1
|
Dsa OC, Kadni TS, N S. From cold chain to ambient temperature: transport of viral specimens- a review. Ann Med 2023; 55:2257711. [PMID: 37725901 PMCID: PMC10512818 DOI: 10.1080/07853890.2023.2257711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
The diagnosis of an aetiology is dependent on the collection, transport, and storage of the infectious sample. The transport of the sample plays a crucial role in the chain of diagnosis. It is important to maintain the biological integrity of the pathogen during the transport of the sample to achieve an accurate diagnosis. This is important, particularly for labile organisms like viruses that are inactivated easily compared to other microorganisms. Many transport media have been utilised to ensure the integrity of the virus during transport. While most of the transport media are focused on preserving the infectious properties of the virus, progress has been made to develop virus transport media to inactivate the virus and obtain the stability of the viral nucleic acid, enabling better molecular diagnosis of the virus aetiologies. This review summarises the various media used for the transport of virus samples and focuses on the need to develop virus transport media that inactivates the virus and preserves the viral nucleic acid.
Collapse
Affiliation(s)
- Oliver Christy Dsa
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Trupti Sathish Kadni
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Sudheesh N
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
2
|
Fukuda K, Baba H, Yoshida M, Kitabayashi K, Katsushima S, Sonehara H, Mizuno K, Kanamori H, Tokuda K, Nakagawa A, Mizuno A. Novel Virus Air Sampler Based on Electrostatic Precipitation and Air Sampling of SARS-CoV-2. Microorganisms 2023; 11:microorganisms11040944. [PMID: 37110367 PMCID: PMC10143856 DOI: 10.3390/microorganisms11040944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
The assessment of airborne viruses in air is a critical step in the design of appropriate prevention and control measures. Hence, herein, we developed a novel wet-type electrostatic air sampler using a viral dissolution buffer containing a radical scavenging agent, and verified the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the air of hospital rooms inhabiting coronavirus disease 2019 (COVID-19) patients and public areas. RNA damage caused by corona discharge was negligible when Buffer AVL was used as the collecting electrode. The viral RNA concentration in the air of the room varied by patient: 3.9 × 103 copy/m3 on the 10th day after onset in a mild case and 1.3 × 103 copy/m3 on the 18th day in a severe case. Viral RNA levels were 7.8 × 102 and 1.9 × 102 copy/m3 in the air of the office and food court, respectively, where people removed their masks when eating and talking, but it remained undetected in the station corridor where all the people were wearing masks. The assessment of airborne SARS-CoV-2 RNA using the proposed sampler can serve as a basis for the safe discontinuation of COVID-19 isolation precautions to identify exposure hotspots and alert individuals at increased infection risks.
Collapse
Affiliation(s)
- Kyohei Fukuda
- AMANO Co., Ltd., 275 Mamedocho, Kohoku-ku, Yokohama 222-8558, Japan
| | - Hiroaki Baba
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Mie Yoshida
- AMANO Co., Ltd., 275 Mamedocho, Kohoku-ku, Yokohama 222-8558, Japan
| | | | | | - Hiroki Sonehara
- Genome Clinic Co., Ltd., 2-5-1 Chuo, Chuo-ku, Chiba 260-0013, Japan
| | - Kazue Mizuno
- MRC LLC, 5-29-12, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Preferred Networks, Inc., 1-6-1 Otemachi Building, Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Koichi Tokuda
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Atsuhiro Nakagawa
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Akira Mizuno
- AMANO Co., Ltd., 275 Mamedocho, Kohoku-ku, Yokohama 222-8558, Japan
- MRC LLC, 5-29-12, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
3
|
Comparison of RT-qPCR and RT-ddPCR with Rift valley fever virus (RVFV) RNA. Sci Rep 2023; 13:3085. [PMID: 36813787 PMCID: PMC9944419 DOI: 10.1038/s41598-023-29023-y] [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: 10/17/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Rift valley fever (RVF) is an important zoonotic disease caused by the Rift valley fever virus (RVFV) which can affect ruminants and humans. In this study, a comparison was done of the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription-droplet digital PCR (RT-ddPCR) assays with synthesized RVFV RNA, cultured viral RNA, and mock clinical RVFV RNA samples. The genomic segments (L, M, and S) of three RVFV strains (BIME01, Kenya56, and ZH548) were synthesized and used as templates for in vitro transcription (IVT). Both the RT-qPCR and RT-ddPCR assays for RVFV did not react with any of the negative reference viral genomes. Thus, both the RT-qPCR and RT-ddPCR assays are specific to RVFV. The comparison of both the RT-qPCR and RT-ddPCR assays with serially diluted templates showed that the LoD of both assays are similar, and a concordant of the results was observed. The LoD of both assays reached the practical measurable minimum concentration. Taken altogether, the sensitivity of the RT-qPCR and RT-ddPCR assays is similar, and the material measured by RT-ddPCR can be used as a reference material for RT-qPCR.
