Circular Whole-Transcriptome Amplification (cWTA) and mNGS Screening Enhanced by a Group Testing Algorithm (mEGA) Enable High-Throughput and Comprehensive Virus Identification
Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative th...
Uložené v:
| Vydané v: | mSphere Ročník 7; číslo 5; s. e0033222 |
|---|---|
| Hlavní autori: | , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
United States
American Society for Microbiology
26.10.2022
|
| Predmet: | |
| ISSN: | 2379-5042, 2379-5042 |
| On-line prístup: | Získať plný text |
| Tagy: |
Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
|
| Abstract | Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample.
Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (
n
= 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput.
IMPORTANCE
Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. |
|---|---|
| AbstractList | Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. ABSTRACT Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam ( = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance.Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. ABSTRACTMetagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput.IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam ( n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance. |
| Author | Patrick Reteng Mizanur Rahman Linh Nguyen Thuy Ana Maria Bispo de Filippis Lan Anh Nguyen Thi Kyoko Hayashida Gabriel Gonzalez William W. Hall Junya Yamagishi Tatsuki Sugi |
| Author_xml | – sequence: 1 givenname: Patrick surname: Reteng fullname: Reteng, Patrick organization: Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan – sequence: 2 givenname: Linh surname: Nguyen Thuy fullname: Nguyen Thuy, Linh organization: Laboratory for Molecular Diagnostics, National Institute of Epidemiology and Health, Hanoi, Vietnam – sequence: 3 givenname: Mizanur orcidid: 0000-0002-0665-7447 surname: Rahman fullname: Rahman, Mizanur organization: Evercare Hospital Dhaka, Dhaka, Bangladesh – sequence: 4 givenname: Ana Maria surname: Bispo de Filippis fullname: Bispo de Filippis, Ana Maria organization: Flavivirus Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil – sequence: 5 givenname: Kyoko surname: Hayashida fullname: Hayashida, Kyoko organization: Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan, International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan – sequence: 6 givenname: Tatsuki surname: Sugi fullname: Sugi, Tatsuki organization: Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan, International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan – sequence: 7 givenname: Gabriel surname: Gonzalez fullname: Gonzalez, Gabriel organization: National Virus Reference Laboratory, University College Dublin, Dublin, Ireland – sequence: 8 givenname: William W. surname: Hall fullname: Hall, William W. organization: School of Medicine and Medical Research, University College Dublin, Dublin, Ireland, Global Virus Network, Baltimore, Maryland, USA – sequence: 9 givenname: Lan Anh surname: Nguyen Thi fullname: Nguyen Thi, Lan Anh organization: Laboratory for Molecular Diagnostics, National Institute of Epidemiology and Health, Hanoi, Vietnam – sequence: 10 givenname: Junya orcidid: 0000-0002-8385-5359 surname: Yamagishi fullname: Yamagishi, Junya organization: Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan, International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan |
| BackLink | https://cir.nii.ac.jp/crid/1873961342875902208$$DView record in CiNii https://www.ncbi.nlm.nih.gov/pubmed/36005385$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9kkFv1DAQhSNUREvpnROyBIflkOLYiZ1ckFarZVupgkMXerRsZ5K4SuxgJ5X6q_iLeLtLaTlwsS3P56c34_c6ObLOQpK8zfB5lpHy0xDGDjycY0wpSQl5kZwQyqu0wDk5enI-Ts5CuMUYZ4wwxtmr5JgyjAtaFifJr5Xxeu6lRzed6yHdemmD9mac3ABoOYy9aYyWk3EWLfTNdvkRSVuj4evmGl1rD2CNbdHadtJqqJG6RxJtvJtHtIUw7WrLvnXeTN2AFsN6E9-vrVQ9oAvTdum2i2zbjfP0ILtyw-ihAxvMHaAfxs8BXdZgp0cTb5KXjewDnB320-T7l_V2dZFefdtcrpZXqWQET6mkDSkriJawUhmXVVPXVBKGuc6kxFlRskaDUjkticaFYhrygoHMQVeaypKeJpd73drJWzF6M0h_L5w04uHC-VZIPxndg9BacaBKEa6bnDe64iVTtSp0waIk1lHr815rnNUAtY79eNk_E31esaYTrbsTVVFVjO3MLA4C3v2c41zFYIKGvpcW3BwE4ZhxgkuWR_T9P-itm72No4oUxTz-fEYile4pGQbyl8iw2CVLHJIlHpIlyI5_97SDR-t_chQBvAe0dyF4aB6R_2h-2D-xxghtdmtWclqxjOak5EWFSWyJ_gaObOpZ |
