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You D, Xu T, Huang BZ, Zhu L, Wu F, Deng LS, Liu ZY, Duan JQ, Wang YM, Ge LP, Liu ZH, Sun J, Zeng X, Lang LQ, Zhou YC, Chen DS, Lai SY, Ai YR, Huang JB, Xu ZW. Rapid, sensitive, and visual detection of swine Japanese encephalitis virus with a one-pot RPA-CRISPR/EsCas13d-based dual readout portable platform. Int J Biol Macromol 2024; 277:134151. [PMID: 39059534 DOI: 10.1016/j.ijbiomac.2024.134151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/20/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Japanese encephalitis (JE), a mosquito-borne zoonotic disease caused by the Japanese encephalitis virus (JEV), poses a serious threat to global public health. The low viremia levels typical in JEV infections make RNA detection challenging, necessitating early and rapid diagnostic methods for effective control and prevention. This study introduces a novel one-pot detection method that combines recombinant enzyme polymerase isothermal amplification (RPA) with CRISPR/EsCas13d targeting, providing visual fluorescence and lateral flow assay (LFA) results. Our portable one-pot RPA-EsCas13d platform can detect as few as two copies of JEV nucleic acid within 1 h, without cross-reactivity with other pathogens. Validation against clinical samples showed 100 % concordance with real-time PCR results, underscoring the method's simplicity, sensitivity, and specificity. This efficacy confirms the platform's suitability as a novel point-of-care testing (POCT) solution for detecting and monitoring the JE virus in clinical and vector samples, especially valuable in remote and resource-limited settings.
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Affiliation(s)
- Dong You
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Tong Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bing-Zhou Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China
| | - Fang Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Li-Shuang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhe-Yan Liu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jia-Qi Duan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuan-Meng Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Liang-Peng Ge
- ChongQing Academy of Animal Sciences, Chongqiing, China
| | - Zuo-Hua Liu
- ChongQing Academy of Animal Sciences, Chongqiing, China
| | - Jing Sun
- ChongQing Academy of Animal Sciences, Chongqiing, China
| | - Xiu Zeng
- ChongQing Academy of Animal Sciences, Chongqiing, China
| | - Li-Qiao Lang
- ChongQing Academy of Animal Sciences, Chongqiing, China
| | - Yuan-Cheng Zhou
- Key Laboratory of Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan, Animal Science Academy, Chengdu, China; Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan, Animal Science Academy, Chengdu, China
| | - Di-Shi Chen
- Sichuan Animal Disease Prevention and Control Center, Chengdu, China
| | - Si-Yuan Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan-Ru Ai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jian-Bo Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Wen Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.
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Milburn J, Suresh R, Doyle R, Jarvis JN. The diagnosis of central nervous system infections in resource-limited settings and the use of novel and molecular diagnostic platforms to improve diagnosis. Expert Rev Mol Diagn 2024; 24:219-230. [PMID: 38369939 DOI: 10.1080/14737159.2024.2317414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Central nervous system infections (CNSI) disproportionately affect individuals in low-resource settings where diagnosis is challenging; large proportions of patients never receive a confirmed microbiological diagnosis resulting in inadequate management and high mortality. The epidemiology of CNSI varies globally and conventional diagnostics deployed in resource-limited settings have significant limitations, with an urgent need for improved diagnostic strategies. AREAS COVERED This review describes molecular platforms and other novel diagnostics used in the diagnosis of CNSI that are applicable to resource-limited settings. An extensive literature search of Medline and PubMed was performed. The emphasis is on investigations targeting infections of relevance to resource-limited settings either due to variation in regional CNSI epidemiology or due to increased prevalence in patients with immunosuppression. This includes commercially available multiplex PCR platforms, mycobacterial PCR platforms, and rapid diagnostics tests. To offer a framework for the optimal implementation in clinical settings, existing evidence highlighting the advantages and limitations of available platforms is reviewed. EXPERT OPINION The implementation of molecular platforms and other novel diagnostics has the potential to transform CNSI diagnosis in resource-limited settings, with several examples of successful rollout of novel diagnostics such as Xpert MTB/RIF Ultra and cryptococcal antigen testing.
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Affiliation(s)
- James Milburn
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Clinical Research, Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Rachita Suresh
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ronan Doyle
- Department of Clinical Research, Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Joseph N Jarvis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Clinical Research, Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Kinsella P, Moso M, Martin G, Karapangiotidis T, Karamalakis D, Nicholson S, Batty M, Jackson K, Marsland M, Thomson T, Manoharan L, O'brien H, Friedman ND, Bond K, Williamson DA, Lim CK. Laboratory evaluation of ELISA and indirect immunofluorescence assay in response to emergence of Japanese encephalitis virus genotype IV in Australia. J Clin Virol 2023; 168:105580. [PMID: 37717487 DOI: 10.1016/j.jcv.2023.105580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 09/19/2023]
Abstract
The unexpected recent emergence of Japanese encephalitis virus (JEV) genotype IV in multiple southern states of Australia necessitated an evaluation of JEV serological tests suitable for diagnosing acute infection and for seroprevalence studies. This study examined the analytical and clinical performance of two high-throughput JEV assays, Euroimmun immunofluorescence assay (IFA) and Euroimmun enzyme-linked immunosorbent assay (ELISA), across four cohorts; (1) surveillance of piggery workers in outbreak areas, (2) surveillance of residents in outbreak areas, (3) acute JEV infection and (4) post-JEV vaccination. ELISA and IFA IgM demonstrated minimal cross-reactivity (0-1.8%) with other endemic flaviviruses, with high sensitivity (100%) for acute JEV infection in this low endemicity setting. Differences in IgG serodynamics between the two assays suggest convalescent and paired testing with IgM are critical in diagnosing acute infection. High assay concordance was observed between ELISA and IFA when used in serosurveillance (97.4% agreement, Cohen' κ 0.74 [95% CI 0.614-0.860]) and vaccination cohorts (91.1% agreement, Cohen's κ 0.806 [95% CI 0.672-0.941]). In conclusion, this study highlights the clinical & epidemiological applications and limitations of these two commercial JEV assays.