Collapse
|
4
|
Cho S, Kim WK, No JS, Lee SH, Jung J, Yi Y, Park HC, Lee GY, Park K, Kim JA, Kim J, Lee J, Lee D, Song DH, Gu SH, Jeong ST, Song JW. Urinary genome detection and tracking of Hantaan virus from hemorrhagic fever with renal syndrome patients using multiplex PCR-based next-generation sequencing. PLoS Negl Trop Dis 2021; 15:e0009707. [PMID: 34582439 PMCID: PMC8478167 DOI: 10.1371/journal.pntd.0009707] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022] Open
Abstract
Background Hantavirus infection occurs through the inhalation of aerosolized excreta, including urine, feces, and saliva of infected rodents. The presence of Hantaan virus (HTNV) RNA or infectious particles in urine specimens of patient with hemorrhagic fever with renal syndrome (HFRS) remains to be investigated. Methodology/Principal findings We collected four urine and serum specimens of Republic of Korea Army (ROKA) patients with HFRS. We performed multiplex PCR-based next-generation sequencing (NGS) to obtain the genome sequences of clinical HTNV in urine specimens containing ultra-low amounts of viral genomes. The epidemiological and phylogenetic analyses of HTNV demonstrated geographically homogenous clustering with those in Apodemus agrarius captured in highly endemic areas, indicating that phylogeographic tracing of HTNV genomes reveals the potential infection sites of patients with HFRS. Genetic exchange analyses showed a genetic configuration compatible with HTNV L segment exchange in nature. Conclusion/Significance Our results suggest that whole or partial genome sequences of HTNV from the urine enabled to track the putative infection sites of patients with HFRS by phylogeographically linking to the zoonotic HTNV from the reservoir host captured at endemic regions. This report raises awareness among physicians for the presence of HTNV in the urine of patients with HFRS. Hantavirus transmission to humans occurs via inhalation of aerosolized excreta, including urine, feces, and saliva of infected rodents. Currently, no report for the etiological evidence associated with urinary Hantaan virus (HTNV) from patients with hemorrhagic fever with renal syndrome (HFRS) is available. Here, we conducted multiplex PCR-based next-generation sequencing (NGS) using urine and serum specimens from four Republic of Korea Army (ROKA) patients with HFRS. The epidemiological and phylogenetic analyses using whole or partial genome sequences of HTNV from urine and serum demonstrated homogenous genetic clustering with HTNV from clinical specimens, circulating at highly endemic sites of patient infection. Among the sequences from ROKA patients, the genomic configuration of ROKA16-10 demonstrated occurrences of the genetic reassortment. Our results suggest that whole or partial genome sequences of HTNV from the urine enabled to track the putative infection sites of patients with HFRS by phylogeographically linking to the zoonotic HTNV from the reservoir host captured at endemic regions. This result provides new insights into presence of HTNV in the urine of patients with HFRS among physicians.
Collapse
Affiliation(s)
- Seungchan Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jin Sun No
- Division of High-risk Pathogens, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Seung-Ho Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaehun Jung
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Yongjin Yi
- Division of Nephrology, Department of Internal Medicine, Dankook University Hospital, Cheonan, Republic of Korea
| | - Hayne Cho Park
- Department of Internal Medicine, Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jeong-Ah Kim
- Division of High-risk Pathogens, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jingyeong Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Daesang Lee
- 4th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Dong Hyun Song
- 4th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Se Hun Gu
- 4th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Seong Tae Jeong
- 4th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|
5
|
Honeywood MJ, Jeffries-Miles S, Wong K, Harrington C, Burns CC, Oberste MS, Bowen MD, Vega E. Use of Guanidine Thiocyanate-Based Nucleic Acid Extraction Buffers to Inactivate Poliovirus in Potentially Infectious Materials. J Virol Methods 2021; 297:114262. [PMID: 34384823 DOI: 10.1016/j.jviromet.2021.114262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 11/15/2022]
Abstract
The efforts of the Global Poliovirus Eradication Initiative (GPEI) have brought about the near elimination of poliovirus worldwide. The World Health Organization has issued guidelines for the safe handling and containment of infectious materials (IM) and potentially infectious materials (PIM) following poliovirus eradication. Inactivation of poliovirus in IM and PIM is needed to prevent inadvertent re-introduction of polioviruses post-eradication. In this study, we investigated the use of guanidine thiocyanate-based nucleic acid extraction buffers from commercially available nucleic acid extraction kits to inactivate poliovirus in cell culture isolates and stool suspensions, two common types of poliovirus IM and PIM, respectively. Incubation with selected nucleic acid extraction buffers or extraction buffers supplemented with ethanol reduced the infectivity of high-titer wild poliovirus type 1 (WPV1), wild poliovirus type 3 (WPV3), Sabin 1 (SL1), and Sabin 3 (SL3) cell culture isolates below the limit of detection in CCID50 assays. Stool suspensions containing WPV1, WPV3, SL1, SL2, or SL3 were also inactivated by the extraction buffers tested. Blind passage of WPV1-spiked stool suspensions confirmed complete inactivation of WPV1 after incubation with extraction buffers. Moreover, treatment with a buffer consisting of 4 M guanidine thiocyanate with 30% ethanol inactivated a high-titer WPV1 culture isolate and a WPV1-spiked stool suspension. Taken together, these results show that guanidine thiocyanate-based nucleic acid extraction buffers are an effective means of inactivating poliovirus IM and PIM, and thus will be instrumental in ensuring containment compliance and preventing potential re-emergence of contained polioviruses.