| Cites_doi | 10.1016/j.biochi.2019.06.003 10.1128/jvi.76.18.9124-9134.2002 10.1016/B978-0-12-375156-0.00023-0 10.4269/ajtmh.16-0667 10.1038/nmeth.1923 10.1186/s12864-017-4428-5 10.1261/rna.078937.121 10.1186/s40168-018-0507-3 10.1155/2017/4248756 10.1073/pnas.202488399 10.1093/nar/20.11.2900 10.1101/gr.377203 10.1186/s40168-019-0658-x 10.1101/gr.113985.110 10.1016/j.bios.2012.09.011 10.1126/science.1229164 10.1038/s41576-019-0113-7 10.1186/1743-422X-10-58 10.1093/bioinformatics/btu808 10.1093/bioinformatics/btu170 10.1093/ofid/ofaa132 10.1093/bioinformatics/bty191 10.1038/s41598-021-98013-9 10.1093/bioinformatics/btp352 10.1186/s12879-019-4185-y 10.1016/j.jmii.2019.05.009 10.1186/1471-2199-9-77 10.1186/1471-2164-9-5 10.14806/ej.17.1.200 10.1128/jcm.30.4.845-853.1992 10.1186/s12915-020-00785-5 10.1128/jcm.30.3.545-551.1992 10.1038/s41467-019-11272-z 10.1371/journal.pone.0205356 10.1016/j.jviromet.2018.02.021 10.1038/s41586-020-2885-5 |
| ContentType | Journal Article |
| Copyright | Copyright © 2022 Reteng et al. Copyright © 2022 Reteng et al. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Copyright © 2022 Reteng et al. 2022 Reteng et al. |
| Copyright_xml | – notice: Copyright © 2022 Reteng et al. – notice: Copyright © 2022 Reteng et al. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: Copyright © 2022 Reteng et al. 2022 Reteng et al. |
| DBID | RYH AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7X7 7XB 8FE 8FH 8FI 8FJ 8FK ABUWG AFKRA AZQEC BBNVY BENPR BHPHI CCPQU COVID DWQXO FYUFA GHDGH GNUQQ HCIFZ K9. LK8 M0S M7P PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS 7X8 5PM DOA |
| DOI | 10.1128/msphere.00332-22 |
| DatabaseName | CiNii Complete CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Health & Medical Collection ProQuest Central (purchase pre-March 2016) ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest Central UK/Ireland ProQuest Central Essentials Biological Science Database ProQuest Central (ProQuest) Natural Science Collection ProQuest One Coronavirus Research Database ProQuest Central Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) ProQuest Biological Science Collection Health & Medical Collection (Alumni Edition) Biological Science Database ProQuest Central Premium ProQuest One Academic (New) Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Publicly Available Content Database ProQuest Central Student ProQuest One Academic Middle East (New) ProQuest Central Essentials ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Central China ProQuest Central ProQuest One Applied & Life Sciences ProQuest Health & Medical Research Collection Health Research Premium Collection Health and Medicine Complete (Alumni Edition) Natural Science Collection ProQuest Central Korea Biological Science Collection ProQuest Central (New) ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Coronavirus Research Database ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest SciTech Collection ProQuest Hospital Collection (Alumni) ProQuest Health & Medical Complete ProQuest One Academic UKI Edition ProQuest One Academic ProQuest One Academic (New) ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic Publicly Available Content Database CrossRef |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: PIMPY name: Publicly Available Content Database url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 2379-5042 |
| Editor | Pipas, James M. |
| Editor_xml | – sequence: 1 givenname: James M. surname: Pipas fullname: Pipas, James M. |
| ExternalDocumentID | oai_doaj_org_article_ccb7e3bb27cf47fc9786bdb5c5656e0c PMC9599668 00332-22 36005385 10_1128_msphere_00332_22 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GeographicLocations | Bangladesh |
