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      Identification of multiple potential viral diseases in a large urban center using wastewater surveillance

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          Abstract

          Viruses are linked to a multitude of human illnesses and can disseminate widely in urbanized environments causing global adverse impacts on communities and healthcare infrastructures. Wastewater-based epidemiology was employed using metagenomics and quantitative polymerase chain reaction (qPCR) assays to identify enteric and non-enteric viruses collected from a large urban area for potential public health monitoring and outbreak analysis. Untreated wastewater samples were collected from November 2017 to February 2018 (n = 54) to evaluate the diversity of human viral pathogens in collected samples. Viruses were classified into virus types based on primary transmission routes and reviewed against viral associated diseases reported in the catchment area. Metagenomics detected the presence of viral pathogens that cause clinically significant diseases reported within the study area during the sampling year. Detected viruses belong to the Adenoviridae, Astroviridae, Caliciviridae, Coronaviridae, Flaviviridae, Hepeviridae, Herpesviridae, Matonaviridae, Papillomaviridae, Parvoviridae, Picornaviridae, Poxviridae, Retroviridae, and Togaviridae families. Furthermore, concentrations of adenovirus, norovirus GII, sapovirus, hepatitis A virus, human herpesvirus 6, and human herpesvirus 8 were measured in wastewater samples and compared to metagenomic findings to confirm detected viral genus. Hepatitis A virus obtained the greatest average viral load (1.86 × 10 7 genome copies/L) in wastewater samples compared to other viruses quantified using qPCR with a 100% detection rate in metagenomic samples. Average concentration of sapovirus (1.36 × 10 6 genome copies/L) was significantly greater than norovirus GII (2.94 × 10 4 genome copies/L) indicating a higher burden within the study area. Findings obtained from this study aid in evaluating the utility of wastewater-based epidemiology for identification and routine monitoring of various viruses in large communities. This methodology has the potential to improve public health responses to large scale outbreaks and viral pandemics.

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          Highlights

          • Optimized sequence alignment and qPCR identified the presence of important viral pathogens.

          • Detected viral pathogens in wastewater associated with reported clinically significant diseases.

          • Wastewater-based epidemiology can be used for identification of viral outbreaks.

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          Is Open Access

          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the Global Burden of Disease Study 2017