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Affiliation(s)
- Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Genevieve Martin
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Theo Karapangiotidis
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Di Karamalakis
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Mitch Batty
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | | | | | | | | | | | - Katherine Bond
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
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4
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Hu X, Feng S, Shi K, Shi Y, Yin Y, Long F, Wei X, Li Z. Development of a quadruplex real-time quantitative RT-PCR for detection and differentiation of PHEV, PRV, CSFV, and JEV. Front Vet Sci 2023; 10:1276505. [PMID: 38026635 PMCID: PMC10643766 DOI: 10.3389/fvets.2023.1276505] [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: 08/12/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV), porcine pseudorabies virus (PRV), classical swine fever virus (CSFV), and Japanese encephalitis virus (JEV) cause similar neurological symptoms in the infected pigs, and their differential diagnosis depends on laboratory testing. Four pairs of specific primers and probes were designed targeting the PHEV N gene, PRV gB gene, CSFV 5' untranslated region (5'UTR), and JEV NS1 gene, respectively, and a quadruplex real-time quantitative RT-PCR (qRT-PCR) was developed to detect and differentiate PHEV, PRV, CSFV, and JEV. The assay showed high sensitivity, with the limit of detection (LOD) of 1.5 × 101 copies/μL for each pathogen. The assay specifically detected only PHEV, PRV, CSFV, and JEV, without cross-reaction with other swine viruses. The coefficients of variation (CVs) of the intra-assay and the inter-assay were less than 1.84%, with great repeatability. A total of 1,977 clinical samples, including tissue samples, and whole blood samples collected from Guangxi province in China, were tested by the developed quadruplex qRT-PCR, and the positivity rates of PHEV, PRV, CSFV, and JEV were 1.57% (31/1,977), 0.35% (7/1,977), 1.06% (21/1,977), and 0.10% (2/1,977), respectively. These 1,977 samples were also tested by the previously reported qRT-PCR assays, and the coincidence rates of these methods were more than 99.90%. The developed assay is demonstrated to be rapid, sensitive, and accurate for detection and differentiation of PHEV, PRV, CSFV, and JEV.
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Affiliation(s)
- Xin Hu
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Shuping Feng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Kaichuang Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Yuwen Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yanwen Yin
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Xiankai Wei
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Zongqiang Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
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Martin GE, Tran T, Papadakis G, Kinsella P, Druce J, Caly L, Williamson DA, Lim CK. A real-time PCR assay for Japanese encephalitis virus (JEV) genotype IV as a public health laboratory response to an emerging outbreak in Australia. Pathology 2023; 55:869-870. [PMID: 37147245 DOI: 10.1016/j.pathol.2023.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/18/2023] [Accepted: 02/14/2023] [Indexed: 05/07/2023]
Affiliation(s)
- Genevieve E Martin
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Georgina Papadakis
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, and Department of Medicine, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.
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Van den Eynde C, Sohier C, Matthijs S, De Regge N. Belgian Anopheles plumbeus Mosquitoes Are Competent for Japanese Encephalitis Virus and Readily Feed on Pigs, Suggesting a High Vectorial Capacity. Microorganisms 2023; 11:1386. [PMID: 37374888 DOI: 10.3390/microorganisms11061386] [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: 04/19/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Anopheles plumbeus, a day-active mosquito known to feed aggressively on humans, was reported as a nuisance species near an abandoned pigsty in Belgium. Since Japanese encephalitis virus (JEV) is an emerging zoonotic flavivirus which uses pigs as amplification hosts, we investigated (1) whether An. plumbeus would feed on pigs and (2) its vector competence for JEV, to investigate whether this species could be a potential vector. Three- to seven-day-old F0-generation adult mosquitoes, emerged from field-collected larvae, were fed on a JEV genotype 3 Nakayama strain spiked blood meal. Blood-fed mosquitoes were subsequently incubated for 14 days at two temperature conditions: a constant 25 °C and a 25/15 °C day/night temperature gradient. Our results show that An. plumbeus is a competent vector for JEV at the 25 °C condition and this with an infection rate of 34.1%, a dissemination rate of 67.7% and a transmission rate of 14.3%. The vector competence showed to be influenced by temperature, with a significantly lower dissemination rate (16.7%) and no transmission when implementing the temperature gradient. Moreover, we demonstrated that An. plumbeus readily feeds on pigs when the opportunity occurs. Therefore, our results suggest that Belgian An. plumbeus mosquitoes may play an important role in the transmission of JEV upon an introduction into our region if temperatures increase with climate change.