| GeographicLocations_xml | – name: Bangladesh |
| GrantInformation_xml | – fundername: MEXT | Japan Society for the Promotion of Science (JSPS) grantid: 120208101 funderid: https://doi.org/10.13039/501100001691 – fundername: MEXT | Japan Society for the Promotion of Science (JSPS) grantid: 15H05272 funderid: https://doi.org/10.13039/501100001691 – fundername: ; grantid: 120208101 – fundername: ; grantid: 15H05272 |
| GroupedDBID | 0R~ 53G 5VS 7X7 8FE 8FH 8FI 8FJ AAFWJ AAGFI AAUOK ABUWG ADBBV AFFHD AFKRA AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS BBNVY BCNDV BENPR BHPHI BPHCQ BVXVI CCPQU DIK EBS FRP FYUFA GROUPED_DOAJ H13 HCIFZ HMCUK HYE KQ8 LK8 M48 M7P M~E O9- OK1 PGMZT PHGZM PHGZT PIMPY PQGLB PQQKQ PROAC R9- RHI RPM RSF RYH UKHRP AAYXX CITATION ALIPV CGR CUY CVF ECM EIF NPM 3V. BBAFP PQEST PQUKI PRINS RHF 7XB 8FK AZQEC COVID DWQXO GNUQQ K9. PJZUB PKEHL PPXIY 7X8 5PM |
| ID | FETCH-LOGICAL-a620t-a3f289eced0bb17a9fdd3a2607c1aa01586fcebb4382c05b6ce456ea4ec9c3a83 |
| IEDL.DBID | 7X7 |
| ISICitedReferencesCount | 1 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000844533700001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 2379-5042 |
| IngestDate | Mon Nov 10 04:30:19 EST 2025 Tue Nov 04 02:07:28 EST 2025 Sun Nov 09 14:23:06 EST 2025 Sat Nov 29 14:51:41 EST 2025 Thu Oct 27 05:09:28 EDT 2022 Thu Apr 03 07:00:31 EDT 2025 Sat Nov 29 03:33:49 EST 2025 Mon Nov 10 09:16:31 EST 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 5 |
| Keywords | metagenomic group testing algorithm comprehensive pathogen detection multiple displacement amplification febrile illness |
| Language | English |
| License | This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. https://creativecommons.org/licenses/by/4.0 This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a620t-a3f289eced0bb17a9fdd3a2607c1aa01586fcebb4382c05b6ce456ea4ec9c3a83 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 The authors declare no conflict of interest. |
| ORCID | 0000-0002-3711-1375 0000-0002-0665-7447 0000-0002-8385-5359 |
| OpenAccessLink | https://www.proquest.com/docview/2730736012?pq-origsite=%requestingapplication% |
| PMID | 36005385 |
| PQID | 2730736012 |
| PQPubID | 2045592 |
| PageCount | 10 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_ccb7e3bb27cf47fc9786bdb5c5656e0c pubmedcentral_primary_oai_pubmedcentral_nih_gov_9599668 proquest_miscellaneous_2706720864 proquest_journals_2730736012 asm2_journals_10_1128_msphere_00332_22 pubmed_primary_36005385 crossref_primary_10_1128_msphere_00332_22 nii_cinii_1873961342875902208 |
| PublicationCentury | 2000 |
| PublicationDate | 2022-10-26 |
| PublicationDateYYYYMMDD | 2022-10-26 |
| PublicationDate_xml | – month: 10 year: 2022 text: 2022-10-26 day: 26 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States – name: 1752 N St., N.W., Washington, DC – name: Washington |
| PublicationTitle | mSphere |
| PublicationTitleAbbrev | mSphere |
| PublicationTitleAlternate | mSphere |
| PublicationYear | 2022 |
| Publisher | American Society for Microbiology |
| Publisher_xml | – name: American Society for Microbiology |
| References | e_1_3_3_17_2 e_1_3_3_16_2 e_1_3_3_19_2 e_1_3_3_38_2 e_1_3_3_18_2 e_1_3_3_13_2 e_1_3_3_36_2 e_1_3_3_12_2 e_1_3_3_37_2 e_1_3_3_34_2 e_1_3_3_14_2 e_1_3_3_35_2 e_1_3_3_32_2 e_1_3_3_33_2 e_1_3_3_11_2 e_1_3_3_30_2 e_1_3_3_10_2 e_1_3_3_31_2 e_1_3_3_6_2 e_1_3_3_5_2 e_1_3_3_8_2 e_1_3_3_7_2 e_1_3_3_28_2 e_1_3_3_9_2 e_1_3_3_27_2 e_1_3_3_29_2 e_1_3_3_24_2 e_1_3_3_23_2 e_1_3_3_26_2 e_1_3_3_25_2 e_1_3_3_2_2 e_1_3_3_20_2 e_1_3_3_4_2 e_1_3_3_22_2 e_1_3_3_3_2 Dorfman R (e_1_3_3_15_2) 1974; 2 e_1_3_3_21_2 Vina-Rodriguez, A, Sachse, K, Ziegler, U, Chaintoutis, SC, Keller, M, Groschup, MH, Eiden, M (B5) 2017; 2017 Li, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N, Marth, G, Abecasis, G, Durbin, R (B25) 2009; 25 Lage, JM, Leamon, JH, Pejovic, T, Hamann, S, Lacey, M, Dillon, D, Segraves, R, Vossbrinck, B, González, A, Pinkel, D, Albertson, DG, Costa, J, Lizardi, PM (B11) 2003; 13 Patel, P, Landt, O, Kaiser, M, Faye, O, Koppe, T, Lass, U, Sall, AA, Niedrig, M (B23) 2013; 10 MacConaill, LE, Burns, RT, Nag, A, Coleman, HA, Slevin, MK, Giorda, K, Light, M, Lai, K, Jarosz, M, McNeill, MS, Ducar, MD, Meyerson, M, Thorner, AR (B18) 2018; 19 Robinson, ML, Manabe, YC (B2) 2017; 96 Chiu, CY, Miller, SA (B4) 2019; 20 Dorfman, R (B14) 1974; 2 Mutesa, L, Ndishimye, P, Butera, Y, Souopgui, J, Uwineza, A, Rutayisire, R, Ndoricimpaye, EL, Musoni, E, Rujeni, N, Nyatanyi, T, Ntagwabira, E, Semakula, M, Musanabaganwa, C, Nyamwasa, D, Ndashimye, M, Ujeneza, E, Mwikarago, IE, Muvunyi, CM, Mazarati, JB, Nsanzimana, S, Turok, N, Ndifon, W (B15) 2021; 589 Djikeng, A, Halpin, R, Kuzmickas, R, DePasse, J, Feldblyum, J, Sengamalay, N, Afonso, C, Zhang, X, Anderson, NG, Ghedin, E, Spiro, DJ (B8) 2008; 9 Martin, M (B26) 2011; 17 Wintersinger, JA, Wasmuth, JD (B37) 2015; 31 Servant, A, Laperche, S, Lallemand, F, Marinho, V, De Saint Maur, G, Meritet, JF, Garbarg-Chenon, A (B32) 2002; 76 Sosa-Jurado, F, Meléndez-Mena, D, Rosas-Murrieta, NH, Guzmán-Flores, B, Mendoza-Torres, MA, Barcenas-Villalobos, R, Márquez-Domínguez, L, Cortés-Hernández, P, Reyes-Leyva, J, Vallejo-Ruiz, V, Santos-López, G (B33) 2018; 13 Sim, JY, Chang, LY, Chen, JM, Lee, PI, Huang, LM, Lu, CY (B16) 2019; 52 Langmead, B, Salzberg, SL (B29) 2012; 9 Reteng, P, Nguyen Thuy, L, Tran Thi Minh, T, Mares-Guia, MAM, de, M, Torres, MC, de Filippis, AMB, Orba, Y, Kobayashi, S, Hayashida, K, Sawa, H, Hall, WW, Nguyen Thi, LA, Yamagishi, J (B19) 2021; 11 Froussard, P (B7) 1992; 20 Burrell, CJ, Howard, CR, Murphy, FA (B17) 2017 Wang, J-H, Cheng, L, Wang, C-H, Ling, W-S, Wang, S-W, Lee, G-B (B35) 2013; 41 Whetsell, AJ, Drew, JB, Milman, G, Hoff, R, Dragon, EA, Adler, K, Hui, J, Otto, P, Gupta, P, Farzadegan, H, Wolinsky, SM (B36) 1992; 30 Soneson, C, Yao, Y, Bratus-Neuenschwander, A, Patrignani, A, Robinson, MD, Hussain, S (B9) 2019; 10 Kumata, R, Ito, J, Takahashi, K, Suzuki, T, Sato, K (B31) 2020; 18 Grünberger, F, Ferreira-Cerca, S, Grohmann, D (B10) 2022; 28 Ning, L, Wang, X, Xu, K, Song, S, Li, Q, Yang, X (B20) 2019; 163 Lanciotti, RS, Calisher, CH, Gubler, DJ, Chang, GJ, Vorndam, AV (B34) 1992; 30 Zong, C, Lu, S, Chapman, AR, Xie, XS (B21) 2012; 338 Hu, H, Jung, K, Wang, Q, Saif, LJ, Vlasova, AN (B6) 2018; 256 Li, H (B24) 2018; 34 Wangdi, K, Kasturiaratchi, K, Nery, SV, Lau, CL, Gray, DJ, Clements, ACA (B1) 2019; 19 Wright, WF, Auwaerter, PG (B3) 2020; 7 Kiełbasa, SM, Wan, R, Sato, K, Horton, P, Frith, MC (B30) 2011; 21 Bolger, AM, Lohse, M, Usadel, B (B27) 2014; 30 Berthet, N, Reinhardt, AK, Leclercq, I, Van Ooyen, S, Batéjat, C, Dickinson, P, Stamboliyska, R, Old, IG, Kong, KA, Dacheux, L, Bourhy, H, Kennedy, GC, Korfhage, C, Cole, ST, Manuguerra, JC (B12) 2008; 9 Parras-Moltó, M, Rodríguez-Galet, A, Suárez-Rodríguez, P, López-Bueno, A (B13) 2018; 6 Breitbart, M, Salamon, P, Andresen, B, Mahaffy, JM, Segall, AM, Mead, D, Azam, F, Rohwer, F (B22) 2002; 99 Clarke, EL, Taylor, LJ, Zhao, C, Connell, A, Lee, J-J, Fett, B, Bushman, FD, Bittinger, K (B28) 2019; 7 |
| References_xml | – ident: e_1_3_3_21_2 doi: 10.1016/j.biochi.2019.06.003 – ident: e_1_3_3_33_2 doi: 10.1128/jvi.76.18.9124-9134.2002 – ident: e_1_3_3_18_2 doi: 10.1016/B978-0-12-375156-0.00023-0 – ident: e_1_3_3_3_2 doi: 10.4269/ajtmh.16-0667 – ident: e_1_3_3_30_2 doi: 10.1038/nmeth.1923 – ident: e_1_3_3_19_2 doi: 10.1186/s12864-017-4428-5 – ident: e_1_3_3_11_2 doi: 10.1261/rna.078937.121 – volume: 2 start-page: 347 year: 1974 ident: e_1_3_3_15_2 article-title: The detection of defective members of large populations publication-title: Statistics (Berlin) – ident: e_1_3_3_14_2 doi: 10.1186/s40168-018-0507-3 – ident: e_1_3_3_6_2 doi: 10.1155/2017/4248756 – ident: e_1_3_3_23_2 doi: 10.1073/pnas.202488399 – ident: e_1_3_3_8_2 doi: 10.1093/nar/20.11.2900 – ident: e_1_3_3_12_2 doi: 10.1101/gr.377203 – ident: e_1_3_3_29_2 doi: 10.1186/s40168-019-0658-x – ident: e_1_3_3_31_2 