            Summary Background Global development goals increasingly rely on country-specific estimates for benchmarking a nation's progress. To meet this need, the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2016 estimated global, regional, national, and, for selected locations, subnational cause-specific mortality beginning in the year 1980. Here we report an update to that study, making use of newly available data and improved methods. GBD 2017 provides a comprehensive assessment of cause-specific mortality for 282 causes in 195 countries and territories from 1980 to 2017. Methods The causes of death database is composed of vital registration (VR), verbal autopsy (VA), registry, survey, police, and surveillance data. GBD 2017 added ten VA studies, 127 country-years of VR data, 502 cancer-registry country-years, and an additional surveillance country-year. Expansions of the GBD cause of death hierarchy resulted in 18 additional causes estimated for GBD 2017. Newly available data led to subnational estimates for five additional countries—Ethiopia, Iran, New Zealand, Norway, and Russia. Deaths assigned International Classification of Diseases (ICD) codes for non-specific, implausible, or intermediate causes of death were reassigned to underlying causes by redistribution algorithms that were incorporated into uncertainty estimation. We used statistical modelling tools developed for GBD, including the Cause of Death Ensemble model (CODEm), to generate cause fractions and cause-specific death rates for each location, year, age, and sex. Instead of using UN estimates as in previous versions, GBD 2017 independently estimated population size and fertility rate for all locations. Years of life lost (YLLs) were then calculated as the sum of each death multiplied by the standard life expectancy at each age. All rates reported here are age-standardised. Findings At the broadest grouping of causes of death (Level 1), non-communicable diseases (NCDs) comprised the greatest fraction of deaths, contributing to 73·4% (95% uncertainty interval [UI] 72·5–74·1) of total deaths in 2017, while communicable, maternal, neonatal, and nutritional (CMNN) causes accounted for 18·6% (17·9–19·6), and injuries 8·0% (7·7–8·2). Total numbers of deaths from NCD causes increased from 2007 to 2017 by 22·7% (21·5–23·9), representing an additional 7·61 million (7·20–8·01) deaths estimated in 2017 versus 2007. The death rate from NCDs decreased globally by 7·9% (7·0–8·8). The number of deaths for CMNN causes decreased by 22·2% (20·0–24·0) and the death rate by 31·8% (30·1–33·3). Total deaths from injuries increased by 2·3% (0·5–4·0) between 2007 and 2017, and the death rate from injuries decreased by 13·7% (12·2–15·1) to 57·9 deaths (55·9–59·2) per 100 000 in 2017. Deaths from substance use disorders also increased, rising from 284 000 deaths (268 000–289 000) globally in 2007 to 352 000 (334 000–363 000) in 2017. Between 2007 and 2017, total deaths from conflict and terrorism increased by 118·0% (88·8–148·6). A greater reduction in total deaths and death rates was observed for some CMNN causes among children younger than 5 years than for older adults, such as a 36·4% (32·2–40·6) reduction in deaths from lower respiratory infections for children younger than 5 years compared with a 33·6% (31·2–36·1) increase in adults older than 70 years. Globally, the number of deaths was greater for men than for women at most ages in 2017, except at ages older than 85 years. Trends in global YLLs reflect an epidemiological transition, with decreases in total YLLs from enteric infections, respiratory infections and tuberculosis, and maternal and neonatal disorders between 1990 and 2017; these were generally greater in magnitude at the lowest levels of the Socio-demographic Index (SDI). At the same time, there were large increases in YLLs from neoplasms and cardiovascular diseases. YLL rates decreased across the five leading Level 2 causes in all SDI quintiles. The leading causes of YLLs in 1990—neonatal disorders, lower respiratory infections, and diarrhoeal diseases—were ranked second, fourth, and fifth, in 2017. Meanwhile, estimated YLLs increased for ischaemic heart disease (ranked first in 2017) and stroke (ranked third), even though YLL rates decreased. Population growth contributed to increased total deaths across the 20 leading Level 2 causes of mortality between 2007 and 2017. Decreases in the cause-specific mortality rate reduced the effect of population growth for all but three causes: substance use disorders, neurological disorders, and skin and subcutaneous diseases. Interpretation Improvements in global health have been unevenly distributed among populations. Deaths due to injuries, substance use disorders, armed conflict and terrorism, neoplasms, and cardiovascular disease are expanding threats to global health. For causes of death such as lower respiratory and enteric infections, more rapid progress occurred for children than for the oldest adults, and there is continuing disparity in mortality rates by sex across age groups. Reductions in the death rate of some common diseases are themselves slowing or have ceased, primarily for NCDs, and the death rate for selected causes has increased in the past decade. Funding Bill & Melinda Gates Foundation.
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              Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges

              Highlights • Emergence of 2019 novel coronavirus (2019-nCoV) in China has caused a large global outbreak and major public health issue. • At 9 February 2020, data from the WHO has shown >37 000 confirmed cases in 28 countries (>99% of cases detected in China). • 2019-nCoV is spread by human-to-human transmission via droplets or direct contact. • Infection estimated to have an incubation period of 2–14 days and a basic reproduction number of 2.24–3.58. • Controlling infection to prevent spread of the 2019-nCoV is the primary intervention being used.
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                Author and article information

                Contributors
                Journal
                Water Res
                Water Res
                Water Research
                Published by Elsevier Ltd.
                0043-1354
                1879-2448
                7 July 2020
                7 July 2020
                : 116160
                Affiliations
                [1]Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
                Author notes
                []Corresponding author. A124 Engineering Research Complex, Michigan State University, East Lansing, MI, 48824, USA. xagorara@ 123456msu.edu
                Article
                S0043-1354(20)30697-7 116160
                10.1016/j.watres.2020.116160
                7342010
                32738707
                40bbabe0-8461-41aa-b4fd-c40d81e3bc63
                © 2020 Published by Elsevier Ltd.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 30 April 2020
                : 27 June 2020
                : 5 July 2020
                Categories
                Article

                Oceanography & Hydrology
                wastewater-based epidemiology,public health,viral diseases,metagenomics,virus diversity,qpcr

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