Microbiome Analysis for Wastewater Surveillance during COVID-19

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ABSTRACT

Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

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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An interactive web-based dashboard to track COVID-19 in real time

Ensheng Dong, Hongru Du, Lauren Gardner (2020)

In December, 2019, a local outbreak of pneumonia of initially unknown cause was detected in Wuhan (Hubei, China), and was quickly determined to be caused by a novel coronavirus, 1 namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The outbreak has since spread to every province of mainland China as well as 27 other countries and regions, with more than 70 000 confirmed cases as of Feb 17, 2020. 2 In response to this ongoing public health emergency, we developed an online interactive dashboard, hosted by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University, Baltimore, MD, USA, to visualise and track reported cases of coronavirus disease 2019 (COVID-19) in real time. The dashboard, first shared publicly on Jan 22, illustrates the location and number of confirmed COVID-19 cases, deaths, and recoveries for all affected countries. It was developed to provide researchers, public health authorities, and the general public with a user-friendly tool to track the outbreak as it unfolds. All data collected and displayed are made freely available, initially through Google Sheets and now through a GitHub repository, along with the feature layers of the dashboard, which are now included in the Esri Living Atlas. The dashboard reports cases at the province level in China; at the city level in the USA, Australia, and Canada; and at the country level otherwise. During Jan 22–31, all data collection and processing were done manually, and updates were typically done twice a day, morning and night (US Eastern Time). As the outbreak evolved, the manual reporting process became unsustainable; therefore, on Feb 1, we adopted a semi-automated living data stream strategy. Our primary data source is DXY, an online platform run by members of the Chinese medical community, which aggregates local media and government reports to provide cumulative totals of COVID-19 cases in near real time at the province level in China and at the country level otherwise. Every 15 min, the cumulative case counts are updated from DXY for all provinces in China and for other affected countries and regions. For countries and regions outside mainland China (including Hong Kong, Macau, and Taiwan), we found DXY cumulative case counts to frequently lag behind other sources; we therefore manually update these case numbers throughout the day when new cases are identified. To identify new cases, we monitor various Twitter feeds, online news services, and direct communication sent through the dashboard. Before manually updating the dashboard, we confirm the case numbers with regional and local health departments, including the respective centres for disease control and prevention (CDC) of China, Taiwan, and Europe, the Hong Kong Department of Health, the Macau Government, and WHO, as well as city-level and state-level health authorities. For city-level case reports in the USA, Australia, and Canada, which we began reporting on Feb 1, we rely on the US CDC, the government of Canada, the Australian Government Department of Health, and various state or territory health authorities. All manual updates (for countries and regions outside mainland China) are coordinated by a team at Johns Hopkins University. The case data reported on the dashboard aligns with the daily Chinese CDC 3 and WHO situation reports 2 for within and outside of mainland China, respectively (figure ). Furthermore, the dashboard is particularly effective at capturing the timing of the first reported case of COVID-19 in new countries or regions (appendix). With the exception of Australia, Hong Kong, and Italy, the CSSE at Johns Hopkins University has reported newly infected countries ahead of WHO, with Hong Kong and Italy reported within hours of the corresponding WHO situation report. Figure Comparison of COVID-19 case reporting from different sources Daily cumulative case numbers (starting Jan 22, 2020) reported by the Johns Hopkins University Center for Systems Science and Engineering (CSSE), WHO situation reports, and the Chinese Center for Disease Control and Prevention (Chinese CDC) for within (A) and outside (B) mainland China. Given the popularity and impact of the dashboard to date, we plan to continue hosting and managing the tool throughout the entirety of the COVID-19 outbreak and to build out its capabilities to establish a standing tool to monitor and report on future outbreaks. We believe our efforts are crucial to help inform modelling efforts and control measures during the earliest stages of the outbreak.

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First Case of 2019 Novel Coronavirus in the United States

Michelle Holshue, Chas DeBolt, Scott Lindquist … (2020)

Summary An outbreak of novel coronavirus (2019-nCoV) that began in Wuhan, China, has spread rapidly, with cases now confirmed in multiple countries. We report the first case of 2019-nCoV infection confirmed in the United States and describe the identification, diagnosis, clinical course, and management of the case, including the patient’s initial mild symptoms at presentation with progression to pneumonia on day 9 of illness. This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.