Collapse
Affiliation(s)
- Michelle J Honeywood
- IHRC, Inc., Contracting Agency to the Centers for Disease Control and Prevention, Atlanta, GA, 30346, USA
| | - Stacey Jeffries-Miles
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Kimberly Wong
- IHRC, Inc., Contracting Agency to the Centers for Disease Control and Prevention, Atlanta, GA, 30346, USA
| | - Chelsea Harrington
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Cara C Burns
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - M Steven Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Michael D Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Everardo Vega
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| |
Collapse
|
6
|
Yan Y, Chang L, Wang L. Laboratory testing of SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures. Rev Med Virol 2020; 30:e2106. [PMID: 32302058 PMCID: PMC7235496 DOI: 10.1002/rmv.2106] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 01/08/2023]
Abstract
Emerging and reemerging infectious diseases are global public concerns. With the outbreak of unknown pneumonia in Wuhan, China in December 2019, a new coronavirus, SARS-CoV-2 has been attracting tremendous attention. Rapid and accurate laboratory testing of SARS-CoV-2 is essential for early discovery, early reporting, early quarantine, early treatment, and cutting off epidemic transmission. The genome structure, transmission, and pathogenesis of SARS-CoV-2 are basically similar to SARS-CoV and MERS-CoV, the other two beta-CoVs of medical importance. During the SARS-CoV and MERS-CoV epidemics, a variety of molecular and serological diagnostic assays were established and should be referred to for SARS-CoV-2. In this review, by summarizing the articles and guidelines about specimen collection, nucleic acid tests (NAT) and serological tests for SARS-CoV, MERS-CoV, and SARS-CoV-2, several suggestions are put forward to improve the laboratory testing of SARS-CoV-2. In summary, for NAT: collecting stool and blood samples at later periods of illness to improve the positive rate if lower respiratory tract specimens are unavailable; increasing template volume to raise the sensitivity of detection; putting samples in reagents containing guanidine salt to inactivate virus as well as protect RNA; setting proper positive, negative and inhibition controls to ensure high-quality results; simultaneously amplifying human RNase P gene to avoid false-negative results. For antibody test, diverse assays targeting different antigens, and collecting paired samples are needed.
Collapse
Affiliation(s)
- Ying Yan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
- Graduate School, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
| |
Collapse
|
7
|
|
8
|
Leandro ADS, Britto ADS, Rios JA, Galvão SR, Kafka R, de Oliveira WF, Neto OF, Silva I, Delai RM, Gonçalves DD, Svoboda WK, Rivas AV, Lopes RD, Trench FJP, de Castro WAC, Sibim AC, Ribas LFDO, Gois FR, Vieira RFDC, Biondo AW. Molecular Detection of Dengue Virus in Mosquitoes as an Early Indicator to Aid in the Prevention of Human Infection in Endemic Areas. Vector Borne Zoonotic Dis 2019; 20:54-59. [PMID: 31697613 DOI: 10.1089/vbz.2018.2411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human cases of dengue virus based on the National Dengue Control Plan were compared with the molecular detection of the dengue virus in trapped mosquitoes, verifying the prediction and efficacy potentials of vector control between the two methodologies in a city with three endemic frontiers. Molecular detection of dengue virus in trapped mosquitoes was significantly higher than in human cases (p = 0.0435). Thus, molecular detection could be used as an early indicator to help prevent more human cases of dengue.
