1
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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2
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Davila-Calderon J, Li ML, Penumutchu SR, Haddad C, Malcolm L, King J, Hargrove AE, Brewer G, Tolbert BS. Enterovirus evolution reveals the mechanism of an RNA-targeted antiviral and determinants of viral replication. SCIENCE ADVANCES 2024; 10:eadg3060. [PMID: 38363831 PMCID: PMC10871541 DOI: 10.1126/sciadv.adg3060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
Selective pressures on viruses provide opportunities to establish target site specificity and mechanisms of antivirals. Enterovirus (EV)-A71 with resistant mutations in the stem loop (SL) II internal ribosome entry site (IRES) (SLIIresist) were selected at low doses of the antiviral dimethylamiloride (DMA)-135. The EV-A71 mutants were resistant to DMA-135 at concentrations that inhibit replication of wild-type virus. EV-A71 IRES structures harboring resistant mutations induced efficient expression of Luciferase messenger RNA in the presence of noncytotoxic doses of DMA-135. Nuclear magnetic resonance indicates that the mutations change the structure of SLII at the binding site of DMA-135 and at the surface recognized by the host protein AU-rich element/poly(U)-binding/degradation factor 1 (AUF1). Biophysical studies of complexes formed between AUF1, DMA-135, and either SLII or SLIIresist show that DMA-135 stabilizes a ternary complex with AUF1-SLII but not AUF1-SLIIresist. This work demonstrates how viral evolution elucidates the (DMA-135)-RNA binding site specificity in cells and provides insights into the viral pathways inhibited by the antiviral.
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Affiliation(s)
| | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | | | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Linzy Malcolm
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Josephine King
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | | | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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3
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Abedeera SM, Davila-Calderon J, Haddad C, Henry B, King J, Penumutchu S, Tolbert BS. The Repurposing of Cellular Proteins during Enterovirus A71 Infection. Viruses 2023; 16:75. [PMID: 38257775 PMCID: PMC10821071 DOI: 10.3390/v16010075] [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: 12/09/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Viruses pose a great threat to people's lives. Enterovirus A71 (EV-A71) infects children and infants all over the world with no FDA-approved treatment to date. Understanding the basic mechanisms of viral processes aids in selecting more efficient drug targets and designing more effective antivirals to thwart this virus. The 5'-untranslated region (5'-UTR) of the viral RNA genome is composed of a cloverleaf structure and an internal ribosome entry site (IRES). Cellular proteins that bind to the cloverleaf structure regulate viral RNA synthesis, while those that bind to the IRES also known as IRES trans-acting factors (ITAFs) regulate viral translation. In this review, we survey the cellular proteins currently known to bind the 5'-UTR and influence viral gene expression with emphasis on comparing proteins' functions and localizations pre- and post-(EV-A71) infection. A comprehensive understanding of how the host cell's machinery is hijacked and reprogrammed by the virus to facilitate its replication is crucial for developing effective antivirals.
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Affiliation(s)
- Sudeshi M. Abedeera
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Jesse Davila-Calderon
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Barrington Henry
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Josephine King
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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4
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Yoo B, Kim MG, Min AY, Seo DW, Kim SH, Kim SH. Optimization of RT-PCR methods for enterovirus detection in groundwater. Heliyon 2023; 9:e23028. [PMID: 38149210 PMCID: PMC10750030 DOI: 10.1016/j.heliyon.2023.e23028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Enteroviruses (EVs), which belong to the Picornaviridae family, infect individuals asymptomatically or cause mild symptoms (fever, runny nose, cough, skin rash, sneezing, mouth blister). Severe cases can cause various diseases, such as acute hemorrhagic conjunctivitis, aseptic meningitis, or myocarditis, especially in infants. These viruses can be transmitted via the fecal-oral route via contaminated water. In this study, we established a polymerase chain reaction (PCR) method for detecting EVs in water sample using Coxsackievirus B5 (CV-B5) and Echovirus 30 (E-30), which belong to species B of the four species of EVs (EV-A to D). Several methods have been investigated and compared for the detection of EVs, including real-time reverse transcription (RT) polymerase chain reaction and conventional RT-PCR. The most sensitive primer sets were selected, and the PCR conditions were modified to increase sensitivity. We also quantified the detection limits of real-time and conventional RT-PCR. The detection limits of conventional RT-PCR were detected in 105-106 copy/mL for CV-B5 and 106-107 copy/mL for E-30, respectively. This optimized method for detecting EVs is expected to contribute substantially to the investigation of EV outbreaks in water samples.
