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Greenman N, Hassouneh SAD, Abdelli LS, Johnston C, Azarian T. Improving Bacterial Metagenomic Research through Long-Read Sequencing. Microorganisms 2024; 12:935. [PMID: 38792764 PMCID: PMC11124196 DOI: 10.3390/microorganisms12050935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Metagenomic sequencing analysis is central to investigating microbial communities in clinical and environmental studies. Short-read sequencing remains the primary approach for metagenomic research; however, long-read sequencing may offer advantages of improved metagenomic assembly and resolved taxonomic identification. To compare the relative performance for metagenomic studies, we simulated short- and long-read datasets using increasingly complex metagenomes comprising 10, 20, and 50 microbial taxa. Additionally, we used an empirical dataset of paired short- and long-read data generated from mouse fecal pellets to assess real-world performance. We compared metagenomic assembly quality, taxonomic classification, and metagenome-assembled genome (MAG) recovery rates. We show that long-read sequencing data significantly improve taxonomic classification and assembly quality. Metagenomic assemblies using simulated long reads were more complete and more contiguous with higher rates of MAG recovery. This resulted in more precise taxonomic classifications. Principal component analysis of empirical data demonstrated that sequencing technology affects compositional results as samples clustered by sequence type, not sample type. Overall, we highlight strengths of long-read metagenomic sequencing for microbiome studies, including improving the accuracy of classification and relative abundance estimates. These results will aid researchers when considering which sequencing approaches to use for metagenomic projects.
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Affiliation(s)
- Noah Greenman
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
| | - Sayf Al-Deen Hassouneh
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
| | - Latifa S. Abdelli
- Department of Health Science, College of Health Professions and Sciences, University of Central Florida, Orlando, FL 32816, USA;
| | - Catherine Johnston
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
| | - Taj Azarian
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
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2
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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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3
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Mejías-Molina C, Pico-Tomàs A, Martínez-Puchol S, Itarte M, Torrell H, Canela N, Borrego CM, Corominas L, Rusiñol M, Bofill-Mas S. Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals. Hum Genomics 2024; 18:10. [PMID: 38303015 PMCID: PMC10832175 DOI: 10.1186/s40246-024-00580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome. RESULTS The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression. CONCLUSIONS This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.
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Affiliation(s)
- Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | | | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | | | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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4
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Sadasivan H, Wadden J, Goliya K, Ranjan P, Dickson RP, Blaauw D, Das R, Narayanasamy S. Rapid Real-time Squiggle Classification for Read until using RawMap. ARCHIVES OF CLINICAL AND BIOMEDICAL RESEARCH 2023; 7:45-57. [PMID: 36938368 PMCID: PMC10022530 DOI: 10.26502/acbr.50170318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively sequence reads of target species in real-time. This enables efficient microbial enrichment for applications such as microbial abundance estimation and is particularly beneficial for metagenomic samples with a very high fraction of non-target reads (> 99% can be human reads). However, read-until requires a fast and accurate software filter that analyzes a short prefix of a read and determines if it belongs to a microbe of interest (target) or not. The baseline Read Until pipeline uses a deep neural network-based basecaller called Guppy and is slow and inaccurate for this task (~60% of bases sequenced are unclassified). We present RawMap, an efficient CPU-only microbial species-agnostic Read Until classifier for filtering non-target human reads in the squiggle space. RawMap uses a Support Vector Machine (SVM), which is trained to distinguish human from microbe using non-linear and non-stationary characteristics of ONT's squiggle output (continuous electrical signals). Compared to the baseline Read Until pipeline, RawMap is a 1327X faster classifier and significantly improves the sequencing time and cost, and compute time savings. We show that RawMap augmented pipelines reduce sequencing time and cost by ~24% and computing cost by 22%. Additionally, since RawMap is agnostic to microbial species, it can also classify microbial species it is not trained on. We also discuss how RawMap may be used as an alternative to the RT-PCR test for viral load quantification of SARS-CoV-2.
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Affiliation(s)
- Harisankar Sadasivan
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Jack Wadden
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Kush Goliya
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Piyush Ranjan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - Robert P Dickson
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - David Blaauw
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Reetuparna Das
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Satish Narayanasamy
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
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5
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Zuckerman NS, Shulman LM. Next-Generation Sequencing in the Study of Infectious Diseases. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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6
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Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics. Viruses 2022; 14:v14112481. [PMID: 36366579 PMCID: PMC9693158 DOI: 10.3390/v14112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.