Collapse
Affiliation(s)
- André de Souza Leandro
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - André da Silva Britto
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - Jean Avemir Rios
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - Sandro Roberto Galvão
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - Rosinei Kafka
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | | | - Orestes Fecci Neto
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - Isaac Silva
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - Robson Michael Delai
- One Health Laboratory at the Three-Border Tropical Medicine Center, Itaiguapy Foundation, Institute of Teaching and Research, Foz do Iguaçu, Paraná, Brazil.,Department of Preventive Veterinary Medicine and Public Health, Paranaense University, Umuarama, Paraná, Brazil
| | - Daniela Dib Gonçalves
- Department of Preventive Veterinary Medicine and Public Health, Paranaense University, Umuarama, Paraná, Brazil
| | - Walfrido Kühl Svoboda
- Latin-American Institute of Life Sciences and Nature, Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - Açucena Veleh Rivas
- Latin-American Institute of Technology, Infrastructure and Territory, Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - Renata Defante Lopes
- Zoonoses Surveillance Unit, Municipal Secretary of Health, Foz do Iguaçu, Paraná, Brazil
| | - Flávia Julyana Pina Trench
- Latin-American Institute of Life Sciences and Nature, Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - Wagner Antônio Chiba de Castro
- Latin-American Institute of Life Sciences and Nature, Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - Alessandra Cristiane Sibim
- Latin-American Institute of Technology, Infrastructure and Territory, Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | | | | | | | - Alexander Welker Biondo
- Department of Veterinary Medicine, Federal University of Paraná, Paraná, Brazil.,Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana
| |
Collapse
|
9
|
Kuisma E, Olson SH, Cameron KN, Reed PE, Karesh WB, Ondzie AI, Akongo MJ, Kaba SD, Fischer RJ, Seifert SN, Muñoz-Fontela C, Becker-Ziaja B, Escudero-Pérez B, Goma-Nkoua C, Munster VJ, Mombouli JV. Long-term wildlife mortality surveillance in northern Congo: a model for the detection of Ebola virus disease epizootics. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180339. [PMID: 31401969 DOI: 10.1098/rstb.2018.0339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ebolavirus (EBOV) has caused disease outbreaks taking thousands of lives, costing billions of dollars in control efforts and threatening great ape populations. EBOV ecology is not fully understood but infected wildlife and consumption of animal carcasses have been linked to human outbreaks, especially in the Congo Basin. Partnering with the Congolese Ministry of Health, we conducted wildlife mortality surveillance and educational outreach in the northern Republic of Congo (RoC). Designed for EBOV detection and to alert public health authorities, we established a low-cost wildlife mortality reporting network covering 50 000 km2. Simultaneously, we delivered educational outreach promoting behavioural change to over 6600 people in rural northern RoC. We achieved specimen collection by training project staff on a safe sampling protocol and equipping geographically distributed bases with sampling kits. We established in-country diagnostics for EBOV testing, reducing diagnostic turnaround time to 3 days and demonstrated the absence of EBOV in 58 carcasses. Central Africa remains a high-risk EBOV region, but RoC, home to the largest remaining populations of great apes, has not had an epidemic since 2005. This effort continues to function as an untested early warning system in RoC, where people and great apes have died from past Ebola virus disease outbreaks. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.
Collapse
Affiliation(s)
- Eeva Kuisma
- Wildlife Conservation Society, Wildlife Health Program, 151 Avenue du General de Gaulle, BP14537 Brazzaville, Republic of Congo
| | - Sarah H Olson
- Wildlife Conservation Society, Wildlife Health Program, 2300 Southern Boulevard, Bronx, New York, NY 10460, USA
| | - Kenneth N Cameron
- Wildlife Conservation Society, Wildlife Health Program, 2300 Southern Boulevard, Bronx, New York, NY 10460, USA
| | - Patricia E Reed
- Wildlife Conservation Society, Wildlife Health Program, 2300 Southern Boulevard, Bronx, New York, NY 10460, USA
| | - William B Karesh
- Health and Policy, EcoHealth Alliance, 460 West 34th Street, New York, NY 10001, USA
| | - Alain I Ondzie
- Wildlife Conservation Society, Wildlife Health Program, 151 Avenue du General de Gaulle, BP14537 Brazzaville, Republic of Congo
| | - Marc-Joël Akongo
- Wildlife Conservation Society, Wildlife Health Program, 151 Avenue du General de Gaulle, BP14537 Brazzaville, Republic of Congo
| | - Serge D Kaba
- Wildlife Conservation Society, Wildlife Health Program, 151 Avenue du General de Gaulle, BP14537 Brazzaville, Republic of Congo
| | - Robert J Fischer
- Laboratory of Virology, Virus Ecology Unit, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, 903s 4th street, Hamilton, MT, USA
| | - Stephanie N Seifert
- Laboratory of Virology, Virus Ecology Unit, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, 903s 4th street, Hamilton, MT, USA
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine and German Center for Infection Research DZIF, Bernhard Nocht Strasse 74, 20359 Hamburg, Germany
| | | | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine and German Center for Infection Research DZIF, Bernhard Nocht Strasse 74, 20359 Hamburg, Germany
| | - Cynthia Goma-Nkoua
- Service d'Epidémiologie Moléculaire, Laboratoire National de Santé Publique, Avenue du General de Gaulle, BP120 Brazzaville, Republic of Congo
| | - Vincent J Munster
- Laboratory of Virology, Virus Ecology Unit, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, 903s 4th street, Hamilton, MT, USA
| | - Jean-Vivien Mombouli
- Service d'Epidémiologie Moléculaire, Laboratoire National de Santé Publique, Avenue du General de Gaulle, BP120 Brazzaville, Republic of Congo
| |
Collapse
|
10
|
Patterson EI, Warmbrod KL, Bouyer DH, Forrester NL. Evaluation of the inactivation of Venezuelan equine encephalitis virus by several common methods. J Virol Methods 2018; 254:31-34. [PMID: 29407211 DOI: 10.1016/j.jviromet.2018.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 12/11/2022]
Abstract
Working with virological samples requires validated inactivation protocols for safe handling and disposal. Although many techniques exist to inactivate samples containing viruses, not all procedures have been properly validated or are compatible with subsequent assays. To aid in the development of inactivation protocols for Alphaviruses, and specifically Venezuelan equine encephalitis virus (VEEV), a variety of methods were evaluated for their ability to completely inactivate a high titer sample of the vaccine strain VEEV TC-83. The methods evaluated include reagents used in RNA extraction, fixation, treatment with a detergent, and heat inactivation. Most methods were successful at inactivating the sample; however, treatment with only Buffer AVL, SDS, and heat inactivation at 58 °C for one hour were not capable of complete inactivation of the virus in the sample. These results provide a substantial framework for identifying techniques that are safe for complete inactivation of Alphaviruses and to advise protocol implementation.