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Affiliation(s)
- Claudia Van den Eynde
- Exotic and Vector-Borne Diseases, Sciensano, Groeselenberg 99, 1180 Brussels, Belgium
| | - Charlotte Sohier
- Exotic and Vector-Borne Diseases, Sciensano, Groeselenberg 99, 1180 Brussels, Belgium
| | - Severine Matthijs
- Viral Re-Emerging Enzootic and Bee Diseases, Sciensano, Groeselenberg 99, 1180 Brussels, Belgium
| | - Nick De Regge
- Exotic and Vector-Borne Diseases, Sciensano, Groeselenberg 99, 1180 Brussels, Belgium
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Thorburn S, Friedman D, Burston J, Kinsella PM, Martin GE, Williamson DA, Jackson J. Sentinel cluster of locally acquired Japanese encephalitis in southern Australia. Intern Med J 2023; 53:835-840. [PMID: 37134258 DOI: 10.1111/imj.16086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/09/2023] [Indexed: 05/05/2023]
Abstract
Prior to January 2022, only a single case of infection with Japanese encephalitis virus (JEV) had been reported on the Australian mainland, acquired in the northern extremity on Cape York. We report the clinical characteristics of the sentinel cluster of cases that confirmed the local acquisition of JEV in southern Australia along the Murray River bordering New South Wales and Victoria.
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Affiliation(s)
- Samuel Thorburn
- Albury Wodonga Health, Albury, New South Wales, Australia
- Infectious Diseases Department, Albury Base Hospital, Albury, New South Wales, Australia
| | - Deborah Friedman
- Public Health Divison, Victorian Department of Health, Melbourne, Victoria, Australia
| | - John Burston
- Albury Wodonga Health, Albury, New South Wales, Australia
- Infectious Diseases Department, Albury Base Hospital, Albury, New South Wales, Australia
| | - Paul M Kinsella
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia
| | - Genevieve E Martin
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia
| | - Justin Jackson
- Albury Wodonga Health, Albury, New South Wales, Australia
- Infectious Diseases Department, Albury Base Hospital, Albury, New South Wales, Australia
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8
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Relevant Day/Night Temperatures Simulating Belgian Summer Conditions Reduce Japanese Encephalitis Virus Dissemination and Transmission in Belgian Field-Collected Culex pipiens Mosquitoes. Viruses 2023; 15:v15030764. [PMID: 36992473 PMCID: PMC10053291 DOI: 10.3390/v15030764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Japanese encephalitis virus (JEV), a zoonotic mosquito-borne Flavivirus, can be considered an emerging infectious disease. Therefore, vector competence studies with indigenous mosquitoes from regions where JEV is not yet endemic are of great importance. In our study, we compared the vector competence of Culex pipiens mosquitoes emerged from Belgian field-caught larvae under two different temperature conditions: a constant 25 °C and a 25/15 °C day/night temperature gradient representing typical summer temperatures in Belgium. Three- to seven-day-old F0-generation mosquitoes were fed on a JEV genotype 3 Nakayama strain spiked blood-meal and incubated for 14 days at the two aforementioned temperature conditions. Similar infection rates of 36.8% and 35.2% were found in both conditions. The observed dissemination rate in the gradient condition was, however, significantly lower compared to the constant temperature condition (8% versus 53.6%, respectively). JEV was detected by RT-qPCR in the saliva of 13.3% of dissemination positive mosquitoes in the 25 °C condition, and this transmission was confirmed by virus isolation in 1 out of 2 RT-qPCR positive samples. No JEV transmission to saliva was detected in the gradient condition. These results suggest that JEV transmission by Culex pipiens mosquitoes upon an accidental introduction in our region is unlikely under current climatic conditions. This could change in the future when temperatures increase due to climate change.
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Sikazwe C, Neave MJ, Michie A, Mileto P, Wang J, Cooper N, Levy A, Imrie A, Baird RW, Currie BJ, Speers D, Mackenzie JS, Smith DW, Williams DT. Molecular detection and characterisation of the first Japanese encephalitis virus belonging to genotype IV acquired in Australia. PLoS Negl Trop Dis 2022; 16:e0010754. [PMID: 36409739 PMCID: PMC9721490 DOI: 10.1371/journal.pntd.0010754] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/05/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A fatal case of Japanese encephalitis (JE) occurred in a resident of the Tiwi Islands, in the Northern Territory of Australia in February 2021, preceding the large JE outbreak in south-eastern Australia in 2022. This study reports the detection, whole genome sequencing and analysis of the virus responsible (designated JEV/Australia/NT_Tiwi Islands/2021). METHODS Reverse transcription quantitative PCR (RT-qPCR) testing was performed on post-mortem brain specimens using a range of JE virus (JEV)-specific assays. Virus isolation from brain specimens was attempted by inoculation of mosquito and mammalian cells or embryonated chicken eggs. Whole genome sequencing was undertaken using a combination of Illumina next generation sequencing methodologies, including a tiling amplicon approach. Phylogenetic and selection analyses were performed using alignments of the Tiwi Islands JEV genome and envelope (E) protein gene sequences and publicly available JEV sequences. RESULTS Virus isolation was unsuccessful and JEV RNA was detected only by RT-qPCR assays capable of detecting all JEV genotypes. Phylogenetic analysis revealed that the Tiwi Islands strain is a divergent member of genotype IV (GIV) and is closely related to the 2022 Australian outbreak virus (99.8% nucleotide identity). The Australian strains share highest levels of nucleotide identity with Indonesian viruses from 2017 and 2019 (96.7-96.8%). The most recent common ancestor of this Australian-Indonesian clade was estimated to have emerged in 2007 (95% HPD range: 1998-2014). Positive selection was detected using two methods (MEME and FEL) at several sites in the E and non-structural protein genes, including a single site in the E protein (S194N) unique to the Australian GIV strains. CONCLUSION This case represents the first detection of GIV JEV acquired in Australia, and only the second confirmed fatal human infection with a GIV JEV strain. The close phylogenetic relationship between the Tiwi Islands strain and recent Indonesian viruses is indicative of the origin of this novel GIV lineage, which we estimate has circulated in the region for several years prior to the Tiwi Islands case.