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7
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35753493 DOI: 10.1101/2022.01.28.21268186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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8
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156932. [PMID: 35753493 PMCID: PMC9225927 DOI: 10.1016/j.scitotenv.2022.156932] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/21/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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9
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Glidden CK, Field LC, Bachhuber S, Hennessey SM, Cates R, Cohen L, Crockett E, Degnin M, Feezell MK, Fulton‐Bennett HK, Pires D, Poirson BN, Randell ZH, White E, Gravem SA. Strategies for managing marine disease. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2643. [PMID: 35470930 PMCID: PMC9786832 DOI: 10.1002/eap.2643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
The incidence of emerging infectious diseases (EIDs) has increased in wildlife populations in recent years and is expected to continue to increase with global environmental change. Marine diseases are relatively understudied compared with terrestrial diseases but warrant parallel attention as they can disrupt ecosystems, cause economic loss, and threaten human livelihoods. Although there are many existing tools to combat the direct and indirect consequences of EIDs, these management strategies are often insufficient or ineffective in marine habitats compared with their terrestrial counterparts, often due to fundamental differences between marine and terrestrial systems. Here, we first illustrate how the marine environment and marine organism life histories present challenges and opportunities for wildlife disease management. We then assess the application of common disease management strategies to marine versus terrestrial systems to identify those that may be most effective for marine disease outbreak prevention, response, and recovery. Finally, we recommend multiple actions that will enable more successful management of marine wildlife disease emergencies in the future. These include prioritizing marine disease research and understanding its links to climate change, improving marine ecosystem health, forming better monitoring and response networks, developing marine veterinary medicine programs, and enacting policy that addresses marine and other wildlife diseases. Overall, we encourage a more proactive rather than reactive approach to marine wildlife disease management and emphasize that multidisciplinary collaborations are crucial to managing marine wildlife health.
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Affiliation(s)
- Caroline K. Glidden
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
- Present address:
Department of BiologyStanford UniversityStanfordCaliforniaUSA
| | - Laurel C. Field
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Silke Bachhuber
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | | | - Robyn Cates
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Lesley Cohen
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Elin Crockett
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Michelle Degnin
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | - Maya K. Feezell
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | | | - Devyn Pires
- College of Veterinary MedicineOregon State UniversityCorvallisOregonUSA
| | | | - Zachary H. Randell
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Erick White
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Sarah A. Gravem
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
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10
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Bartlow AW, Stromberg ZR, Gleasner CD, Hu B, Davenport KW, Jakhar S, Li PE, Vosburg M, Garimella M, Chain PSG, Erkkila TH, Fair JM, Mukundan H. Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000811. [PMID: 36962439 PMCID: PMC10022352 DOI: 10.1371/journal.pgph.0000811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/29/2022] [Indexed: 11/18/2022]
Abstract
Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.
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Affiliation(s)
- Andrew W. Bartlow
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Zachary R. Stromberg
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cheryl D. Gleasner
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bin Hu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Karen W. Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Shailja Jakhar
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Po-E Li
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Molly Vosburg
- Medical Associates of Northern New Mexico, Los Alamos, New Mexico, United States of America
| | - Madhavi Garimella
- Medical Associates of Northern New Mexico, Los Alamos, New Mexico, United States of America
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tracy H. Erkkila
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeanne M. Fair
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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11
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Lee HJ, Jeong RD. Metatranscriptomic Analysis of Plant Viruses in Imported Pear and Kiwifruit Pollen. THE PLANT PATHOLOGY JOURNAL 2022; 38:220-228. [PMID: 35678055 PMCID: PMC9343911 DOI: 10.5423/ppj.oa.03.2022.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Pollen is a vector for viral transmission. Pollen-mediated viruses cause serious economic losses in the fruit industry. Despite the commercial importance of pollen-associated viruses, the diversity of such viruses is yet to be fully explored. In this study, we performed metatranscriptomic analyses using RNA sequencing to investigate the viral diversity in imported apple and kiwifruit pollen. We identified 665 virus-associated contigs, which corresponded to four different virus species. We identified one virus, the apple stem grooving virus, from pear pollen and three viruses, including citrus leaf blotch virus, cucumber mosaic virus, and lychnis mottle virus in kiwifruit pollen. The assembled viral genome sequences were analyzed to determine phylogenetic relationships. These findings will expand our knowledge of the virosphere in fruit pollen and lead to appropriate management of international pollen trade. However, the pathogenic mechanisms of pollen-associated viruses in fruit trees should be further investigated.
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Affiliation(s)
| | - Rae-Dong Jeong
- Corresponding author. Phone) +82-62-530-2075, FAX) +82-62-530-2069, E-mail)
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12
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Chen Y, Liu F, Lee LP. Quantitative and ultrasensitive in situ immunoassay technology for SARS-CoV-2 detection in saliva. SCIENCE ADVANCES 2022; 8:eabn3481. [PMID: 35613342 PMCID: PMC9132547 DOI: 10.1126/sciadv.abn3481] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has become an immense global health crisis. However, the lack of efficient and sensitive on-site testing methods limits early detection for timely isolation and intervention. Here, we present a quantitative and ultrasensitive in situ immunoassay technology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in saliva (QUIT SARS-CoV-2). Our nanoporous membrane resonator generates a rapid oscillating flow to purify and concentrate fully intact SARS-CoV-2 virus in saliva by 40-fold for in situ detection of viral antigens based on chemiluminescent immunoassay within 20 min. This method can not only achieve a detection sensitivity below 100 copies/ml of virus, comparable to the bench-top PCR equipment; it can also improve detection specificity via direct monitoring of viral loads. The integrated portable QUIT SARS-CoV-2 system, which enables rapid and accurate on-site viral screening with a high-throughput sample pooling strategy, can be performed in primary care settings and substantially improve the detection and prevention of COVID-19.