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Affiliation(s)
- Boeun Yoo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Mi-Gyeong Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - A Young Min
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Doo Won Seo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Seung Hwan Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Soon Han Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
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5
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Kim MJ, Lee JE, Kim KG, Park DW, Cho SJ, Kim TS, Kee HY, Kim SH, Park HJ, Seo MH, Chung JK, Seo JJ. Long-term sentinel surveillance of enteroviruses in Gwangju, South Korea, 2011-2020. Sci Rep 2023; 13:2798. [PMID: 36797345 PMCID: PMC9933826 DOI: 10.1038/s41598-023-29461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Human enteroviruses (EVs) are associated with a broad spectrum of diseases. To understand EV epidemiology, we present longitudinal data reflecting changing EV prevalence patterns in South Korea. We collected 7160 specimens from patients with suspected EV infections in ten hospitals in Gwangju, Korea during 2011-2020. RNA extraction and real-time reverse transcription polymerase chain reaction using EV-specific probes and primers were performed. EV genotyping and phylogenetic analysis were performed; EVs were detected in 3076 samples (43.0%), and the annual EV detection rate varied. EV infection rates did not differ with sex, and children aged ≤ 4 years were the most prone to EV infection; this trend did not change over time. Overall, 35 different EV types belonging to four distinctive species and rhinoviruses were identified. Although serotype distribution changed annually, the most frequently observed EVs were EV-A71 (13.1% of the cases), CVA6 (8.3%), CVB5 (7.6%), CVA16 (7.6%), CVA10 (7.5%), E18 (7.5%), E30 (7.0%), and E11 (5.0%) during 2011-2020. The predominant EV genotypes by clinical manifestation were CVB5 for aseptic meningitis; EV-A71 for hand, foot, and mouth disease cases; and CVA10 for herpangina. These results will aid the development of vaccines against EV infection and allow comprehensive disease control.
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Affiliation(s)
- Min Ji Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea, 61954.
| | - Ji-eun Lee
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Kwang gon Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Duck Woong Park
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Sun Ju Cho
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Tae sun Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Hye-young Kee
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Sun-Hee Kim
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Hye jung Park
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Mi Hee Seo
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Jae Keun Chung
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
| | - Jin-jong Seo
- Department of Infectious Disease Research, Health & Environment Research Institute of Gwangju, 584 Mujin-Daero, Seogu, Gwangju, Republic of Korea 61954
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6
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Cui G, Wang H, Yang C, Zhou X, Wang J, Wang T, Ma T. Berberine prevents lethal EV71 neurological infection in newborn mice. Front Pharmacol 2022; 13:1027566. [PMID: 36386168 PMCID: PMC9640474 DOI: 10.3389/fphar.2022.1027566] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/14/2022] [Indexed: 12/01/2022] Open
Abstract
Enterovirus 71 (EV71) is the major pathogen causing fatal neurological complications of hand, foot, and mouth disease (HFMD) in young children. Currently no effective antiviral therapy is available. In the present study, we found that natural compound Berberine (BBR) displayed potent inhibitory effects on EV71 replication in various neural cells (IC50 of 2.79–4.03 μM). In a newborn mouse model of lethal EV71 infection, Berberine at 2–5 mg/kg markedly reduced mortality and clinical scores. Consistently, the replication of EV71 and pathological changes were attenuated in various infected organs including brain and lung with BBR treatment. Interestingly, EV71 infection in the brain mainly localized in the peripheral zone of