doi: 10.1101/gr.113985.110 – ident: e_1_3_3_36_2 doi: 10.1016/j.bios.2012.09.011 – ident: e_1_3_3_22_2 doi: 10.1126/science.1229164 – ident: e_1_3_3_5_2 doi: 10.1038/s41576-019-0113-7 – ident: e_1_3_3_24_2 doi: 10.1186/1743-422X-10-58 – ident: e_1_3_3_38_2 doi: 10.1093/bioinformatics/btu808 – ident: e_1_3_3_28_2 doi: 10.1093/bioinformatics/btu170 – ident: e_1_3_3_4_2 doi: 10.1093/ofid/ofaa132 – ident: e_1_3_3_25_2 doi: 10.1093/bioinformatics/bty191 – ident: e_1_3_3_20_2 doi: 10.1038/s41598-021-98013-9 – ident: e_1_3_3_26_2 doi: 10.1093/bioinformatics/btp352 – ident: e_1_3_3_2_2 doi: 10.1186/s12879-019-4185-y – ident: e_1_3_3_17_2 doi: 10.1016/j.jmii.2019.05.009 – ident: e_1_3_3_13_2 doi: 10.1186/1471-2199-9-77 – ident: e_1_3_3_9_2 doi: 10.1186/1471-2164-9-5 – ident: e_1_3_3_27_2 doi: 10.14806/ej.17.1.200 – ident: e_1_3_3_37_2 doi: 10.1128/jcm.30.4.845-853.1992 – ident: e_1_3_3_32_2 doi: 10.1186/s12915-020-00785-5 – ident: e_1_3_3_35_2 doi: 10.1128/jcm.30.3.545-551.1992 – ident: e_1_3_3_10_2 doi: 10.1038/s41467-019-11272-z – ident: e_1_3_3_34_2 doi: 10.1371/journal.pone.0205356 – ident: e_1_3_3_7_2 doi: 10.1016/j.jviromet.2018.02.021 – ident: e_1_3_3_16_2 doi: 10.1038/s41586-020-2885-5 – volume: 11 start-page: 1 year: 2021 end-page: 9 ident: B19 article-title: A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses publication-title: Sci Rep doi: 10.1038/s41598-021-98013-9 – volume: 52 start-page: 534 year: 2019 end-page: 541 ident: B16 article-title: Human parvovirus B19 infection in patients with or without underlying diseases publication-title: J Microbiol Immunol Infect doi: 10.1016/j.jmii.2019.05.009 – volume: 9 start-page: 77 year: 2008 end-page: 77 ident: B12 article-title: ϕ29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR publication-title: BMC Mol Biol doi: 10.1186/1471-2199-9-77 – volume: 76 start-page: 9124 year: 2002 end-page: 9134 ident: B32 article-title: Genetic diversity within human erythroviruses: identification of three genotypes publication-title: J Virol doi: 10.1128/jvi.76.18.9124-9134.2002 – volume: 9 start-page: 5 year: 2008 end-page: 9 ident: B8 article-title: Viral genome sequencing by random priming methods publication-title: BMC Genomics doi: 10.1186/1471-2164-9-5 – volume: 19 start-page: 1 year: 2018 end-page: 10 ident: B18 article-title: Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing publication-title: BMC Genomics doi: 10.1186/s12864-017-4428-5 – volume: 13 year: 2018 ident: B33 article-title: Effectiveness of PCR primers for the detection of occult hepatitis B virus infection in Mexican patients publication-title: PLoS One doi: 10.1371/journal.pone.0205356 – volume: 256 start-page: 116 year: 2018 end-page: 122 ident: B6 article-title: Development of a one-step RT-PCR assay for detection of pancoronaviruses (α-, β-, γ-, and δ-coronaviruses) using newly designed degenerate primers for porcine and avian fecal samples publication-title: J Virol Methods doi: 10.1016/j.jviromet.2018.02.021 – volume: 2 start-page: 347 year: 1974 end-page: 370 ident: B14 article-title: The detection of defective members of large populations publication-title: Statistics (Berlin) – volume: 20 start-page: 341 year: 2019 end-page: 355 ident: B4 article-title: Clinical metagenomics publication-title: Nat Rev Genet doi: 10.1038/s41576-019-0113-7 – volume: 17 start-page: 10 year: 2011 ident: B26 article-title: Cutadapt removes adapter sequences from high-throughput sequencing reads publication-title: EMBnet J doi: 10.14806/ej.17.1.200 – volume: 30 start-page: 845 year: 1992 end-page: 853 ident: B36 article-title: Comparison of three nonradioisotopic polymerase chain reaction-based methods for detection of human immunodeficiency virus type 1 publication-title: J Clin Microbiol doi: 10.1128/jcm.30.4.845-853.1992 – volume: 30 start-page: 2114 year: 2014 end-page: 2120 ident: B27 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu170 – volume: 41 start-page: 484 year: 2013 end-page: 491 ident: B35 article-title: An