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Affiliation(s)
- Chisha Sikazwe
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Matthew J. Neave
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Alice Michie
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Patrick Mileto
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Jianning Wang
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Natalie Cooper
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Avram Levy
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Allison Imrie
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Robert W. Baird
- Pathology and Infectious Diseases Departments, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Pathology and Infectious Diseases Departments, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David Speers
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - John S. Mackenzie
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia
| | - David W. Smith
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- * E-mail: (DWS); (DTW)
| | - David T. Williams
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
- * E-mail: (DWS); (DTW)
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Bharucha T, Ayhan N, Pastorino B, Rattanavong S, Vongsouvath M, Mayxay M, Changthongthip A, Sengvilaipaseuth O, Phonemixay O, Pommier JD, Gorman C, Zitzmann N, Newton PN, de Lamballerie X, Dubot-Pérès A. Immunoglobulin M seroneutralization for improved confirmation of Japanese encephalitis virus infection in a flavivirus-endemic area. Trans R Soc Trop Med Hyg 2022; 116:1032-1042. [PMID: 35593182 PMCID: PMC9623734 DOI: 10.1093/trstmh/trac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/21/2022] [Accepted: 03/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The mainstay of diagnostic confirmation of acute Japanese encephalitis (JE) involves detection of anti-JE virus (JEV) immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA). Limitations in the specificity of this test are increasingly apparent with the introduction of JEV vaccinations and the endemicity of other cross-reactive flaviviruses. Virus neutralization testing (VNT) is considered the gold standard, but it is challenging to implement and interpret. We performed a pilot study to assess IgG depletion prior to VNT for detection of anti-JEV IgM neutralizing antibodies (IgM-VNT) as compared with standard VNT. METHODS We evaluated IgM-VNT in paired sera from anti-JEV IgM ELISA-positive patients (JE n=35) and negative controls of healthy flavivirus-naïve (n=10) as well as confirmed dengue (n=12) and Zika virus (n=4) patient sera. IgM-VNT was subsequently performed on single sera from additional JE patients (n=76). RESULTS Anti-JEV IgG was detectable in admission serum of 58% of JE patients. The positive, negative and overall percentage agreement of IgM-VNT as compared with standard VNT was 100%. A total of 12/14 (86%) patient samples were unclassified by VNT and, with sufficient sample available for IgG depletion and IgG ELISA confirming depletion, were classified by IgM-VNT. IgM-VNT enabled JE case classification in 72/76 (95%) patients for whom only a single sample was available. CONCLUSIONS The novel approach has been readily adapted for high-throughput testing of single patient samples and it holds promise for incorporation into algorithms for use in reference centres.
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Affiliation(s)
- Tehmina Bharucha
- Department of Biochemistry, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Nazli Ayhan
- Unité des Virus Émergents, Aix-Marseille Univ-IRD 190-Inserm 1207, Marseille, France
| | - Boris Pastorino
- Unité des Virus Émergents, Aix-Marseille Univ-IRD 190-Inserm 1207, Marseille, France
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Institute of Research and Education Development, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anisone Changthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Ooyanong Phonemixay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Jean-David Pommier
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- Institut Pasteur, Biology of Infection Unit, Paris, France
- Inserm U1117, Paris, France
- Intensive Care Department, University Hospital of Guadeloupe, France
| | | | - Nicole Zitzmann
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xavier de Lamballerie
- Unité des Virus Émergents, Aix-Marseille Univ-IRD 190-Inserm 1207, Marseille, France
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust-Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Unité des Virus Émergents, Aix-Marseille Univ-IRD 190-Inserm 1207, Marseille, France
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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11
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CRISPR-Cas-mediated diagnostics. Trends Biotechnol 2022; 40:1326-1345. [PMID: 35595574 DOI: 10.1016/j.tibtech.2022.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023]
Abstract
An ideal molecular diagnostic method should be sensitive, specific, low cost, rapid, portable, and easy to operate. Traditional nucleic acid detection methods based mainly on PCR technology have not only high sensitivity and specificity, but also some limitations, such as the need for expensive equipment and skilled technicians, being both time and labor intensive, and difficult to implement in some regions. However, with the continuous development of CRISPR-Cas technology and its application in molecular diagnosis, new approaches have been used for the construction of molecular diagnostic systems. In this review, we discuss recent advances in CRISPR-based molecular diagnostic technologies and highlight the revolution they bring to the field of molecular diagnostics.