brainstem and largely in astrocytes. Primary culture of astrocytes from newborn mouse brain confirmed the efficient EV71 replication that was mostly inhibited by BBR treatment at 5 μM. Further investigations revealed remarkably elevated cellular reactive oxygen species (ROS) levels that coincided with EV71 replication in primary cultured astrocytes and various cell lines. BBR largely abolished the virus-elevated ROS production and greatly diminished EV71 replication by up-regulating NFE2 like bZIP transcription factor 2 (Nrf2) via the kelch like ECH associated protein 1 (Keap)-Nrf2 axis. The nuclear localization of Nrf2 and expression of downstream antioxidant enzymes heme oxygenase 1 (HO-1) and NAD(P)H quinone dehydrogenase 1 (NQO1) were increased significantly by BBR treatment. Collectively, our findings revealed that BBR prevents lethal EV71 neurological infection via inhibiting virus replication through regulating Keap-Nrf2 axis and ROS generation in astrocytes of brainstem, thus providing a potential antiviral treatment for severe EV71 infection associated with neurological complications.
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7
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Chen Z, Bao L, Zhu B, Fu H, Zhu S, Ji T, Xue Y, Liu C, Wang X, Li F, Lv Q, Qi F, Yu P, Deng W, Xu W, Qin C, Liu H, Jin Q. Structural and functional analysis of a potent human neutralizing antibody against enterovirus A71. SCIENCE CHINA LIFE SCIENCES 2022; 65:2517-2526. [PMID: 35696017 PMCID: PMC9189450 DOI: 10.1007/s11427-021-2095-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/22/2022] [Indexed: 10/29/2022]
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8
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Qin B, Craven GB, Hou P, Chesti J, Lu X, Child ES, Morgan RML, Niu W, Zhao L, Armstrong A, Mann DJ, Cui S. Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 71 3C and SARS-CoV-2 main protease. Acta Pharm Sin B 2022; 12:3924-3933. [PMID: 35702321 PMCID: PMC9181371 DOI: 10.1016/j.apsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
RNA viruses are critically dependent upon virally encoded proteases to cleave the viral polyproteins into functional proteins. Many of these proteases exhibit a similar fold and contain an essential catalytic cysteine, offering the opportunity to inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold and a similar active site. The hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity. We demonstrate that targeting the active site cysteine of Mpro can have profound allosteric effects, distorting secondary structures to disrupt the active dimeric unit.
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Affiliation(s)
- Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, China
| | - Gregory B Craven
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Pengjiao Hou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, China
| | - Julian Chesti
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Xinran Lu
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Emma S Child
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Rhodri M L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Wenchao Niu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - David J Mann
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, China
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Nhu LNT, Nhan LNT, Anh NT, Hong NTT, Van HMT, Thanh TT, Hang VTT, Han DDK, Ny NTH, Nguyet LA, Quy DT, Qui PT, Khanh TH, Hung NT, Tuan HM, Chau NVV, Thwaites G, van Doorn HR, Tan LV. Coxsackievirus A16 in Southern Vietnam. Front Microbiol 2021; 12:689658. [PMID: 34248913 PMCID: PMC8265502 DOI: 10.3389/fmicb.2021.689658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/11/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Hand, Foot and Mouth Disease (HFMD) is a major public health concern in the Asia-Pacific region. Most recent HFMD outbreaks have been caused by enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), CVA10, and CVA6. There has been no report regarding the epidemiology and genetic diversity of CVA16 in Vietnam. Such knowledge is critical to inform the development of intervention strategies. Materials and Methods: From 2011 to 2017, clinical samples were collected from in- and outpatients enrolled in a HFMD research program conducted at three referral hospitals in Ho Chi Minh City (HCMC), Vietnam. Throat or rectal swabs positive for CVA16 with sufficient viral load were selected for whole genome sequencing and evolutionary analysis. Results: Throughout the study period, 320 CVA16 positive samples were collected from 2808 HFMD patients (11.4%). 