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Affiliation(s)
- Yuchao Chen
- WellSIM Biomedical Technologies Inc., 626 Bancroft Way, Suite A, Berkeley, CA, USA
| | - Fei Liu
- WellSIM Biomedical Technologies Inc., 626 Bancroft Way, Suite A, Berkeley, CA, USA
| | - Luke P. Lee
- Harvard Medical School, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Bioengineering and Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
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13
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Varkoly K, Tan S, Beladi R, Fonseca D, Zanetti IR, Kraberger S, Shah C, Yaron JR, Zhang L, Juby M, Fath A, Ambadapadi S, House M, Maranian P, Pepine CJ, Varsani A, Moreb J, Schultz-Cherry S, Lucas AR. RNA Virus Gene Signatures Detected in Patients With Cardiomyopathy After Chemotherapy; A Pilot Study. Front Cardiovasc Med 2022; 9:821162. [PMID: 35360008 PMCID: PMC8962958 DOI: 10.3389/fcvm.2022.821162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background Viral infections are pervasive and leading causes of myocarditis. Immune-suppression after chemotherapy increases opportunistic infections, but the incidence of virus-induced myocarditis is unknown. Objective An unbiased, blinded screening for RNA viruses was performed after chemotherapy with correlation to cardiac function. Methods High-throughput sequencing of RNA isolated from blood samples was analyzed following chemotherapy for hematological malignancies (N = 28) and compared with left ventricular ejection fraction (LVEF). Results On initial rigorous analysis, low levels of influenza orthomyxovirus and avian paramyxovirus sequences were detectable, but without significant correlation to LVEF (r = 0.208). A secondary broad data mining analysis for virus sequences, without filtering human sequences, detected significant correlations for paramyxovirus with LVEF after chemotherapy (r = 0.592, P < 0.0096). Correlations were similar for LVEF pre- and post- chemotherapy for orthomyxovirus (R = 0.483, P < 0.0421). Retrovirus detection also correlated with LVEF post (r = 0.453, p < 0.0591), but not pre-chemotherapy, but is suspect due to potential host contamination. Detectable phage and anellovirus had no correlation. Combined sequence reads (all viruses) demonstrated significant correlation (r = 0.621, P < 0.0078). Reduced LVEF was not associated with chemotherapy (P = NS). Conclusions This is the first report of RNA virus screening in circulating blood and association with changes in cardiac function among patients post chemotherapy, using unbiased, blinded, high-throughput sequencing. Influenza orthomyxovirus, avian paramyxovirus and retrovirus sequences were detectable in patients with reduced LVEF. Further analysis for RNA virus infections in patients with cardiomyopathy after chemotherapy is warranted.
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Affiliation(s)
- Kyle Varkoly
- Department of Internal Medicine, McLaren Macomb Hospital- Michigan State University College of Human Medicine, Mt Clemens, MI, United States
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Shaoyuan Tan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Roxana Beladi
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Department of Neurological Surgery, Ascension Providence Hospital- Michigan State University College of Human Medicine, Southfield, MI, United States
| | - David Fonseca
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Isabela Rivabem Zanetti
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Simona Kraberger
- The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Chintan Shah
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Jordan R. Yaron
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School for Engineering of Matter, Transport and Energy, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, United States
| | - Liqiang Zhang
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael Juby
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Ayman Fath
- Department of Internal Medicine, Dignity Health, Creighton University, Phoenix, AZ, United States
| | - Sriram Ambadapadi
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Melanie House
- Department of Internal Medicine, Dignity Health, Creighton University, Phoenix, AZ, United States
| | - Paul Maranian
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Carl J. Pepine
- Division of Cardiology, Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Division of Cardiology, Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Jan Moreb
- Hematologic Malignancies, Transplantation and Cellular Therapy Program, Forsyth Medical Center, Derrick L Davis Cancer Center, Winston-Salem, NC, United States
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Alexandra R. Lucas
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Division of Cardiology, Department of Medicine, University of Florida, Gainesville, FL, United States
- Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- *Correspondence: Alexandra R. Lucas
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14
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Negrey JD, Mitani JC, Wrangham RW, Otali E, Reddy RB, Pappas TE, Grindle KA, Gern JE, Machanda ZP, Muller MN, Langergraber KE, Thompson ME, Goldberg TL. Viruses associated with ill health in wild chimpanzees. Am J Primatol 2022; 84:e23358. [PMID: 35015311 PMCID: PMC8853648 DOI: 10.1002/ajp.23358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023]
Abstract
Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.
