehensive analysis of COVID-19 in Western New York (WNY), integrating individual patient-level genomic sequencing data with a spatially informed agent-based disease Susceptible-Exposed-Infectious-Recovered (SEIR) computational model. The integration of genomic and spatial data enables a multi-faceted exploration of the factors influencing the transmission patterns of COVID-19, including genetic variations in the viral genomes, population density, and movement dynamics in New York State (NYS). Our genomic analyses provide insights into the genetic heterogeneity of SARS-CoV-2 within a single lineage, at region-specific resolutions, while our population analyses provide models for SARS-CoV-2 lineage transmission. Together, our findings shed light on localized dynamics of the pandemic, revealing potential cross-county transmission networks. This interdisciplinary approach, bridging genomics and spatial modeling, contributes to a more comprehensive understanding of COVID-19 dynamics. The results of this study have implications for future public health strategies, including guiding targeted interventions and resource allocations to control the spread of similar viruses. 

The sequencing of human virus genomes from wastewater samples is an efficient method for tracking viral transmission and evolution at the community level. However, this requires the recovery of viral nucleic acids of high quality. We developed a reusable tangential-flow filtration system to concentrate and purify viruses from wastewater for genome sequencing. A pilot study was conducted with 94 wastewater samples from four local sewersheds, from which viral nucleic acids were extracted, and the whole genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was sequenced using the ARTIC V4.0 primers. Our method yielded a high probability (0.9) of recovering complete or near-complete SARS-CoV-2 genomes (>90% coverage at 10× depth) from wastewater when the COVID-19 incidence rate exceeded 33 cases per 100 000 people. The relative abundances of sequenced SARS-CoV-2 variants followed the trends observed from patient-derived samples. We also identified SARS-CoV-2 lineages in wastewater that were underrepresented or not present in the clinical whole-genome sequencing data. The developed tangential-flow filtration system can be easily adopted for the sequencing of other viruses in wastewater, particularly those at low concentrations. 

In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglobin, the oxygen-transport system of virtually all vertebrates. Here, we integrate paleoclimate records with an extensive phylogenomic dataset of notothenioid fishes to understand the evolution of trait loss associated with climate change. In contrast to buoyancy adaptations in this clade, we find relaxed selection on the genetic regions controlling erythropoiesis evolved only after sustained cooling in the SO. This pattern is seen not only within icefishes but also occurred independently in other high-latitude notothenioids. We show that one species of the red-blooded dragonfish clade evolved a spherocytic anemia that phenocopies human patients with this disease via orthologous mutations. The genomic imprint of SO climate change is biased toward erythrocyte-associated conserved noncoding elements (CNEs) rather than to coding regions, which are largely preserved through pleiotropy. The drift in CNEs is specifically enriched near genes that are preferentially expressed late in erythropoiesis. Furthermore, we find that the hematopoietic marrow of icefish species retained proerythroblasts, which indicates that early erythroid development remains intact. Our results provide a framework for understanding the interactions between development and the genome in shaping the response of species to climate change. 

During the development of mouse embryonic stem cells (ESC) to neuronal committed cells (NCC), coordinated changes in the expression of 2851 genes take place, mediated by the nuclear form of FGFR1. In this paper, widespread differences are demonstrated in the ESC and NCC inter- and intra-chromosomal interactions, chromatin looping, the formation of CTCF- and nFGFR1-linked Topologically Associating Domains (TADs) on a genome-wide scale and in exemplary HoxA-D loci. The analysis centered on HoxA cluster shows that blocking FGFR1 disrupts the loop formation. FGFR1 binding and genome locales are predictive of the genome interactions; likewise, chromatin interactions along with nFGFR1 binding are predictive of the genome function and correlate with genome regulatory attributes and gene expression. This study advances a topologically integrated genome archipelago model that undergoes structural transformations through the formation of nFGFR1-associated TADs. The makeover of the TAD islands serves to recruit distinct ontogenic programs during the development of the ESC to NCC.