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Author and article information

Contributors

Rita R. Colwell:

ORCID: https://orcid.org/0000-0001-5432-1502

Michele S. Swanson: Role: Editor

Journal

Journal ID (nlm-ta): mBio

Journal ID (iso-abbrev): mBio

Journal ID (publisher-id): mbio

Title: mBio

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2150-7511

Publication date (Electronic, pub): 21 June 2022

Publication date (Electronic, collection): Jul-Aug 2022

Publication date PMC-release: 21 June 2022

Volume: 13

Issue: 4

Electronic Location Identifier: e00591-22

Affiliations

[a ] Maryland Pathogen Research Institute, University of Maryland, College Parkgrid.164295.d, , Maryland, USA

[b ] University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Parkgrid.164295.d, , Maryland, USA

[c ] Essential Environmental and Engineering Systems, Huntington Beach, California, USA

[d ] Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Floridagrid.15276.37, , Gainesville, Florida, USA

[e ] Joseph Cotruvo and Associates LLC, Washington, DC, USA

[f ] Maryland Department of Environment, Baltimore, Maryland, USA

[g ] CosmosID Inc., Germantown, Maryland, USA

[h ] Inspection Experts Inc., Columbia, Maryland, USA

University of Michigan-Ann Arbor

Author notes

The authors declare the following potential conflicts of interest, with respect to the research, authorship, and/or publication of this article: R.R.C. is the founder of CosmosID, Inc., Rockville, MD and Distinguished University Professor, University of Maryland, College Park, MD; K.G., M.D., B.F., I.Z., and N.R. were employed by CosmosID, Inc. and M.W., D.J., R.A., and C.W. were employed by Inspection Experts, Inc., at the time this work was completed; J.A.C. is the founder of Joseph Cotruvo and Associates LLC, Washington, DC; M.L. is the founder of Essential Environmental and Engineering Systems, Huntington Beach. Specific roles of these authors are articulated in the 'Acknowledgements' section. This does not alter our decision to publish or adherence to policies on sharing data and materials.

Author information

Kyle D. Brumfield https://orcid.org/0000-0002-3234-3337

Rita R. Colwell https://orcid.org/0000-0001-5432-1502

Article

Publisher ID: 00591-22 Publisher ID: mbio.00591-22

DOI: 10.1128/mbio.00591-22

PMC ID: 9426581

PubMed ID: 35726918

SO-VID: e01f758e-8cf7-43d5-b685-d42fb1e38ac8

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 4 March 2022

Date accepted : 16 May 2022

Page count

supplementary-material: 10, Figures: 7, Tables: 1, Equations: 0, References: 130, Pages: 25, Words: 16945

Funding

Funded by: HHS | National Institutes of Health (NIH), FundRef https://doi.org/10.13039/100000002;

Award ID: R01ES030317A

Award Recipient : Anwar Huq

Funded by: National Science Foundation (NSF), FundRef https://doi.org/10.13039/100000001;

Award ID: OCE1839171

Award Recipient : Anwar Huq

Funded by: National Science Foundation (NSF), FundRef https://doi.org/10.13039/100000001;

Award ID: CCF1918749

Award Recipient : Rita R. Colwell

Funded by: National Science Foundation (NSF), FundRef https://doi.org/10.13039/100000001;

Award ID: CBET1751854

Award Recipient : Antarpreet Jutla

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cover-date July/August 2022

ScienceOpen disciplines: Life sciences

Keywords: covid-19,sars-cov-2,wastewater,microbiome,wastewater-based epidemiology,wastewater monitoring,wastewater surveillance,rt-qpcr,dna sequencing,rna sequencing,metagenomics,whole metagenome sequencing,metatranscriptomics,shotgun sequencing,risk assessment,environmental risk

Data availability:

ScienceOpen disciplines: Life sciences

Keywords: covid-19, sars-cov-2, wastewater, microbiome, wastewater-based epidemiology, wastewater monitoring, wastewater surveillance, rt-qpcr, dna sequencing, rna sequencing, metagenomics, whole metagenome sequencing, metatranscriptomics, shotgun sequencing, risk assessment, environmental risk

Microbiome Analysis for Wastewater Surveillance during COVID-19

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ABSTRACT

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Novel Coronavirus Disease COVID-19

Most cited references 123

Trimmomatic: a flexible trimmer for Illumina sequence data

An interactive web-based dashboard to track COVID-19 in real time

First Case of 2019 Novel Coronavirus in the United States

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