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Affiliation(s)
- Jacob D. Negrey
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - John C. Mitani
- Department of Anthropology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Richard W. Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | - Rachna B. Reddy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Tressa E. Pappas
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Kristine A. Grindle
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Zarin P. Machanda
- Department of Anthropology, Tufts University, Medford, MA, 02155, USA
| | - Martin N. Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kevin E. Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
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15
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Mertens J, Coppens J, Loens K, Le Mercier M, Xavier BB, Lammens C, Vandamme S, Jansens H, Goossens H, Matheeussen V. Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Clin Microbiol Infect 2022; 28:124-129. [PMID: 34537361 PMCID: PMC8444474 DOI: 10.1016/j.cmi.2021.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To evaluate a testing algorithm for the rapid identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that includes the use of PCR-based targeted single nucleotide polymorphism (SNP) detection assays preceded by a multiplex PCR sensitive to S-Gene Target Failure (SGTF). METHODS PCR SNP assays targeting SARS-CoV-2 S-gene mutations ΔH69-V70, L452R, E484K, N501Y, H655Y and P681R using melting curve analysis were performed on 567 samples in which SARS-CoV-2 viral RNA was detected by a multiplex PCR. Viral whole-genome sequencing (WGS) was performed to confirm the presence of SNPs and to identify the Pangolin lineage. Additionally, 1133 SARS-CoV-2 positive samples with SGTF were further assessed by WGS to determine the presence of ΔH69-V70. RESULTS The N501Y-specific assay (n = 567) had an overall percentage agreement (OPA) of 98.5%. The ΔH69-V70-specific (n = 178) and E484K-specific (n = 401) assays had OPA of 96.6% and 99.7%, respectively. Assessment of H655Y (n = 139) yielded a 100.0% concordance when applied in the proposed algorithm. The L452R-specific (n = 67) and P681R-specific (n = 62) assays had an OPA of 98.2% and 98.1%, respectively. The proposed algorithm identified six variants of concern/interest (VOC/VOI)-Alpha (n = 149), Beta (n = 65), Gamma (n = 86), Delta (n = 49), Eta (n = 6), Kappa (n = 6)-and 205 non-VOC/VOI strains-including the variants under monitoring B.1.214.2 (n = 43) and B.1.1.318 (n = 18) and Epsilon (n = 1). An excellent concordance was observed for the identification of all SARS-CoV-2 lineages evaluated. CONCLUSIONS We present a flexible testing algorithm for the rapid detection of current and emerging SARS-CoV-2 VOC/VOIs, which can be easily adapted based on the local endemicity of specific variants.
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Affiliation(s)
- Joachim Mertens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Jasmine Coppens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Katherine Loens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Marie Le Mercier
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Sarah Vandamme
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium
| | - Hilde Jansens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Herman Goossens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Veerle Matheeussen
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, University Hospital Antwerp, Edegem, Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Antwerp, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Wilrijk, Antwerp, Belgium.
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16
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Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak. PLoS One 2021; 16:e0255663. [PMID: 34506497 PMCID: PMC8432851 DOI: 10.1371/journal.pone.0255663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 07/21/2021] [Indexed: 11/19/2022] Open
Abstract
Measles outbreaks escalated globally despite worldwide elimination efforts. Molecular epidemiological investigations utilizing partial measles virus (MeV) genomes are challenged by reduction in global genotypes and low evolutionary rates. Greater resolution was reached using MeV complete genomes, however time and costs limit the application to numerous samples. We developed an approach to unbiasedly sequence complete MeV genomes directly from patient urine samples. Samples were enriched for MeV using filtration or nucleases and the minimal number of sequence reads to allocate per sample based on its MeV content was assessed using in-silico reduction of sequencing depth. Application of limited-resource sequencing to treated MeV-positive samples demonstrated that 1–5 million sequences for samples with high/medium MeV quantities and 10–15 million sequences for samples with lower MeV quantities are sufficient to obtain >98% MeV genome coverage and over X50 average depth. This approach enables real-time high-resolution molecular epidemiological investigations of large-scale MeV outbreaks.
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17
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Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res 2021; 31:635-644. [PMID: 33602693 PMCID: PMC8015855 DOI: 10.1101/gr.268961.120] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/12/2021] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we investigated 129 RNA-seq data sets and 6928 consensus genomes to contrast the intra-host and inter-host diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights intra-host single nucleotide variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael D Jochum
- Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA
| | - Yunxi Liu
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - R A Leo Elworth
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Qi Wang
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University, Houston, Texas 77005, USA
| | - Dreycey Albin
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University, Houston, Texas 77005, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, California 94043, USA
- Blue Marble Space Institute of Science, Seattle, Washington 98104, USA
| | - Sonia Villapol
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Kyle M Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | | | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, California 94035, USA
| | | | - Kjersti M Aagaard
- Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
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18
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Yuan D, Yan Z, Li M, Wang Y, Su M, Sun D. Isolation and Characterization of a Porcine Transmissible Gastroenteritis Coronavirus in Northeast China. Front Vet Sci 2021; 8:611721. [PMID: 33738304 PMCID: PMC7960647 DOI: 10.3389/fvets.2021.611721] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/05/2021] [Indexed: 12/26/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is a coronavirus (CoV) that is a major pathogenity of viral enteritis and diarrhea in suckling piglets, causing high morbidity and mortality. In this study, a TGEV strain HQ2016 was isolated from northeast China and characterized its genome sequence and pathogenicity. The phylogenetic analysis indicated that the TGEV HQ2016 strain was more similar to the TGEV Purdue cluster than to the Miller cluster. Both recombination and phylogenetic analysis based on each structural and non-structural gene revealed no recombination event in the HQ2016 strain. Experimental infection study using colostrum-deprived newborn piglets successfully showed that the HQ2016 can cause clinical symptoms including anorexia and yellow-to-whitish watery diarrhea, which are characteristics of TGE, in the inoculated piglets 48 h post-inoculation. These results provide valuable information about the evolution of the porcine CoVs.