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12
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Lan Z, Guo Y, Wang K, Zhang Y, Chen Y, Zheng D, Xu X, Wu W. Hundreds-Dollar-Level Multiplex Integrated RT-qPCR Quantitative System for Field Detection. BIOSENSORS 2022; 12:706. [PMID: 36140090 PMCID: PMC9496240 DOI: 10.3390/bios12090706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic poses a threat to global health. Due to its high sensitivity, specificity, and stability, real-time fluorescence quantitative (real-time PCR) detection has become the most extensively used approach for diagnosing SARS-CoV-2 pneumonia. According to a report from the World Health Organization, emerging and underdeveloped nations lack nucleic acid detection kits and polymerase chain reaction (PCR) instruments for molecular biological detection. In addition, sending samples to a laboratory for testing may result in considerable delays between sampling and diagnosis, which is not favorable to the timely prevention and control of new crown outbreaks. Concurrently, there is an urgent demand for accurate PCR devices that do not require a laboratory setting, are more portable, and are capable of completing testing on-site. Hence, we report on HDLRT-qPCR, a new, low-cost, multiplexed real-time fluorescence detection apparatus that we have developed for on-site testing investigations of diverse diseases in developing nations. This apparatus can complete on-site testing rapidly and sensitively. The entire cost of this instrument does not exceed USD 760. In order to demonstrate the applicability of our PCR instrument, we conducted testing that revealed that we achieved gradient amplification and melting curves comparable to those of commercially available equipment. Good consistency characterized the testing outcomes. The successful detection of target genes demonstrates the reliability of our inexpensive PCR diagnostic technique. With this apparatus, there is no need to transport samples to a central laboratory; instead, we conduct testing at the sampling site. This saves time on transportation, substantially accelerates overall testing speed, and provides results within 40 min.
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Affiliation(s)
- Zhihao Lan
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510075, China
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510075, China
| | - Yipeng Zhang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510075, China
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - Youyun Chen
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510075, China
| | - Dezhou Zheng
- College of Applied Physics and Materials, Wuyi University, Jiangmen 529000, China
| | - Xiaolong Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529000, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510075, China
- State Key Laboratory of ASIC and Systems, Fudan University, Shanghai 200433, China
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13
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Pham D, Howard-Jones AR, Hueston L, Jeoffreys N, Doggett S, Rockett R, Eden JS, Sintchenko V, Chen SCA, O’Sullivan MV, Maddocks S, Dwyer DE, Kok J. Emergence of Japanese encephalitis in Australia: a diagnostic perspective. Pathology 2022; 54:669-677. [DOI: 10.1016/j.pathol.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
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Zhang Y, Li Y, Guan Z, Yang Y, Zhang J, Sun Q, Li B, Qiu Y, Liu K, Shao D, Ma Z, Wei J, Li P. Rapid Differential Detection of Japanese Encephalitis Virus and Getah Virus in Pigs or Mosquitos by a Duplex TaqMan Real-Time RT-PCR Assay. Front Vet Sci 2022; 9:839443. [PMID: 35464361 PMCID: PMC9023051 DOI: 10.3389/fvets.2022.839443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/18/2022] [Indexed: 11/20/2022] Open
Abstract
Both JEV (Japanese encephalitis virus) and GETV (Getah virus) pose huge threats to the safety of animals and public health. Pigs and mosquitoes play a primary role in JEV and GETV transmission. However, there is no way to quickly distinguish between JEV and GETV. In this study, we established a one-step duplex TaqMan RT-qPCR for rapid identification and detection of JEV and GETV. Primers and probes located in the NS1 gene of JEV and the E2 gene of GETV that could specifically distinguish JEV from GETV were selected for duplex TaqMan RT-qPCR. In duplex real-time RT-qPCR detection, the correlation coefficients (R2) of the two viruses were higher than 0.999. The RT-qPCR assay demonstrated high sensitivity, extreme specificity, and excellent repeatability. Detection of JEV and GETV in field mosquito and pig samples was 100 times and 10 times more sensitive than using traditional PCR, respectively. In addition, the new test took less time and could be completed in under an hour. Clinical sample testing revealed the prevalence of JEV and GETV in mosquitoes and pig herds in China. This complete duplex TaqMan RT-qPCR assay provided a fast, efficient, specific, and sensitive tool for the detection and differentiation of JEV and GETV.
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Affiliation(s)
- Yan Zhang
- College of Animal Science, Yangtze University, Jingzhou, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yuhao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhixin Guan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yang Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Junjie Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Qing Sun
- College of Animal Science, Yangtze University, Jingzhou, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Peng Li
- College of Animal Science, Yangtze University, Jingzhou, China
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15
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Ghosh S, Straus DL, Good C, Phuntumart V. Development and comparison of loop-mediated isothermal amplification with quantitative PCR for the specific detection of Saprolegnia spp. PLoS One 2021; 16:e0250808. [PMID: 34898622 PMCID: PMC8668100 DOI: 10.1371/journal.pone.0250808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Saprolegniasis is an important disease in freshwater aquaculture, and is associated with oomycete pathogens in the genus Saprolegnia. Early detection of significant levels of Saprolegnia spp. pathogens would allow informed decisions for treatment which could significantly reduce losses. This study is the first to report the development of loop-mediated isothermal amplification (LAMP) for the detection of Saprolegnia spp. and compares it with quantitative PCR (qPCR). The developed protocols targeted the internal transcribed spacer (ITS) region of ribosomal DNA and the cytochrome C oxidase subunit 1 (CoxI) gene and was shown to be specific only to Saprolegnia genus. This LAMP method can detect as low as 10 fg of S. salmonis DNA while the qPCR method has a detection limit of 2 pg of S. salmonis DNA, indicating the superior sensitivity of LAMP compared to qPCR. When applied to detect the pathogen in water samples, both methods could detect the pathogen when only one zoospore of Saprolegnia was present. We propose LAMP as a quick (about 20–60 minutes) and sensitive molecular diagnostic tool for the detection of Saprolegnia spp. suitable for on-site applications.