Collapse
Affiliation(s)
- Edward I Patterson
- Institute for Human Infections and Immunity, Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Kelsey L Warmbrod
- Institute for Human Infections and Immunity, Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Donald H Bouyer
- Institute for Human Infections and Immunity, Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Naomi L Forrester
- Institute for Human Infections and Immunity, Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
11
|
Stability of Zika virus in urine: Specimen processing considerations and implications for the detection of RNA targets in urine. J Virol Methods 2017; 248:66-70. [DOI: 10.1016/j.jviromet.2017.04.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 12/31/2022]
|
12
|
The Effect of Nucleic Acid Extraction Platforms and Sample Storage on the Integrity of Viral RNA for Use in Whole Genome Sequencing. J Mol Diagn 2016; 19:303-312. [PMID: 28041870 DOI: 10.1016/j.jmoldx.2016.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 11/24/2022] Open
Abstract
Extraction of viral RNA and the storage of sample material are extremely important factors in the detection and whole genome sequencing (WGS) of viral pathogens. Although PCR-based detection methods focus on small amplicons, viral WGS applications require RNA of high quality and integrity for adequate sequence coverage and depth. This study examined the fitness of one manual and four automated RNA extraction platforms commonly used in diagnostic laboratories for use in metagenomic sequencing, how the practice of storing sample material in Qiagen buffer AVL before extraction affected the integrity of viral RNA and its suitability for use in amplicon-based WGS methods, and how the addition of Triton X-100 to buffer AVL affected the capability of the extraction platforms and the integrity of viral RNA in stored samples. This study found that the EZ1 platform gave the best performance of the automated platforms and gave comparable results to the frequently used manual Qiagen extraction protocol when extracted viral RNA was used in metagenomics sequencing. To maintain high levels of viral RNA integrity suitable for amplicon-based WGS, nucleic acid should be extracted from samples immediately, because even short storage periods in buffer AVL have a severe effect on integrity, and the addition of Triton X-100 had little effect on the quality of viral material for WGS.
Collapse
|
13
|
Folarin OA, Ehichioya D, Schaffner SF, Winnicki SM, Wohl S, Eromon P, West KL, Gladden-Young A, Oyejide NE, Matranga CB, Deme AB, James A, Tomkins-Tinch C, Onyewurunwa K, Ladner JT, Palacios G, Nosamiefan I, Andersen KG, Omilabu S, Park DJ, Yozwiak NL, Nasidi A, Garry RF, Tomori O, Sabeti PC, Happi CT. Ebola Virus Epidemiology and Evolution in Nigeria. J Infect Dis 2016; 214:S102-S109. [PMID: 27377746 PMCID: PMC5050462 DOI: 10.1093/infdis/jiw190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Containment limited the 2014 Nigerian Ebola virus (EBOV) disease outbreak to 20 reported cases and 8 fatalities. We present here clinical data and contact information for at least 19 case patients, and full-length EBOV genome sequences for 12 of the 20. The detailed contact data permits nearly complete reconstruction of the transmission tree for the outbreak. The EBOV genomic data are consistent with that tree. It confirms that there was a single source for the Nigerian infections, shows that the Nigerian EBOV lineage nests within a lineage previously seen in Liberia but is genetically distinct from it, and supports the conclusion that transmission from Nigeria to elsewhere did not occur.
Collapse
Affiliation(s)
- Onikepe A Folarin
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | - Deborah Ehichioya
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | - Stephen F Schaffner
- Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | - Sarah M Winnicki
- Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | - Shirlee Wohl
- Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | - Philomena Eromon
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | | | | | | | | | - Awa Bineta Deme
- Department de Parasitologie et Mycologie, Université Cheikh Anta Diop de Dakar, Fann, Dakar, Senegal
| | | | | | - Kenneth Onyewurunwa
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | - Jason T Ladner
- Department of Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, Massachusetts
| | - Gustavo Palacios
- Department of Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, Massachusetts
| | | | - Kristian G Andersen
- Department of The Scripps Research Institute, Scripps Translational Science Institute, La Jolla, California
| | - Sunday Omilabu
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos
| | - Daniel J Park
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Broad Institute of Harvard and MIT
| | - Nathan L Yozwiak
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | | | - Robert F Garry
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana
| | - Oyewale Tomori
- Department of Biological Sciences Department of Nigerian Academy of Science, Akoka-Yaba, Lagos
| | - Pardis C Sabeti
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Department of Howard Hughes Medical Institute, Chevy Chase
| | - Christian T Happi
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| |
Collapse
|
14
|
Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JLB, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 2014; 345:1369-72. [PMID: 25214632 PMCID: PMC4431643 DOI: 10.1126/science.1259657] [Citation(s) in RCA: 828] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.