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Affiliation(s)
- Dongwei Yuan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China.,Daqing Center of Inspection and Testing for Agricultural Products Ministry of Agriculture, Daqing, China
| | - Zihan Yan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mingyue Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yi Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mingjun Su
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dongbo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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19
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Lee L, Liu F, Chen Y, Roma G. Quantitative and Ultrasensitive In-situ Immunoassay Technology for SARS-CoV-2 Detection in Saliva. RESEARCH SQUARE 2021. [PMID: 33469572 PMCID: PMC7814831 DOI: 10.21203/rs.3.rs-138025/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic has become an immense global health crisis. However, the lack of efficient and sensitive on-site testing methods limits early detection for timely isolation and intervention. Here, we present a Quantitative and Ultrasensitive in-situ Immunoassay Technology for SARS-CoV-2 detection in saliva (QUIT SARS-CoV-2). Our nanoporous membrane resonator generates a rapid oscillating flow to purify and concentrate SARS-CoV-2 virus in saliva by 40 folds for in-situ detection of viral antigens based on chemiluminescent immunoassay within 20 min. This method achieved a detection sensitivity below 100 copies/mL viral load, comparable to the bench-top PCR equipment. The portable QUIT SARS-CoV-2 system, allowing rapid and accurate on-site viral screen with high-throughput sample pooling strategy, can be performed at the primary care settings and substantially improve the detection and prevention of COVID-19.
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20
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Jansen SA, Nijhuis W, Leavis HL, Riezebos-Brilman A, Lindemans CA, Schuurman R. Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics. Front Microbiol 2020; 11:560179. [PMID: 33281758 PMCID: PMC7705093 DOI: 10.3389/fmicb.2020.560179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Pediatric allogeneic hematopoietic stem cell transplantation (HSCT) patients often suffer from gastro-intestinal (GI) disease caused by viruses, Graft-versus-Host Disease (GVHD) or a combination of the two. Currently, the GI eukaryotic virome of HSCT recipients remains relatively understudied, which complicates the understanding of its role in GVHD pathogenicity. As decisions regarding immunosuppressive therapy in the treatment of virus infection or GVHD, respectively, can be completely contradicting, it is crucial to better understand the prevalence and relevance of viruses in the GI tract in the HSCT setting. A real time PCR panel for a set of specific viruses widely used to diagnose the most common causes of GI viral gastroenteritis is possibly insufficient to grasp the full extent of viruses present. Therefore, we applied the targeted sequence capture method ViroCap to residual fecal samples of 11 pediatric allogeneic HSCT recipients with GI symptoms and a suspicion of GVHD, to enrich for nucleic acids of viruses that are known to infect vertebrate hosts. After enrichment, NGS was applied to broadly detect viral sequences. Using ViroCap, we were able to detect viruses such as norovirus and adenovirus (ADV), that had been previously detected using clinical diagnostic PCR on the same sample. In addition, multiple, some of which clinically relevant viruses were detected, including ADV, human rhinovirus (HRV) and BK polyomavirus (BKV). Interestingly, in samples in which specific PCR testing for regular viral GI pathogens did not result in a diagnosis, the ViroCap pipeline led to the detection of viral sequences of human herpesvirus (HHV)-7, BKV, HRV, KI polyomavirus and astrovirus. The latter was an only recently described variant and showed extensive sequence mismatches with the applied real time PCR primers and would therefore not have been detected if tested. Our results indicate that target enrichment of viral nucleic acids through ViroCap leads to sensitive and broad possibly clinically relevant virus detection, including the detection of newer variants in clinical HSCT recipient samples. As such, ViroCap could be a useful detection tool clinically, but also in studying the associations between viral presence and GVHD.