59.4% of patients were male. The median age was 20.8 months (IQR, 14.96–31.41). Patients resided in HCMC (55.3%), Mekong Delta (22.2%), and South East Vietnam (22.5%). 10% of CVA16 infected patients had moderately severe or severe HFMD. CVA16 positive samples from 153 patients were selected for whole genome sequencing, and 66 complete genomes were obtained. Phylogenetic analysis demonstrated that Vietnamese CVA16 strains belong to a single genogroup B1a that clusters together with isolates from China, Japan, Thailand, Malaysia, France and Australia. The CVA16 strains of the present study were circulating in Vietnam some 4 years prior to its detection in HFMD cases. Conclusion: We report for the first time on the molecular epidemiology of CVA16 in Vietnam. Unlike EV-A71, which showed frequent replacement between subgenogroups B5 and C4 every 2–3 years in Vietnam, CVA16 displays a less pronounced genetic alternation with only subgenogroup B1a circulating in Vietnam since 2011. Our collective findings emphasize the importance of active surveillance for viral circulation in HFMD endemic countries, critical to informing outbreak response and vaccine development.
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Affiliation(s)
| | | | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Hoang Minh Tu Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Children's Hospital 2, Ho Chi Minh City, Vietnam
| | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ty Hang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do Duong Kim Han
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Du Tuan Quy
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Phan Tu Qui
- Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | | | | | - Ha Manh Tuan
- Children's Hospital 2, Ho Chi Minh City, Vietnam
| | | | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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10
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Brouwer L, Moreni G, Wolthers KC, Pajkrt D. World-Wide Prevalence and Genotype Distribution of Enteroviruses. Viruses 2021; 13:v13030434. [PMID: 33800518 PMCID: PMC7999254 DOI: 10.3390/v13030434] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/18/2022] Open
Abstract
Enteroviruses (EVs) are highly prevalent viruses world-wide, causing a wide range of diseases in both children and adults. Insight in the global prevalence of EVs is important to define their clinical significance and total disease burden, and assists in making therapeutic decisions. While many studies have been conducted to describe epidemiology of EVs in specific (sub)populations and patient cohorts, little effort has been made to aggregate the available evidence. In the current study, we conducted a search in the PubMed and Embase (Ovid) databases to identify articles reporting EV prevalence and type distribution. We summarized the findings of 153 included studies. We found that EVs are highly prevalent viruses in all continents. Enterovirus B was the most detected species worldwide, while the other species showed continent-specific differences, with Enterovirus C more detected in Africa and Enterovirus A more detected in Asia. Echovirus 30 was by far the most detected type, especially in studies conducted in Europe. EV types in species Enterovirus B-including echovirus 30-were often detected in patient groups with neurological infections and in cerebrospinal fluid, while Enterovirus C types were often found in stool samples.
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Affiliation(s)
- Lieke Brouwer
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (G.M.); (K.C.W.)
- Department of Pediatric Infectious Diseases, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
- Correspondence:
| | - Giulia Moreni
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (G.M.); (K.C.W.)
- Department of Pediatric Infectious Diseases, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Katja C. Wolthers
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (G.M.); (K.C.W.)
