Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.
Mathis Hjort Hjelmsø,Sarah Mollerup,Randi Holm Jensen,Carlotta Pietroni,Oksana Lukjancenko,Anna Charlotte Schultz,Frank Møller Aarestrup,Anders J. Hansen +7 more
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TLDR
It is believed that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.Abstract:
Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.read more
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Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens
Sandra Martínez-Puchol,Marta Rusiñol,Xavier Fernandez-Cassi,Natàlia Timoneda,Marta Itarte,Cristina Andrés,Andrés Antón,Josep F. Abril,Rosina Girones,Sílvia Bofill-Mas +9 more
TL;DR: TES is the best strategy to obtain a broad picture of human viruses present in complex samples such as sewage, and other NGS strategies are useful for studying the virome of complex samples when also targeting viruses infecting plants, bacteria, invertebrates or fungi.
Journal ArticleDOI
Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
Rene S. Hendriksen,Oksana Lukjancenko,Patrick Munk,Mathis Hjort Hjelmsø,Jennifer R. Verani,Eric Ng’eno,Godfrey Bigogo,Samuel Kiplangat,Traoré Oumar,Lasse Bergmark,Timo Röder,John Neatherlin,Onyango Clayton,Tine Hald,Susanne Karlsmose,Sünje Johanna Pamp,Barry S. Fields,Joel M. Montgomery,Frank Møller Aarestrup +18 more
TL;DR: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement and may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.
Journal ArticleDOI
Computational Structural Biology: Successes, Future Directions, and Challenges.
TL;DR: A broad, yet concise, sketch of modern aspects of computational biology, with a special focus on computational structural biology, is provided to forecast the areas that computational structural Biology will embrace in the future and the challenges that it may face.
Posted ContentDOI
Library preparation and sequencing platform introduce bias in metagenomics characterisation of microbial communities
TL;DR: It is recommended that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions, and library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure.
Journal ArticleDOI
Suitability of aircraft wastewater for pathogen detection and public health surveillance
David L. Jones,Jennifer Rhymes,Matthew J. Wade,Jessica L. Kevill,Shelagh K. Malham,Jasmine M. S. Grimsley,Charlotte Doyle,Andrew J. Weightman,Kata Farkas +8 more
TL;DR: In this article , the authors quantified the likelihood of defecation prior to departure, on the aircraft and upon arrival on both short- and long-haul flights of SARS-CoV-2.
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