integrated chip capable of performing sample pretreatment and nucleic acid amplification for HIV-1 detection publication-title: Biosens Bioelectron doi: 10.1016/j.bios.2012.09.011 – volume: 2017 start-page: 4248756 year: 2017 ident: B5 article-title: A novel pan-flavivirus detection and identification assay based on RT-qPCR and microarray publication-title: Biomed Res Int doi: 10.1155/2017/4248756 – volume: 10 start-page: 1 year: 2019 end-page: 14 ident: B9 article-title: A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes publication-title: Nat Commun doi: 10.1038/s41467-019-11272-z – volume: 9 start-page: 357 year: 2012 end-page: 359 ident: B29 article-title: Fast gapped-read alignment with Bowtie 2 publication-title: Nat Methods doi: 10.1038/nmeth.1923 – volume: 31 start-page: 1305 year: 2015 end-page: 1306 ident: B37 article-title: Kablammo: an interactive, web-based BLAST results visualizer publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu808 – volume: 13 start-page: 294 year: 2003 end-page: 307 ident: B11 article-title: Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH publication-title: Genome Res doi: 10.1101/gr.377203 – volume: 30 start-page: 545 year: 1992 end-page: 551 ident: B34 article-title: Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction publication-title: J Clin Microbiol doi: 10.1128/jcm.30.3.545-551.1992 – volume: 96 start-page: 1285 year: 2017 end-page: 1295 ident: B2 article-title: Reducing uncertainty for acute febrile illness in resource-limited settings: the current diagnostic landscape publication-title: Am J Trop Med Hyg doi: 10.4269/ajtmh.16-0667 – volume: 10 start-page: 58 year: 2013 ident: B23 article-title: Development of one-step quantitative reverse transcription PCR for the rapid detection of flaviviruses publication-title: Virol J doi: 10.1186/1743-422X-10-58 – volume: 338 start-page: 1622 year: 2012 end-page: 1626 ident: B21 article-title: Genome-wide detection of single-nucleotide and copy-number variations of a single human cell publication-title: Science doi: 10.1126/science.1229164 – volume: 25 start-page: 2078 year: 2009 end-page: 2079 ident: B25 article-title: The Sequence Alignment/Map format and SAMtools publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp352 – start-page: 317 year: 2017 end-page: 344 ident: B17 publication-title: Fenner and White’s Medical Virology ;5th ed ;Academic Press ;London, England – volume: 34 start-page: 3094 year: 2018 end-page: 3100 ident: B24 article-title: Minimap2: pairwise alignment for nucleotide sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty191 – volume: 20 start-page: 2900 year: 1992 ident: B7 article-title: A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA publication-title: Nucleic Acids Res doi: 10.1093/nar/20.11.2900 – volume: 19 start-page: 577 year: 2019 ident: B1 article-title: Diversity of infectious aetiologies of acute undifferentiated febrile illnesses in South and Southeast Asia: a systematic review publication-title: BMC Infect Dis doi: 10.1186/s12879-019-4185-y – volume: 7 start-page: ofaa132 year: 2020 ident: B3 article-title: Fever and fever of unknown origin: review, recent advances, and lingering dogma publication-title: Open Forum Infect Dis doi: 10.1093/ofid/ofaa132 – volume: 163 start-page: 137 year: 2019 end-page: 141 ident: B20 article-title: A novel isothermal method using rolling circle reverse transcription for accurate amplification of small RNA sequences publication-title: Biochimie doi: 10.1016/j.biochi.2019.06.003 – volume: 7 start-page: 46 year: 2019 ident: B28 article-title: Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments publication-title: Microbiome doi: 10.1186/s40168-019-0658-x – volume: 28 start-page: 400 year: 2022 end-page: 417 ident: B10 article-title: Nanopore sequencing of RNA and cDNA molecules in Escherichia coli publication-title: RNA doi: 10.1261/rna.078937.121 – volume: 589 start-page: 276 year: 2021 end-page: 280 ident: B15 article-title: A pooled