1. Adriaenssens, Evelien M. and Farkas, Kata and McDonald, James E. and Jones, David L. and Allison, Heather E. and McCarthy, Alan J. (2021) Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity. Water Research 203: 117568 https://doi.org/10.1016/j.watres.2021.117568, ScienceDirect Full Text PDF:C\:\\Users\\alyss\\Zotero\\storage\\BRSZXHDU\\Adriaenssens et al. - 2021 - Tracing the fate of wastewater viruses reveals cat.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\alyss\\Zotero\\storage\\68TCAXMQ\\S0043135421007636.html:text/html, aquatic viruses, shellfish viruses, viral diversity, Viromics, virus ecology, wastewater contamination, wastewater viruses, September, 2023-01-04, en, The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition. To explore this, we used viromic analysis of RNA and DNA virus-like particles to holistically track virus communities entering and leaving wastewater treatment plants and the connecting river catchment system and estuary. We reconstructed {\textgreater}40 000 partial viral genomes into 10 149 species-level groups, dominated by dsDNA and ( +)ssRNA bacteriophages (Caudoviricetes and Leviviricetes) and a small number of genomes that could pose a risk to human health. We found substantial viral diversity and geographically distinct virus communities associated with different wastewater treatment plants. River and estuarine water bodies harboured more diverse viral communities in downstream locations, influenced by tidal movement and proximity to wastewater treatment plants. Shellfish and beach sand were enriched in viral communities when compared with the surrounding water, acting as entrapment matrices for virus particles. Extensive phylogenetic analyses of environmental-derived and reference sequences showed the presence of human-associated sapovirus GII in all sample types, multiple rotavirus A strains in wastewater and a diverse set of picorna-like viruses associated with shellfish. We conclude that wastewater-derived viral genetic material is commonly deposited in the environment and can be traced throughout the freshwater-marine continuum of the river catchment, where it is influenced by local geography, weather events and tidal effects. Our data illustrate the utility of viromic analyses for wastewater- and environment-based ecology and epidemiology, and we present a conceptual model for the circulation of all types of viruses in a freshwater catchment., https://www.sciencedirect.com/science/article/pii/S0043135421007636, 0043-1354
2. Wastewater-{Based} {Epidemiological} {Surveillance} of {Respiratory} {Pathogens} {\textbar} {Frontiers} {Research} {Topic}. Wastewater-Based Epidemiological Surveillance of Respiratory Pathogens | Frontiers Research Topic:C\:\\Users\\alyss\\Zotero\\storage\\2XDE53F2\\wastewater-based-epidemiological-surveillance-of-respiratory-pathogens.html:text/html, 2023-01-04, https://www.frontiersin.org/research-topics/40952/wastewater-based-epidemiological-surveillance-of-respiratory-pathogens
3. Detection of a {SARS}-{CoV}-2 {Beta}-like {Variant} with {Additional} {Mutations} in {Coastal} {Kenya} after {\textgreater}1 {Year} of {Disappearance}. Snapshot:C\:\\Users\\alyss\\Zotero\\storage\\H7VA27MT\\910.html:text/html, 2022, November, Virological, 2023-01-04, en, Arnold W. Lambisia1, *, Joyce U. Nyiro1, John M. Morobe1, Timothy N. Makori1, Leonard Ndwiga1, Maureen W. Mburu1, Edidah O. Moraa1, Jennifer Musyoki1, Nickson Murunga1, Philip Bejon1,2, Lynette Isabella Ochola-Oyier1,2, D. James Nokes1,3, Charles N. Agoti 1,4 and George Githinji1,5, * Affiliations. Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya. Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom. School of Life Scie..., https://virological.org/t/detection-of-a-sars-cov-2-beta-like-variant-with-additional-mutations-in-coastal-kenya-after-1-year-of-disappearance/910
4. Demystifying {Science} {Around} {Wastewater} {Surveillance} {Epidemiology}. Snapshot:C\:\\Users\\alyss\\Zotero\\storage\\LIFJUBA8\\demystifying-science-around-wastewater-surveillance-epidemiology.html:text/html, 2022, November, National Collaborating Centre for Infectious Diseases, 2022-12-23, en-CA, This webinar presents findings from the 2022 Royal Society of Canada policy brief on wastewater surveillance for SARS-CoV-2 RNA in Canada. Discussants elaborate on the application of this scientifi …, https://nccid.ca/webcast/demystifying-science-around-wastewater-surveillance-epidemiology/
5. Cao, Yunlong and Jian, Fanchong and Wang, Jing and Yu, Yuanling and Song, Weiliang and Yisimayi, Ayijiang and Wang, Jing and An, Ran and Zhang, Na and Wang, Yao and Wang, Peng and Zhao, Lijuan and Sun, Haiyan and Yu, Lingling and Yang, Sijie and Niu, Xiao and Xiao, Tianhe and Gu, Qingqing and Shao, Fei and Hao, Xiaohua and Xu, Yanli and Jin, Ronghua and Wang, Youchun and Xie, Xiaoliang Sunney. Imprinted {SARS}-{CoV}-2 humoral immunity induces convergent {Omicron} {RBD} evolution. Pages: 2022.09.15.507787 Section: New Results. Full Text PDF:C\:\\Users\\alyss\\Zotero\\storage\\WMJBIGT8\\Cao et al. - 2022 - Imprinted SARS-CoV-2 humoral immunity induces conv.pdf:application/pdf, 2022, October, bioRxiv, 2022-12-23, en, Continuous evolution of Omicron has led to numerous subvariants that exhibit growth advantage over BA.5. Such rapid and simultaneous emergence of variants with enormous advantages is unprecedented. Despite their rapidly divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots, including R346, K356, K444, L452, N460K and F486. The driving force and destination of such convergent evolution and its impact on humoral immunity established by vaccination and infection remain unclear. Here, we demonstrate that these convergent mutations can cause striking evasion of convalescent plasma, including those from BA.5 breakthrough infection, and existing antibody drugs, including Evusheld and Bebtelovimab. BR.2, CA.1, BQ.1.1, BM.1.1.1, and especially XBB, are the most antibody-evasive strain tested, far exceeding BA.5 and approaching SARS-CoV-1 level. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies (mAbs) isolated from BA.2 and BA.5 breakthrough-infection convalescents. Importantly, due to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection caused significant reductions in the epitope diversity of neutralizing antibodies and increased proportion of non-neutralizing mAbs, which in turn concentrated humoral immune pressure and promoted the convergent RBD evolution. Additionally, the precise convergent RBD mutations and evolution trends of BA.2.75/BA.5 subvariants could be inferred by integrating the neutralization-weighted DMS profiles of mAbs from various immune histories (3051 mAbs in total). Moreover, we demonstrated that as few as five additional convergent mutations based on BA.5 or BA.2.75 could completely evade most plasma samples, including those from BA.5 breakthrough infection, while retaining sufficient hACE2-binding affinity. These results suggest that current herd immunity and BA.5 vaccine boosters may not provide sufficiently broad protection against infection. Broad-spectrum SARS-CoV-2 vaccines and NAb drugs development should be of high priority, and the constructed convergent mutants could serve to examine their effectiveness in advance., 10.1101/2022.09.15.507787, https://www.biorxiv.org/content/10.1101/2022.09.15.507787v3, © 2022, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/