Collapse
Affiliation(s)
- Stephen K Gire
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kristian G Andersen
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rachel S G Sealfon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Mambu Momoh
- Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone
| | - Mohamed Fullah
- Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Shirlee Wohl
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lina M Moses
- Tulane University Medical Center, New Orleans, LA 70112, USA
| | - Nathan L Yozwiak
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Winnicki
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Stephen F Schaffner
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiao Yang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pan-Pan Jiang
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mahan Nekoui
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andres Colubri
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Mbalu Fonnie
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Alex Moigboi
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | - Edwin Konuwa
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Sidiki Saffa
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | - Alice Kovoma
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | - Momoh Foday
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | | | | | | | - Cheryl Murphy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Sahr M Gevao
- University of Sierra Leone, Freetown, Sierra Leone
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Robert F Garry
- Tulane University Medical Center, New Orleans, LA 70112, USA
| | | | - Pardis C Sabeti
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
15
|
Development and clinical evaluation of a novel fully automated qualitative PCR assay for the diagnosis of anogenital herpes simplex virus infection. Diagn Microbiol Infect Dis 2014; 80:102-6. [PMID: 25128985 DOI: 10.1016/j.diagmicrobio.2014.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/02/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022]
Abstract
Molecular detection of viral infections has the potential to improve microbial diagnostics, particularly with the emergence of rapid automated systems. We describe the design of the IDbox fully automated cassette-based system for nucleic acid extraction and real-time PCR amplification and perform a clinical evaluation for the diagnosis of genital herpes simplex infections. At optimal cutoff values determined by receiver-operator curves, the IDbox showed sensitivities of 94.9% (95% confidence interval [CI] 84.9-98.7%) and 97.0% (95% CI 88.5-99.5%) and specificities of 96.7% (95% CI 91.2-98.9%) and 97.3% (95% CI 91.9-99.3%) relative to herpes simplex virus culture and PCR, respectively. We discuss relevant design characteristics and approaches used for each step of the analytical process to enhance assay sensitivity and provide accurate results in the presence of potential cross-reactive organisms and interfering substances.
Collapse
|
16
|
Stabilization of biothreat diagnostic samples through vitrification matrices. J Microbiol Methods 2014; 101:81-5. [DOI: 10.1016/j.mimet.2014.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 11/22/2022]
|
17
|
Liu H, Gan Y, Wu Y, Weng H, Lei P, Shen G. Effects of different lysis buffers of nucleic acid purification kit on the stability of influenza virus RNA. Future Virol 2014. [DOI: 10.2217/fvl.14.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Aim: Under suboptimal storage and transport conditions, influenza virus (flu-v) RNA is prone to degradation and lysis buffers from RNA extraction kits have a potential to stabilize RNA. The aim of this study was to investigate the effects of different lysis buffers on the stability of flu-v RNA. Materials & methods: Aliquots of flu-v suspension were processed in parallel with two lysis buffers, and then underwent cyclic freeze–thaw or prolonged storage at 4, 22 and -20°C. The viral RNA was analyzed by using real-time and conventional RT-PCR amplifying, respectively, partial and full-length sequences of the flu-v matrix gene. Results: The viral RNA remained intact in samples treated with either of the two lysis buffers for at least 7 days at 4°C, 90 days at -20°C or following seven freeze–thaw cycles, but buffer A was superior to buffer B in protecting RNA from degradation at 4°C and 22°C, or following a further increase of freeze–thaw cycles. Conclusion: Lysis buffer preservatives provide viral RNA stabilization, whereas different lysis buffers vary in their ability to stabilize viral RNA, and thus their performance characteristics should be evaluated prior to their application in clinical practice.