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Affiliation(s)
- Suze A Jansen
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Wouter Nijhuis
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Caroline A Lindemans
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
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21
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Zhu N, Wong PK. Advances in Viral Diagnostic Technologies for Combating COVID-19 and Future Pandemics. SLAS Technol 2020; 25:513-521. [PMID: 32833548 PMCID: PMC8960186 DOI: 10.1177/2472630320953798] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/17/2020] [Accepted: 08/08/2020] [Indexed: 12/26/2022]
Abstract
The emergence of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens the health of the global population and challenges our preparedness for pandemic threats. Previous outbreaks of coronaviruses and other viruses have suggested the importance of diagnostic technologies in fighting viral outbreaks. Nucleic acid detection techniques are the gold standard for detecting SARS-CoV-2. Viral antigen tests and serological tests that detect host antibodies have also been developed for studying the epidemiology of COVID-19 and estimating the population that may have immunity to SARS-CoV-2. Nevertheless, the availability, cost, and performance of existing viral diagnostic technologies limit their practicality, and novel approaches are required for improving our readiness for global pandemics. Here, we review the principles and limitations of major viral diagnostic technologies and highlight recent advances of molecular assays for COVID-19. In addition, we discuss emerging technologies, such as clustered regularly interspaced short palindromic repeats (CRISPR) systems, high-throughput sequencing, and single-cell and single-molecule analysis, for improving our ability to understand, trace, and contain viral outbreaks. The prospects of viral diagnostic technologies for combating future pandemic threats are presented.
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Affiliation(s)
- Ninghao Zhu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
- Department of Mechanical Engineering and Department of Surgery, The Pennsylvania State University, University Park, PA, USA
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22
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Negrey JD, Thompson ME, Langergraber KE, Machanda ZP, Mitani JC, Muller MN, Otali E, Owens LA, Wrangham RW, Goldberg TL. Demography, life-history trade-offs, and the gastrointestinal virome of wild chimpanzees. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190613. [PMID: 32951554 PMCID: PMC7540950 DOI: 10.1098/rstb.2019.0613] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 12/11/2022] Open
Abstract
In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates-even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)-are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the faeces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We identified 12 viruses from at least four viral families possessing genomes of both single-stranded RNA and single-stranded DNA. Faecal viromes of both sexes varied with chimpanzee age, but viral richness increased with age only in males. This effect was largely due to three viruses, salivirus, porprismacovirus and chimpanzee stool-associated RNA virus (chisavirus), which occurred most frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Faecal viromes are therefore useful for studying processes related to the divergent reproductive strategies of males and females, ageing, and sex differences in longevity. This article is part of the theme issue 'Evolution of the primate ageing process'.
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Affiliation(s)
| | | | | | | | | | | | | | - Leah A. Owens
- University of Wisconsin-Madison, Madison, WI 53706, USA
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23
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Tan S, Dvorak CMT, Murtaugh MP. Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model. Viruses 2020; 12:v12101136. [PMID: 33036361 PMCID: PMC7600144 DOI: 10.3390/v12101136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases.
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24
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Abstract
When a mosquito feeds on a host, it ingests not only its blood meal but also an assortment of microorganisms that are present in the blood, thus acting as an environmental sampler. By using specific tests, it is possible to detect arthropod-borne viruses (arboviruses) like dengue and West Nile viruses in mosquito excreta. Here, we explored the use of next-generation sequencing (NGS) for unbiased detection of RNA viruses present in excreta from experimentally infected and field-collected mosquitoes. We have demonstrated that mosquito excreta provide a suitable template for NGS and that it is possible to recover and assemble near-full-length genomes of both arboviruses and insect-borne viruses, including potentially novel ones. These results importantly show the direct practicality of the use of mosquito excreta for NGS, which in the future could be used for virus discovery, environmental virome sampling, and arbovirus surveillance. Traditional screening for arboviruses in mosquitoes requires a priori knowledge and the utilization of appropriate assays for their detection. Mosquitoes can also provide other valuable information, including unexpected or novel arboviruses, nonarboviral pathogens ingested from hosts they feed on, and their own genetic material. Metagenomic analysis using next-generation sequencing (NGS) is a rapidly advancing technology that allows us to potentially obtain all this information from a mosquito sample without any prior knowledge of virus, host, or vector. Moreover, it has been recently demonstrated that pathogens, including arboviruses and parasites, can be detected in mosquito excreta by molecular methods. In this study, we investigated whether RNA viruses could be detected in mosquito excreta by NGS. Excreta samples were collected from Aedes vigilax and Culex annulirostris experimentally exposed to either Ross River or West Nile viruses and from field mosquitoes collected across Queensland, Australia. Total RNA was extracted from the excreta samples, reverse transcribed to cDNA, and sequenced using the Illumina NextSeq 500 platform. Bioinformatic analyses from the generated reads demonstrate that mosquito excreta provide sufficient RNA for NGS, allowing the assembly of near-full-length viral genomes. We detected Australian Anopheles totivirus, Wuhan insect virus 33, and Hubei odonate virus 5 and identified seven potentially novel viruses closely related to members of the order Picornavirales (2/7) and to previously described, but unclassified, RNA viruses (5/7). Our results suggest that metagenomic analysis of mosquito excreta has great potential for virus discovery and for unbiased arbovirus surveillance in the near future. IMPORTANCE When a mosquito feeds on a host, it ingests not only its blood meal but also an assortment of microorganisms that are present in the blood, thus acting as an environmental sampler. By using specific tests, it is possible to detect arthropod-borne viruses (arboviruses) like dengue and West Nile viruses in mosquito excreta. Here, we explored the use of next-generation sequencing (NGS) for unbiased detection of RNA viruses present in excreta from experimentally infected and field-collected mosquitoes. We have demonstrated that mosquito excreta provide a suitable template for NGS and that it is possible to recover and assemble near-full-length genomes of both arboviruses and insect-borne viruses, including potentially novel ones. These results importantly show the direct practicality of the use of mosquito excreta for NGS, which in the future could be used for virus discovery, environmental virome sampling, and arbovirus surveillance.