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Affiliation(s)
- Satyaki Ghosh
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - David L. Straus
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree-Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, United States of America
| | - Christopher Good
- The Conservation Fund’s Freshwater Institute, Shepherdstown, West Virginia, United States of America
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
- * E-mail:
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Navien TN, Yeoh TS, Anna A, Tang TH, Citartan M. Aptamers isolated against mosquito-borne pathogens. World J Microbiol Biotechnol 2021; 37:131. [PMID: 34240263 DOI: 10.1007/s11274-021-03097-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 11/27/2022]
Abstract
Mosquito-borne diseases are a major threat to public health. The shortcomings of diagnostic tools, especially those that are antibody-based, have been blamed in part for the rising annual morbidity and mortality caused by these diseases. Antibodies harbor a number of disadvantages that can be clearly addressed by aptamers as the more promising molecular recognition elements. Aptamers are defined as single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit high binding affinity and specificity against a wide variety of target molecules based on their unique structural conformations. A number of aptamers were developed against mosquito-borne pathogens such as Dengue virus, Zika virus, Chikungunya virus, Plasmodium parasite, Francisella tularensis, Japanese encephalitis virus, Venezuelan equine encephalitis virus, Rift Valley fever virus and Yellow fever virus. Intrigued by these achievements, we carry out a comprehensive overview of the aptamers developed against these mosquito-borne infectious agents. Characteristics of the aptamers and their roles in diagnostic, therapeutic as well as other applications are emphasized.
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Affiliation(s)
- Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Tzi Shien Yeoh
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Andrew Anna
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak (UNIMAS), 94300, Kota Samarahan, Sarawak, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Improvement in the sensitivity of viroid detection by adapting the reverse transcription step in one-step RT-qPCR assays. J Virol Methods 2021; 292:114123. [PMID: 33711376 DOI: 10.1016/j.jviromet.2021.114123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/11/2020] [Accepted: 03/07/2021] [Indexed: 11/22/2022]
Abstract
Over the course of developing and applying a new real-time PCR assay for the detection of the newly described apple chlorotic fruit spot viroid (ACFSVd), slight modifications of the reverse transcription (RT) step were found to improve significantly the detection limit of the assay. To prove this hypothesis, three different one-step RT-qPCR kits for the detection of three plant viroids and three plant viruses were compared. The results showed both extension of the RT reaction time from 10 or 15 min-30 min or the increase in reaction temperature from 49 to 52 °C for the cDNA synthesis step results in a 10 times higher sensitivity for potato spindle tuber viroid and apple scar skin viroid one-step RT-qPCR assay and 45 higher sensitivity for ACFSVd one-step RT-qPCR assay. No variation in the detection limit was observed when the modifications were tested on tomato brown rugose fruit virus, plum pox virus and tomato ringspot virus assays. This finding is highly valuable for the investigation of viroids in general and could contribute to enhance sensitivity in their detection and to benefit regulatory outcomes for national plant protection organisations.
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18
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Rapid and simultaneous detection of Japanese encephalitis virus by real-time nucleic acid sequence-based amplification. Microb Pathog 2021; 150:104724. [PMID: 33400988 DOI: 10.1016/j.micpath.2020.104724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 11/23/2022]
Abstract
Japaneses encephalitis (JE) is most common zoonoses caused by Japanese encephalitis virus (JEV) with a high mortality and disability rate. To take timely preventive and control measures, early and rapid detection of JE RNA is necessary. But due to characteristic brief and low viraemia, JE RNA detection remains challenging. In this study, a real-time nucleic acid sequence-based amplification (RT-NASBA) was developed for rapid and simultaneous detection of JEV. Four pairs of primer were designed using a multiple genome alignment of all JEV strains from GenBank. NASBA assay established and optimal reaction conditions were confirmed by using primers and probe on ns1 gene of JEV. The specificity and sensitivity of the assay were compared with RT-PCR by using serial RNA and virus cultivation dilutions. The results showed that JEV RT-NASBA assay was established, and robust signals could be observed in 10 min with high specificity. The limit of dectetion of RT-NASBA was 6 copies per reaction. The assay was thus 100 to 1, 000 times more sensitive than RT-PCR. The cross-reaction was performed with other porcine pathogens, and negative amplification results indicated the high specificity of this method. The novel JEV RT-NASBA assay could be used as an efficient molecular biology tool to diagnose JEV, which would facilitate the surveillance of reproductive failure disease in swine and would be beneficial for public health security.
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Investigation of Japanese encephalitis virus as a cause of acute encephalitis in southern Pakistan, April 2015-January 2018. PLoS One 2020; 15:e0234584. [PMID: 32530966 PMCID: PMC7292402 DOI: 10.1371/journal.pone.0234584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Background Japanese encephalitis (JE) occurs in fewer than 1% of JE virus (JEV) infections, often with catastrophic sequelae including death and neuropsychiatric disability. JEV transmission in Pakistan was documented in 1980s and 1990s, but recent evidence is lacking. Our objective was to investigate JEV as a cause of acute encephalitis in Pakistan. Methods Persons aged ≥1 month with possible JE admitted to two acute care hospitals in Karachi, Pakistan from April 2015 to January 2018 were enrolled. Cerebrospinal fluid (CSF) or serum samples were tested for JEV immunoglobulin M (IgM) using the InBios JE DetectTM assay. Positive or equivocal samples had confirmatory testing using plaque reduction neutralization tests. Results Among 227 patients, testing was performed on CSF in 174 (77%) and on serum in 53 (23%) patients. Six of eight patient samples positive or equivocal for JEV IgM had sufficient volume for confirmatory testing. One patient had evidence of recent West Nile virus (WNV) neurologic infection based on CSF testing. One patient each had recent dengue virus (DENV) infection and WNV infection based on serum results. Recent flavivirus infections were identified in two persons, one each based on CSF and serum results. Specific flaviviruses could not be identified due to serologic cross-reactivity. For the sixth person, JEV neutralizing antibodies were confirmed in CSF but there was insufficient volume for further testing. Conclusions Hospital-based JE surveillance in Karachi, Pakistan could not confirm or exclude local JEV transmission. Nonetheless, Pakistan remains at risk for JE due to presence of the mosquito vector, amplifying hosts, and rice irrigation. Laboratory surveillance for JE should continue among persons with acute encephalitis. However, in view of serological cross-reactivity, confirmatory testing of JE IgM positive samples at a reference laboratory is essential.