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
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11
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Luciani L, Morand A, Zandotti C, Piorkowski G, Boutin A, Mazenq J, Minodier P, Ninove L, Nougairède A. Circulation of enterovirus A71 during 2019-2020, Marseille, France. J Med Virol 2021; 93:5163-5166. [PMID: 33605462 DOI: 10.1002/jmv.26893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/11/2022]
Abstract
Enteroviruses A71 (EVs-A71) are known to cause serious neurological infections, especially in the pediatric population. We report here eight cases of EV-A71 infection diagnosed in Marseille over the past 2 years (seven cases in 2019 and one case in 2020). Only children under 5 years of age were affected, including one case of acute flaccid paralysis. Viral RNA was detected by RT-PCR in peripheral samples for all cases (feces and upper respiratory samples). Phylogenetic analyses based on VP1 and 2C3C coding regions revealed that all these cases of EV-A71 infection were caused by viruses belonging to the subgenogroup C1 that currently circulates in Europe and that these viruses are genetically closed to other EVs-A71 recently detected in European countries. These data therefore reinforce the usefulness of the enterovirus surveillance network and the need for systematic screening for EV-A71 in case of an enteroviral infection. This study therefore suggests that the systematic screening for EV-A71 in case of enteroviral infection could provide additional data for enterovirus surveillance networks.
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Affiliation(s)
- Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
| | - Aurélie Morand
- Service de médecine infantile et pédiatrie spécialisée, CHU Timone, AP-HM, Marseille, France.,Aix Marseille University, IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - Christine Zandotti
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France
| | - Aurélie Boutin
- Service des urgences pédiatriques, CHU Timone AP-HM, Marseille, France
| | - Julie Mazenq
- Service des urgences pédiatriques, CHU Timone AP-HM, Marseille, France
| | - Philippe Minodier
- Service des urgences pédiatriques, CHU Nord AP-HM, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
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12
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Pan Q, Liu F, Zhang J, Zhao X, Hu Y, Fan C, Yang F, Chang Z, Xiao X. Regional-level risk factors for severe hand-foot-and-mouth disease: an ecological study from mainland China. Environ Health Prev Med 2021; 26:4. [PMID: 33419405 PMCID: PMC7792012 DOI: 10.1186/s12199-020-00927-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
Background Severe hand-foot-and-mouth disease (HFMD) is a life-threatening contagious disease among young children and infants. Although enterovirus A71 has been well acknowledged to be the dominant cause of severe HFMD, there still remain other unidentified risk factors for severe HFMD. Previous studies mainly focused on identifying the individual-level risk factors from a clinical perspective, while rare studies aimed to clarify the association between regional-level risk factors and severe HFMD, which may be more important from a public health perspective. Methods We retrieved the clinical HFMD counts between 2008 and 2014 from the Chinese Center for Disease Control and Prevention, which were used to calculated the case-severity rate in 143 prefectural-level cities in mainland China. For each of those 143 cities, we further obtained city-specific characteristics from the China City Statistical Yearbook (social and economic variables) and the national meteorological monitoring system (meteorological variables). A Poisson regression model was then used to estimate the associations between city-specific characteristics (reduced by the principal component analysis to avoid multicollinearity) and the case-severity rate of HFMD. The above analysis was further stratified by age and gender to examine potential modifying effects and vulnerable sub-populations. Results We found that the case-severity rate of HFMD varied dramatically between cities, ranging from 0 to 8.09%. Cities with high case-severity rates were mainly clustered in Central China. By relating the case-severity rate to city-specific characteristics, we found that both the principal component characterized by a high level of social and economic development (RR = 0.823, 95%CI 0.739, 0.916) and another that characterized by warm and humid climate (RR = 0.771, 95%CI 0.619, 0.960) were negatively associated with the case-severity rate of HFMD. These estimations were consistent across age and gender sub-populations. Conclusion Except for the type of infected pathogen, the case-severity rate of HFMD was closely related to city development and meteorological factor. These findings suggest that social and environmental factors may also play an important role in the progress of severe HFMD. Supplementary Information The online version contains supplementary material available at 10.1186/s12199-020-00927-9.