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25
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Samson R, Navale GR, Dharne MS. Biosensors: frontiers in rapid detection of COVID-19. 3 Biotech 2020; 10:385. [PMID: 32818132 PMCID: PMC7417775 DOI: 10.1007/s13205-020-02369-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/27/2020] [Indexed: 12/23/2022] Open
Abstract
The rapid community-spread of novel human coronavirus 2019 (nCOVID19 or SARS-Cov2) and morbidity statistics has put forth an unprecedented urge for rapid diagnostics for quick and sensitive detection followed by contact tracing and containment strategies, especially when no vaccine or therapeutics are known. Currently, quantitative real-time polymerase chain reaction (qRT-PCR) is being used widely to detect COVID-19 from various types of biological specimens, which is time-consuming, labor-intensive and may not be rapidly deployable in remote or resource-limited settings. This might lead to hindrance in acquiring realistic data of infectivity and community spread of SARS-CoV-2 in the population. This review summarizes the existing status of current diagnostic methods, their possible limitations, and the advantages of biosensor-based diagnostics over the conventional ones for the detection of SARS-Cov-2. Novel biosensors used to detect RNA-viruses include CRISPR-Cas9 based paper strip, nucleic-acid based, aptamer-based, antigen-Au/Ag nanoparticles-based electrochemical biosensor, optical biosensor, and Surface Plasmon Resonance. These could be effective tools for rapid, authentic, portable, and more promising diagnosis in the current pandemic that has affected the world economies and humanity. Present challenges and future perspectives of developing robust biosensors devices for rapid, scalable, and sensitive detection and management of COVID-19 are presented in light of the test-test-test theme of the World Health Organization (WHO).
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Affiliation(s)
- Rachel Samson
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-National Chemical, Laboratory, National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, Pune, India
| | - Govinda R. Navale
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-National Chemical, Laboratory, National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, Pune, India
| | - Mahesh S. Dharne
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-National Chemical, Laboratory, National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, Pune, India
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26
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Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck F, Treangen TJ. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.02.184481. [PMID: 32637955 PMCID: PMC7337385 DOI: 10.1101/2020.07.02.184481] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Michael D. Jochum
- Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Qi Wang
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Houston, TX
| | - Dreycey Albin
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Houston, TX
| | - Huw Ogilvie
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Michael D. Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA
- Blue Marble Space Institute of Science, Seattle, WA
| | | | - Kyle M. Hernandez
- Department of Medicine, University of Chicago, Chicago, IL
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | | | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA
| | - Krista Ternus
- Signature Science, LLC, 8329 North Mopac Expressway, Austin TX 78759
| | | | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology School of Biology, University of Vigo, Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Fritz Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
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27
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Tochetto C, de Lima DA, Varela APM, Ortiz LC, Loiko MR, Scheffer CM, Paim WP, Cibulski SP, Cerva C, Herpich J, Schmidt C, Franco AC, Mayer FQ, Roehe PM. Investigation on porcine circovirus type 3 in serum of farrowing sows with stillbirths. Microb Pathog 2020; 149:104316. [PMID: 32531497 DOI: 10.1016/j.micpath.2020.104316] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/26/2022]
Abstract
Since its first identification in 2016, porcine circovirus 3 (PCV3) has been detected in healthy and/or diseased swine in many countries worldwide. In a previous study by our group, PCV3 was detected in sera of sows which had at least one stillborn piglet in the last parturition. As such, it became important to investigate if the presence of PCV3 in sows' sera could be associated to the occurrence of stillbirths. With that aim, the frequency of PCV3 infections and viral DNA loads in sows' sera was investigated through a real-time quantitative PCR in 89 serum samples of just farrowed sows with or without stillbirths. PCV3 genomes were identified in most samples, with genome loads ranging between less than 10 to 200,000 copies per mL of serum. No significant differences were observed either in the frequency of infection or PCV3 viral loads in sows with or without stillbirths. Thus, no association could be established between PCV3 infection of sows at farrowing and stillbirths' occurrence.
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Affiliation(s)
- Caroline Tochetto
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diane Alves de Lima
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Paula Muterle Varela
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lucía Cano Ortiz
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Márcia Regina Loiko
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Camila Mengue Scheffer
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Willian Pinto Paim
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Paulo Cibulski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristine Cerva
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Juliana Herpich
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Candice Schmidt
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Claúdia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil.