testing strategy for identifying SARS-CoV-2 at low prevalence publication-title: Nature doi: 10.1038/s41586-020-2885-5 – volume: 21 start-page: 487 year: 2011 end-page: 493 ident: B30 article-title: Adaptive seeds tame genomic sequence comparison publication-title: Genome Res doi: 10.1101/gr.113985.110 – volume: 18 start-page: 55 year: 2020 ident: B31 article-title: A tissue level atlas of the healthy human virome publication-title: BMC Biol doi: 10.1186/s12915-020-00785-5 – volume: 99 start-page: 14250 year: 2002 end-page: 14255 ident: B22 article-title: Genomic analysis of uncultured marine viral communities publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.202488399 – volume: 6 start-page: 119 year: 2018 ident: B13 article-title: Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses publication-title: Microbiome doi: 10.1186/s40168-018-0507-3 |
| SSID | ssj0001626676 |
| Score | 2.206071 |
| Snippet | Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the... Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in... ABSTRACTMetagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in... ABSTRACT Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis,... |
| SourceID | doaj pubmedcentral proquest asm2 pubmed crossref nii |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Publisher |
| StartPage | e0033222 |
| SubjectTerms | Algorithms Chikungunya virus Clinical Microbiology comprehensive pathogen detection Dengue fever Diagnosis Feasibility studies febrile illness Genomes group testing algorithm Hepatitis B High-Throughput Nucleotide Sequencing High-Throughput Nucleotide Sequencing - methods High-throughput screening Humans Infectious diseases metagenomic Metagenomics Microbiology multiple displacement amplification Next-generation sequencing Nucleic Acids Parvoviruses Pathogens QR1-502 Research Article RNA Transcriptome Transcriptomes Viruses |
| SummonAdditionalLinks | – databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3db9MwELdQBRIviG_CNmQkhLaHsNT5sP1Ypm48VUgrbG-RfXFoJJJOaYq0v2r_IndOWlqE4IWXKIqd6Jw734d9_h1j76R2FkCo0CQxhGih8E4VMhQ2IXw5WWS69MUm5Gymrq_1551SX5QT1sMD9z_uFMBKF1srJJSJLAGjnswWNgXyRFwEpH0jqXeCKb-6gn56Jrf7kkKd1is6pu8-UPEyEVKt3JFZ1WLPHHnUfjQyTVX9yeH8PW9yxxCdP2aPBg-ST3rKn7B7rnnKHvQ1JW-fsbuzqvW5pfyKSt-G3hh51bCsHZ9QAnk5rNPxY7iaT064aQpezy4u-SVQFg4aMz5tFj41gNtbbrhfoOJzAuTAtsn3b8u26hY1P66nF_j-1J-_4pQyEs77uj83685_ltRN6xZ9ljz_WrXrFe_PBm-IeM6-nE_nZ5_CoSpDaDIRdaGJSwzSHJIQWTuWRpdFERsMiySMjUHvQmUlOGtphxGi1Gbg0ElzJnGgITYqfsFGzbJxrxiPbKojQAfKJEmSWmHROUpQeKwuM-OyKGDviUf5MK1WuY9YhMoHZuaembkQATvZcDG_6VE6_tL3I7F524_wtf0DlLp8kLr8X1IXsCMUkhwquo6VjDW6RRR9EhqOiFTADjfi84t6HCgqVIyAkYa322aczrRHYxq3XFMf2hvHODMJ2Mte2raU4quoMlUaMLknh3tD2W9pqoWHDNeEwpOp1_9j7AfsoaAzIGjARXbIRl27dkfsPvzoqlX7xs_Dn6VcOjc priority: 102 providerName: Directory of Open Access Journals |
| Title | Circular Whole-Transcriptome Amplification (cWTA) and mNGS Screening Enhanced by a Group Testing Algorithm (mEGA) Enable High-Throughput and Comprehensive Virus Identification |
| URI | https://cir.nii.ac.jp/crid/1873961342875902208 https://www.ncbi.nlm.nih.gov/pubmed/36005385 https://journals.asm.org/doi/10.1128/msphere.00332-22 https://www.proquest.com/docview/2730736012 https://www.proquest.com/docview/2706720864 https://pubmed.ncbi.nlm.nih.gov/PMC9599668 https://doaj.org/article/ccb7e3bb27cf47fc9786bdb5c5656e0c |
| Volume | 7 |
| WOSCitedRecordID | wos000844533700001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 2379-5042 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001626676 issn: 2379-5042 databaseCode: DOA dateStart: 20160101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 2379-5042 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001626676 issn: 2379-5042 databaseCode: M~E dateStart: 20160101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 2379-5042 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001626676 issn: 2379-5042 databaseCode: M7P dateStart: 20150101 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 2379-5042 