Collapse
Affiliation(s)
- Hongbo Liu
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, China
- Virology Laboratory, Center for Disease Control and Prevention of Zhongshan, Zhongshan, China
| | - Yan Gan
- Neuroimmunology Laboratory, Barrow Neurological Institute, St Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Yanheng Wu
- Virology Laboratory, Center for Disease Control and Prevention of Zhongshan, Zhongshan, China
| | - Hui Weng
- Department of Immunology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Ping Lei
- Department of Immunology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Guanxin Shen
- Department of Immunology, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| |
Collapse
|
18
|
Shafagati N, Patanarut A, Luchini A, Lundberg L, Bailey C, Petricoin E, Liotta L, Narayanan A, Lepene B, Kehn-Hall K. The use of Nanotrap particles for biodefense and emerging infectious disease diagnostics. Pathog Dis 2014; 71:164-76. [PMID: 24449537 PMCID: PMC7108521 DOI: 10.1111/2049-632x.12136] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 11/28/2022] Open
Abstract
Detection of early infectious disease may be challenging due to the low copy number of organisms present. To overcome this limitation and rapidly measure low concentrations of the pathogen, we developed a novel technology: Nanotrap particles, which are designed to capture, concentrate, and protect biomarkers from complex biofluids. Nanotrap particles are thermoresponsive hydrogels that are capable of antigen capture through the coupling of affinity baits to the particles. Here, we describe recent findings demonstrating that Nanotrap particles are able to capture live infectious virus, viral RNA, and viral proteins. Capture is possible even in complex mixtures such as serum and allows the concentration and protection of these analytes, providing increased performance of downstream assays. The Nanotrap particles are a versatile sample preparation technology that has far reaching implications for biomarker discovery and diagnostic assays.
Collapse
Affiliation(s)
- Nazly Shafagati
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Johnson BJ, Melde BJ, Dinderman MA, Lin B. Stabilization of RNA through absorption by functionalized mesoporous silicate nanospheres. PLoS One 2012; 7:e50356. [PMID: 23226266 PMCID: PMC3511576 DOI: 10.1371/journal.pone.0050356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 10/24/2012] [Indexed: 11/29/2022] Open
Abstract
The potential for encapsulating RNA within tunable, semi-permeable structures for storage and transportation purposes offers an interesting approach to the reduction of stringent storage requirements that often hamper the field application of genetic analysis methods. In this study, we assessed the potential for application of functionalized, porous silicate sorbents in maintaining nucleic acid integrity. Mesoporous silica nanoparticles (MSNs) with and without incorporated stabilizing reagents were used to encapsulate triosephosphate isomerase mRNA of Arabidopsis thaliana. The absorption, elution, and the long-term stability of the RNA were monitored by using quantitative real-time RT-PCR. The results indicate that adsorbed RNA can be eluted from the sorbents using simple buffers and employed directly for downstream molecular diagnostic assays without any further processing. RNA integrity can be maintained for extended time periods under refrigeration temperatures in the presence of covalently immobilized stabilizing compounds. This study provides initial evidence of the potential for application of MSNs in transportation and storage. They may also have utility in sample collection and processing in restrictive environments.
Collapse
Affiliation(s)
| | | | | | - Baochuan Lin
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington D.C., United States of America
- * E-mail:
| |
Collapse
|
20
|
Roiz D, Vázquez A, Rosso F, Arnoldi D, Girardi M, Cuevas L, Perez-Pastrana E, Sánchez-Seco MP, Tenorio A, Rizzoli A. Detection of a new insect flavivirus and isolation of Aedes flavivirus in Northern Italy. Parasit Vectors 2012; 5:223. [PMID: 23043958 PMCID: PMC3481474 DOI: 10.1186/1756-3305-5-223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/28/2012] [Indexed: 11/16/2022] Open
Abstract
Background During recent years, numerous novel ‘insect flaviviruses’ have been discovered in natural mosquito populations. In a previous study we described the presence of flavivirus DNA sequences integrated in Aedes albopictus (Asian tiger mosquito) populations from Northern Italy in 2007. Methods During 2008 we collected and tested Aedes females for flavivirus presence and developed phylogenetic analysis, virus isolation, electron microscopy studies and RNAse treatments. Results We detected a high prevalence of flavivirus in Ae. albopictus (77.5%). The phylogenetic analysis identified the insect flavivirus sequences as Aedes flavivirus (AEFV) recently described in Japan, and that may have been introduced in Italy travelling with the tiger mosquito. Some of these pools grew in C6/36 cells, producing cytopathic effects, and the RNase treatment results showed the presence of the detected sequences in RNA forms. Furthermore, we detected a new insect flavivirus in one pool of Aedes cinereus/geminus mosquitoes. Phylogenetic analysis of this virus shows that it forms a distinct cluster within the clade of insect flavivirus. Conclusions This is the first study to report a high prevalence, to describe the seasonal activity and an isolation of the insect flavivirus Aedes flavivirus in Europe. Moreover we describe the detection of a new insect flavivirus detected from Ae. cinereus mosquitoes from Italy. These flavivirus may be common, ubiquitous and diverse in nature and we discuss the implications of the insect flavivirus group in virus evolution and transmission.