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20
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An J, Jiang Y, Shi B, Wu D, Wu W. Low-Cost Battery-Powered and User-Friendly Real-Time Quantitative PCR System for the Detection of Multigene. MICROMACHINES 2020; 11:mi11040435. [PMID: 32326194 PMCID: PMC7231343 DOI: 10.3390/mi11040435] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022]
Abstract
Real-time polymerase chain reaction (PCR) is the standard for nucleic acid detection and plays an important role in many fields. A new chip design is proposed in this study to avoid the use of expensive instruments for hydrophobic treatment of the surface, and a new injection method solves the issue of bubbles formed during the temperature cycle. We built a battery-powered real-time PCR device to follow polymerase chain reaction using fluorescence detection and developed an independently designed electromechanical control system and a fluorescence analysis software to control the temperature cycle, the photoelectric detection coupling, and the automatic analysis of the experimental data. The microchips and the temperature cycling system cost USD 100. All the elements of the device are available through open access, and there are no technical barriers. The simple structure and manipulation allows beginners to build instruments and perform PCR tests after only a short tutorial. The device is used for analysis of the amplification curve and the melting curve of multiple target genes to demonstrate that our instrument has the same accuracy and stability as a commercial instrument.
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Affiliation(s)
- Junru An
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
| | - Bing Shi
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Di Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Correspondence: ; Tel.: +86-431-8670-8159
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21
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A need to raise the bar - A systematic review of temporal trends in diagnostics for Japanese encephalitis virus infection, and perspectives for future research. Int J Infect Dis 2020; 95:444-456. [PMID: 32205287 PMCID: PMC7294235 DOI: 10.1016/j.ijid.2020.03.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/09/2020] [Accepted: 03/15/2020] [Indexed: 12/14/2022] Open
Abstract
Japanese encephalitis virus (JEV) remains a leading cause of neurological infection in Asia. A systematic review identified 20,212 published human cases of laboratory-confirmed JEV infections from 205 studies. 15,167 (75%) of cases were confirmed with the lowest confidence diagnostic test, i.e., level 3 or 4, or level 4. Only 109 (53%) of the studies reported contemporaneous testing for dengue-specific antibodies. A fundamental pre-requisite for the control of JE is lacking — that of a simple and specific diagnostic procedure that can be adapted for point-of-care tests and readily used throughout JE endemic regions of the world.
Objective Japanese encephalitis virus infection (JE) remains a leading cause of neurological disease in Asia, mainly involving individuals living in remote areas with limited access to treatment centers and diagnostic facilities. Laboratory confirmation is fundamental for the justification and implementation of vaccination programs. We reviewed the literature on historical developments and current diagnostic capability worldwide, to identify knowledge gaps and instill urgency to address them. Methods Searches were performed in Web of Science and PubMed using the term 'Japanese encephalitis' up to 13th October 2019. Studies reporting laboratory-confirmed symptomatic JE cases in humans were included, and data on details of diagnostic tests were extracted. A JE case was classified according to confirmatory levels (Fischer et al., 2008; Campbell et al., 2011; Pearce et al., 2018; Heffelfinger et al., 2017), where level 1 represented the highest level of confidence. Findings 20,212 published JE cases were identified from 205 studies. 15,167 (75%) of these positive cases were confirmed with the lowest-confidence diagnostic tests (level 3 or 4, or level 4). Only 109 (53%) of the studies reported contemporaneous testing for dengue-specific antibodies. Conclusion A fundamental pre-requisite for the control of JEV is lacking — that of a simple and specific diagnostic procedure that can be adapted for point-of-care tests and readily used throughout JE-endemic regions of the world.