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001626676 issn: 2379-5042 databaseCode: 7X7 dateStart: 20150101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 2379-5042 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001626676 issn: 2379-5042 databaseCode: BENPR dateStart: 20150101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database customDbUrl: eissn: 2379-5042 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0001626676 issn: 2379-5042 databaseCode: PIMPY dateStart: 20150101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1bb9MwFLagA4kX7rDAVhkJoe0hLHMudp5QN2WDB6qKFVaeIttx1khLWpIWab-Kv8g5TtpShPbCS1TFTnXSfj43H5-PkLc8NkprJlwZ-NoFCwWfRMZdpgLsL8ezKM4t2QQfDsVkEo-6hFvTlVWudKJV1NlMY478CMwsoBHCB_Zh_sNF1ijcXe0oNO6SHaTNRpzzCd_kWMBbj_h6d5KJo7LBw_rmPVKYMRcZc3uyKdmWUbK9-8HUVEXxL7fz7-rJP8zR2aP_fZHH5GHniNJBi5wn5I6pnpL7LTXlzTPy67SobYkqvUQGXdfaNKthZqWhA6xDz7t0Hz3Ql-PBIZVVRsvh-QW90FjMAzaRJtXUVhhQdUMltXkuOsa-HjA2uL4CsRbTkh6UyTk8n9hjXBQrT9xxSx80Xy7s16LWqs20Lban34p62dD2iPFKiOfk61kyPv3oduQOroyYt3Cln0OsZ0AET6ljLuM8y3wJ0RXXx1KCkyKiXBulcKNSe6GKtAFfz8jA6Fj7UvgvSK-aVWaXUE-Fsafhd5VBEISKKfCxAsCgivNImshzyDv8k9NudTapDXyYSDs0pBYNKWMOOVzBIJ23zT5umXuCOFnPwzbd9sasvkq7VZ9qrbjxlWJc5wHPNYTskcpUqNGNNp52yD6gLNUFXhHAMXhXGMRiUx3mCYfsrTC0kX4DIIe8WQ-DVsCtHlmZ2RLn4BY7hKuBQ162cF1LCo-C5hWhQ_gWkLdeZXukKqa283iMzXwi8ep2sV6TBwwPiYCFZ9Ee6S3qpdkn9_TPRdHUfbtE7VX0yc5JMhx96dtMSB_rbkdwb_Tp8-j7b0kqTIM |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1bb9MwFLZGB4IX7pfABkYCtD2EpU4aJw8IldFt1baq0jo2noLtOGskkpa0BfVPwV_kHCdpKUJ72wMvURU7ket852Yfn4-QVzzUUikW2MJzlQ0WCn4FMbeZ9LC-HI_9MDFkE7zXC87Pw_4a-VmfhcG0ylonGkUdjxSuke-AmQU0QvjA3o-_2cgahburNYVGCYtDPf8BIdvkXfcjfN_XjO11BrsHdsUqYAufOVNbuAkEGVrp2JGyyUWYxLErwK3nqikEWMfAT5SWEnfIlNOSvtLgZGjhaRUqVwQuvPcaWfcA7E6DrPe7x_3Py1UdiA98vtgPZcFONsHyAPotkqYxGzl6G2KSsRUzaNgCwLjlafovR_fvfM0_DODenf9t6u6S25WrTdulbNwjazq_T26U5JvzB-TXblqYJFx6hhzBtrHaRoeOMk3bmGmfVAuadEudDdrbVOQxzXr7J_REYboSWH3ayYcmh4LKORXUrOTRAVYugbb21wuYhukwo1tZZx-e75iDahRza-xBSZA0nk3Na1EvF3pYHiegn9JiNqHlIep6EA_J6ZXM1iPSyEe5fkKoI1uho-A7Cs_zWpJJ8CI9kDIZJr7QvmORNwiqqNI_k8iEdiyIKvRFBn0RYxbZrmEXjctyJpf0_YC4XPTDQuTmxqi4iCq9FikluXalZFwlHk9UyANfxrKlMFDQjrLIJqA6UilemwF3Q_AfMUzHskHMCSyyUWN2OfolYC3yctEMeg83s0SuRzPsg0kEEJB7FnlcisdipPAo2JagZRG-Ijgrf2W1JU-HprZ6iOWK_ODp5cN6QW4eDI6PoqNu7_AZucXwSAz4M8zfII1pMdOb5Lr6Pk0nxfNKQVDy5aoF6zfa-ag3 |
| linkToPdf | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V3Nb9MwFLdGB4gL3x-BDYwEaDuEpk4aJweEuq0d01BVsY7tFmzHWSORtCQtqH8Vd_463nPSliK02w5coip2Itf5vS_7-f0IecVDLZVigS08V9lgoeBXEHObSQ_ry_HYDxNDNsH7_eD8PBxskF-LszCYVrnQiUZRx2OFa-RNMLOARggfWDOp0yIGB733k282MkjhTuuCTqOCyLGe_4DwrXx3dADf-jVjve5w_4NdMwzYwmfO1BZuAgGHVjp2pGxxESZx7Apw8blqCQGWMvATpaXE3TLltKWvNDgcWnhahcoVgQvvvUY2uQtBT4Ns7nX7g0-rFR6IFXy-3BtlQTMrsVSAfosEasxGvt6GKDO2ZhINcwAYujxN_-X0_p27-Ycx7N35n6fxLrldu-C0U8nMPbKh8_vkRkXKOX9Afu6nhUnOpWfIHWwba2506zjTtIMZ-Em90El31Nmws0tFHtOsf3hCTxSmMYE3QLv5yORWUDmngpoVPjrEiibQ1vl6AdMwHWV0J-sewvNdc4CNYs6NPayIkyazqXkt6utCj6pjBvRzWsxKWh2uXgziITm9ktl6RBr5ONdPCHVkO3QUfFPheV5bMgnepQfSJ8PEF9p3LPIGARbVeqmMTMjHgqhGYmSQGDFmkd0FBKNJVebkkr57iNFlPyxQbm6Mi4uo1neRUpJrV0rGVeLxRIU88GUs2woDCO0oi2wDwiOV4rUVgASBX4nhO5YTYk5gka0FflejX4HXIi-XzaAPcZNL5Ho8wz6YXACBumeRx5WoLEcKj4LNCdoW4WtCtPZX1lvydGRqrodYxsgPnl4-rBfkJkhT9PGof_yM3GJ4UgbcHOZvkca0mOltcl19n6Zl8bzWFZR8uWq5-g3NcrDR |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Circular+Whole-Transcriptome+Amplification+%28cWTA%29+and+mNGS+Screening+Enhanced+by+a+Group+Testing+Algorithm+%28mEGA%29+Enable+High-Throughput+and+Comprehensive+Virus+Identification&rft.jtitle=mSphere&rft.au=Reteng%2C+Patrick&rft.au=Nguyen+Thuy%2C+Linh&rft.au=Rahman%2C+Mizanur&rft.au=Bispo+de+Filippis%2C+Ana+Maria&rft.date=2022-10-26&rft.issn=2379-5042&rft.eissn=2379-5042&rft.volume=7&rft.issue=5&rft.spage=e0033222&rft_id=info:doi/10.1128%2Fmsphere.00332-22&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2379-5042&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2379-5042&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2379-5042&client=summon |