Collapse
Affiliation(s)
- David Roiz
- Wetland Ecology Department, Doñana Biological Station, CSIC, Sevilla, Spain.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Evaluation and clinical validation of an alcohol-based transport medium for preservation and inactivation of respiratory viruses. J Clin Microbiol 2011; 49:2138-42. [PMID: 21508158 DOI: 10.1128/jcm.00327-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The clinical and public health importance of influenza and other respiratory viruses has accelerated the development of highly sensitive molecular diagnostics, but data are limited regarding preanalytical stages of diagnostic testing. We evaluated CyMol, an alcohol-based transport medium, for its ability to maintain specimen integrity for up to 21 days of storage at various temperatures; for its ability to inactivate virus; and for its compatibility with antigen- or nucleic acid-based diagnostics for respiratory viruses in clinical samples. In mock-infected samples, both universal transport medium (UTM-RT) and CyMol maintained equivalent viral quantities for at least 14 days at room temperature or colder, whereas a dry swab collection maintained viral quantities only if refrigerated or frozen. CyMol inactivated influenza virus within 5 min of sample immersion. UTM-RT- and CyMol-collected nasal swab specimens from 73 symptomatic students attending a campus health clinic were positive for a respiratory virus in 56.2% of subjects by multiplex PCR testing, including influenza A and B viruses, rhinovirus/enteroviruses, coronaviruses, respiratory syncytial virus, parainfluenza viruses, metapneumovirus, and adenovirus. Detection by PCR was equivalent in UTM-RT- and CyMol-collected specimens and in self- and staff-collected swabs. Direct fluorescent antibody (DFA) testing was substantially less sensitive (23.3%) than multiplex PCR, and DFA testing from UTM-RT-collected swabs was more sensitive than that from CyMol-collected swabs. These data indicate that an alcohol-based transport medium such as CyMol preserves respiratory virus integrity, rapidly inactivates viruses, and is compatible with PCR-based respiratory diagnostics.
Collapse
|
22
|
Sampling and RNA quality for diagnosis of honey bee viruses using quantitative PCR. J Virol Methods 2011; 174:150-2. [PMID: 21473885 DOI: 10.1016/j.jviromet.2011.03.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 03/23/2011] [Accepted: 03/28/2011] [Indexed: 11/22/2022]
Abstract
Molecular diagnoses of pathogens via ribonucleic acid (RNA) signatures are used widely in honey bee pathology. Such diagnoses can be compromised by ubiquitous and endogenous RNA-degrading enzymes activated after the death of sampled bees. RNA degradation can be minimized by storage at ultra-cold temperatures or by immersion in high-salt buffers. However, these methods are not always available in the field or are costly, driving a search for alternative methods to store and transport bees for RNA analyses. While the impact of storage conditions on RNA integrity has been evaluated, the tolerance of standard RT-qPCR diagnostic methods of honey bee pathogens for suboptimal collection and storage is unknown. Given the short regions of RNA used for pathogen diagnosis (generally amplified regions of 100-200 nucleotides), it is conceivable that even degraded RNA will provide a template for precise diagnosis. In this study, the impact of the two most convenient sample storage and handling methods (+4°C and ambient temperature) for identifying honey bee virus infections was evaluated by RT-qPCR. The aim was to streamline the methods needed to collect, transport, and store honey bee samples destined for pathogen diagnosis. The data show that samples held at room temperature for times anticipated for sample transport for up to 5 days are suitable for diagnosis of two of the most common and prevalent honey bee viruses, deformed wing virus (DWV) and black queen cell virus (BQCV). The results will be useful for the standardisation of sampling methods across countries and laboratories.
Collapse
|
23
|
A clinical specimen collection and transport medium for molecular diagnostic and genomic applications. Epidemiol Infect 2010; 139:1764-73. [DOI: 10.1017/s0950268810002384] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYPathogen detection and genetic characterization has dramatically changed in recent years. Clinical laboratories are transitioning from traditional culture and primer-specific sequencing to more robust and rapid nucleic acid testing such as real-time PCR and meta-genomic characterization, respectively. Specimen collection is the first step in any downstream molecular diagnostic procedure. PrimeStore Molecular Transport Medium (MTM) is an optimized blend of nucleic acid stabilizing reagents that includes a non-specific internal positive control that can be amplified using real-time RT–PCR for tracking the integrity of a specimen from the point of collection to detection. PrimeStore MTM is shown here to effectively kill pathogens, including highly pathogenic H5 influenza virus, inactivate nucleases and to protect and preserve released RNA at ambient temperature for up to 30 days for downstream real-time and traditional RT–PCR detection and genetic characterization. PrimeStore MTM is also compatible with a variety of commercial extraction kits. PrimeStore is suited for routine clinical specimens and has added utility for field collection in remote areas, triage centres, border crossings and during pandemics where cold-chain, transport, and dissemination of potentially infectious pathogens are a concern.
Collapse
|
24
|
Dacheux L, Wacharapluesadee S, Hemachudha T, Meslin FX, Buchy P, Reynes JM, Bourhy H. More accurate insight into the incidence of human rabies in developing countries through validated laboratory techniques. PLoS Negl Trop Dis 2010; 4:e765. [PMID: 21152054 PMCID: PMC2994914 DOI: 10.1371/journal.pntd.0000765] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Laurent Dacheux
- Institut Pasteur, Dynamics and Host Adaptation Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Paris, France.
| | | | | | | | | | | | | |
Collapse
|