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Drews SJ, Makowski K, Wood H, Dimitrova K, Yan MTS, Young D, Skeate R, Ng M, Hawes G, Fearon M, Bigham M. A case series of inactivated Japanese encephalitis virus vaccination associated with positive West Nile virus blood donor screening nucleic acid tests. Transfusion 2020; 60:1097-1103. [PMID: 32154927 DOI: 10.1111/trf.15744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND West Nile Virus (WNV) is a member of the Japanese Encephalitis (JE) serocomplex within the Flaviviridae family. We report four whole blood donors and one plasma donor with WNV nucleic acid test (NAT)-reactive donations between September 2018 and November 2019, following recent Japanese Encephalitis virus (JEV) vaccination. CASE SERIES Cases 1 and 4 had reactive WNV NAT donations 1 day after receiving the JEV vaccine. Case 2 had a reactive WNV donation 3 days after receiving the JEV vaccine. Case 3 had a reactive WNV NAT donation 3 days after returning from Arizona and 1 day after receiving the JEV vaccine. Case 5 had a reactive WNV donation the same day as receiving the JEV vaccine. STUDY DESIGN AND METHODS WNV screening used the Roche cobas WNV nucleic acid test (NAT) (Roche Molecular Systems). Reference testing on WNV-reactive donations was carried out by the National Microbiology Laboratory (NML). JEV vaccine dilutions were also analyzed. RESULTS Supplemental NAT was negative for WNV and JEV for Cases 1, 3, and 5. Case 2 had a weak amplification curve for one of two JEV NAT targets. Case 4 was JEV NAT-positive, WNV NAT-negative. Serologic testing on donation specimens for Cases 2, 4, and 5 did not support recent or remote WNV infection. JEV vaccine dilutions were detected by both cobas and supplemental NAT. CONCLUSIONS We recommend implementing a temporary blood donor deferral following a JEV vaccination, if screening utilizes a WNV assay with the capability of detecting other members of the JE serocomplex.
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Affiliation(s)
- Steven J Drews
- Canadian Blood Services, Edmonton, Alberta, Canada.,Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kai Makowski
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Heidi Wood
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | | | - Matthew T S Yan
- Canadian Blood Services, Vancouver, British Columbia, Canada
| | - Dale Young
- Canadian Blood Services, Calgary, Alberta, Canada
| | | | - Michiko Ng
- Canadian Blood Services, Calgary, Alberta, Canada
| | - Gordon Hawes
- Canadian Blood Services, Brampton, Ontario, Canada
| | | | - Mark Bigham
- Canadian Blood Services, Vancouver, British Columbia, Canada
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Review of Emerging Japanese Encephalitis Virus: New Aspects and Concepts about Entry into the Brain and Inter-Cellular Spreading. Pathogens 2019; 8:pathogens8030111. [PMID: 31357540 PMCID: PMC6789543 DOI: 10.3390/pathogens8030111] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Japanese encephalitis virus (JEV) is an emerging flavivirus of the Asia-Pacific region. More than two billion people live in endemic or epidemic areas and are at risk of infection. Recently, the first autochthonous human case was recorded in Africa, and infected birds have been found in Europe. JEV may spread even further to other continents. The first section of this review covers established and new information about the epidemiology of JEV. The subsequent sections focus on the impact of JEV on humans, including the natural course and immunity. Furthermore, new concepts are discussed about JEV’s entry into the brain. Finally, interactions of JEV and host cells are covered, as well as how JEV may spread in the body through latently infected immune cells and cell-to-cell transmission of virions or via other infectious material, including JEV genomic RNA.
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Bharucha T, Sengvilaipaseuth O, Seephonelee M, Vongsouvath M, Vongsouvath M, Rattanavong S, Piorkowski G, Lecuit M, Gorman C, Pommier JD, Garson JA, Newton PN, de Lamballerie X, Dubot-Pérès A. Viral RNA Degradation Makes Urine a Challenging Specimen for Detection of Japanese Encephalitis Virus in Patients With Suspected CNS Infection. Open Forum Infect Dis 2019; 6:ofz048. [PMID: 30882014 PMCID: PMC6411208 DOI: 10.1093/ofid/ofz048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/14/2022] Open
Abstract
Background Japanese encephalitis virus (JEV) is a leading cause of central nervous system (CNS) infections in Asia and results in significant morbidity and mortality. JEV RNA is rarely detected in serum or cerebrospinal fluid (CSF), and diagnosis of JEV infection is usually based on serological tests that are frequently difficult to interpret. Unlike serum or CSF, urine is relatively easy to obtain, but, to date, there has been minimal work on the feasibility of testing urine for JEV RNA. Methods We investigated the use of lysis buffer and a Microsep device to optimize urine storage for detection of JEV RNA by reverse transcription real-time polymerase chain reaction (RT-qPCR). The best of the studied methods was then evaluated in consecutive patients admitted to the hospital with suspected CNS infections in Laos. Results We demonstrated degradation of JEV RNA in urine after even short storage periods at 4°C or –80°C. Although there was no advantage in using a Microsep concentration device alone, immediate addition of lysis buffer to fresh urine improved the detection of JEV RNA at the limit of detection. Conclusions In 2 studies of 41 patients with acute encephalitis syndrome, 11 (27%) were positive for JEV IgM in CSF and/or serum, and 2 (4.9%) were JEV RT-qPCR positive from throat swabs. JEV RNA was not detected in any of these patients’ urine samples. However, lysis buffer was only used during a prospective study, that is, for only 17/41 (41%) patient urine samples. Our findings suggest a need for larger studies testing urine for JEV RNA, with urine collected at different times from symptom onset, and using lysis buffer, which stabilizes RNA, for storage.
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Affiliation(s)
- Tehmina Bharucha
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R.,Division of Infection and Immunity, University College London, London, UK
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Malee Seephonelee
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Malavanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Marc Lecuit
- Biology of Infection Unit, Inserm U1117, Institut Pasteur, Paris, France.,Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Paris Descartes University, Paris, France
| | - Christopher Gorman
- Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Jean-David Pommier
- Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Jeremy A Garson
- Division of Infection and Immunity, University College London, London, UK.,Transfusion Microbiology, NHS Blood and Transplant, London, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Churchill Hospital, Oxford, UK
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Churchill Hospital, Oxford, UK.,Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
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