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básica da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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28
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Martínez-Puchol S, Rusiñol M, Fernández-Cassi X, Timoneda N, Itarte M, Andrés C, Antón A, Abril JF, Girones R, Bofill-Mas S. Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136604. [PMID: 31955099 DOI: 10.1016/j.scitotenv.2020.136604] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 04/14/2023]
Abstract
NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before NGS. The selection of appropriate NGS tools is important for reliable identification of viral diversity among the population. We have compared different NGS methodologies (Untargeted Viral Metagenomics, Target Enrichment Sequencing and Amplicon Deep Sequencing) for the detection and characterisation of viruses in urban sewage, focusing on three important human pathogens: papillomaviruses, adenoviruses and enteroviruses. A full picture of excreted viruses was obtained by applying Untargeted Viral Metagenomics, which detected members of four different vertebrate viral families in addition to bacteriophages, plant viruses and viruses infecting other hosts. Target Enrichment Sequencing, using specific vertebrate viral probes, allowed the detection of up to eight families containing human viruses, with high variety of types within the families and with a high genome coverage. By applying Amplicon Deep Sequencing, the diversity of enteroviruses, adenoviruses and papillomaviruses observed was higher than when applying the other two strategies and this technique allowed the subtyping of an enterovirus A71 C1 strain related to a brainstem encephalitis outbreak occurring at the same time in the sampling area. From the data obtained, we concluded that the different strategies studied provided different levels of analysis: TES is the best strategy to obtain a broad picture of human viruses present in complex samples such as sewage. Other NGS strategies are useful for studying the virome of complex samples when also targeting viruses infecting plants, bacteria, invertebrates or fungi (Untargeted Viral Metagenomics) or when observing the variety within a sole viral family is the objective of the study (Amplicon Deep Sequencing).
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Affiliation(s)
- Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Fernández-Cassi
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep F Abril
- Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
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29
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Ehmann R, Brandes K, Antwerpen M, Walter M, V Schlippenbach K, Stegmaier E, Essbauer S, Bugert J, Teifke JP, Meyer H. Molecular and genomic characterization of a novel equine molluscum contagiosum-like virus. J Gen Virol 2020; 102. [PMID: 31922947 PMCID: PMC8515872 DOI: 10.1099/jgv.0.001357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cases of pox-like lesions in horses and donkeys have been associated with poxviruses belonging to different genera of the family Poxviridae. These include the orthopoxviruses vaccinia virus (VACV), horsepoxvirus (HPXV) and cowpoxvirus (CPXV), as well as a potentially novel parapoxvirus and molluscum contagiosum virus (MOCV). However, with the exception of VACV, HPXV and CPXV, the genomic characterization of the causative agents remains largely elusive with only single short genome fragments available. Here we present the first full-length genome sequence of an equine molluscum contagiosum-like virus (EMCLV) directly determined from skin biopsies of a horse with generalized papular dermatitis. Histopathological analysis of the lesions revealed severe epidermal hyperplasia with numerous eosinophilic inclusion bodies within keratinocytes. Virions were detected in the lesions in embedded tissue by transmission electron microscopy. The genome sequence determined by next- and third-generation sequencing comprises 166 843 nt with inverted terminal repeats (ITRs) of 3473 nt. Overall, 20 of the predicted 159 ORFs have no equivalents in other poxviruses. Intriguingly, two of these ORFs were identified to encode homologues of mammalian proteins involved in immune signalling pathways, namely secreted and transmembrane protein 1 (SECTM1) and insulin growth factor-like family receptor 1 (IGFLR1), that were not described in any virus family so far. Phylogenetic analysis with all relevant representatives of the Poxviridae suggests that EMCLV should be nominated as a new species within the genus Molluscipoxvirus.
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Affiliation(s)
- Rosina Ehmann
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - K Brandes
- Animal Pathology Augsburg, Augsburg, Germany
| | - M Antwerpen
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - M Walter
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - S Essbauer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - J Bugert
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - J P Teifke
- Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - H Meyer
- Bundeswehr Institute of Microbiology, Munich, Germany
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Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools. Viruses 2019; 11:v11121132. [PMID: 31817886 PMCID: PMC6950593 DOI: 10.3390/v11121132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Prompt detection and effective control of porcine reproductive and respiratory syndrome virus (PRRSV) during outbreaks is important given its immense adverse impact on the swine industry. However, the diagnostic process can be challenging due to the high genetic diversity and high mutation rate of PRRSV. A diagnostic method that can provide more detailed genetic information about pathogens is urgently needed. In this study, we evaluated the ability of Oxford Nanopore MinION direct RNA sequencing to generate a PRRSV whole genome sequence and detect and discriminate virus at the strain-level. A nearly full length PRRSV genome was successfully generated from raw sequence reads, achieving an accuracy of 96% after consensus genome generation. Direct RNA sequencing reliably detected the PRRSV strain present with an accuracy of 99.9% using as few as 5 raw sequencing reads and successfully differentiated multiple co-infecting strains present in a sample. In addition, PRRSV strain information was obtained from clinical samples containing 104 to 106 viral copies or more within 6 hours of sequencing. Overall, direct viral RNA sequencing followed by bioinformatic analysis proves to be a promising approach for identification of the viral strain or strains involved in clinical infections, allowing for more precise prevention and control strategies during PRRSV outbreaks.
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