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Affiliation(s)
- Qing Pan
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Fengfeng Liu
- Division of Infectious Disease & Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Juying Zhang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Xing Zhao
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Yifan Hu
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Chaonan Fan
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Fan Yang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Zhaorui Chang
- Division of Infectious Disease & Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China.
| | - Xiong Xiao
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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13
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Nguyet LA, Thanh TT, Nhan LNT, Hong NTT, Nhu LNT, Van HMT, Ny NTH, Anh NT, Han DDK, Tuan HM, Huy VQ, Viet HL, Cuong HQ, Thao NTT, Viet DC, Khanh TH, Thwaites L, Clapham H, Hung NT, Chau NVV, Thwaites G, Ha DQ, van Doorn HR, Tan LV. Neutralizing Antibodies against Enteroviruses in Patients with Hand, Foot and Mouth Disease. Emerg Infect Dis 2021; 26:298-306. [PMID: 31961293 PMCID: PMC6986819 DOI: 10.3201/eid2602.190721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hand, foot and mouth disease (HFMD) is an emerging infection with pandemic potential. Knowledge of neutralizing antibody responses among its pathogens is essential to inform vaccine development and epidemiologic research. We used 120 paired-plasma samples collected at enrollment and >7 days after the onset of illness from HFMD patients infected with enterovirus A71 (EV-A71), coxsackievirus A (CVA) 6, CVA10, and CVA16 to study cross neutralization. For homotypic viruses, seropositivity increased from <60% at enrollment to 97%-100% at follow-up, corresponding to seroconversion rates of 57%-93%. Seroconversion for heterotypic viruses was recorded in only 3%-23% of patients. All plasma samples from patients infected with EV-A71 subgenogroup B5 could neutralize the emerging EV-A71 subgenogroup C4. Collectively, our results support previous reports about the potential benefit of EV-A71 vaccine but highlight the necessity of multivalent vaccines to control HFMD.
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14
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Brown DM, Zhang Y, Scheuermann RH. Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses. Microorganisms 2020; 8:microorganisms8121856. [PMID: 33255654 PMCID: PMC7759938 DOI: 10.3390/microorganisms8121856] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) are positive-sense RNA viruses, with over 50,000 nucleotide sequences publicly available. While most human infections are typically associated with mild respiratory symptoms, several different EV types have also been associated with severe human disease, especially acute flaccid paralysis (AFP), particularly with endemic members of the EV-B species and two pandemic types—EV-A71 and EV-D68—that appear to be responsible for recent widespread outbreaks. Here we review the recent literature on the prevalence, characteristics, and circulation dynamics of different enterovirus types and combine this with an analysis of the sequence coverage of different EV types in public databases (e.g., the Virus Pathogen Resource). This evaluation reveals temporal and geographic differences in EV circulation and sequence distribution, highlighting recent EV outbreaks and revealing gaps in sequence coverage. Phylogenetic analysis of the EV genus shows the relatedness of different EV types. Recombination analysis of the EV-A species provides evidence for recombination as a mechanism of genomic diversification. The absence of broadly protective vaccines and effective antivirals makes human enteroviruses important pathogens of public health concern.
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Affiliation(s)
- David M Brown
- Department of Synthetic Biology, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- La Jolla Institute for Immunology, La Jolla, CA 92065, USA
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15
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Hoa-Tran TN, Dao ATH, Nguyen AT, Kataoka C, Takemura T, Pham CH, Vu HM, Hong TTT, Ha NTV, Duong TN, Thanh NTH, Shimizu H. Coxsackieviruses A6 and A16 associated with hand, foot, and mouth disease in Vietnam, 2008-2017: Essential information for rational vaccine design. Vaccine 2020; 38:8273-8285. [PMID: 33223308 DOI: 10.1016/j.vaccine.2020.11.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 12/20/2022]
Abstract
Development of multivalent hand, foot, and mouth disease (HFMD) vaccines against enterovirus A71 (EV-A71) and several non-EV-A71 enteroviruses is needed for this life-threatening disease with a huge economic burden in Asia-Pacific countries. Comprehensive studies on the molecular epidemiology and genetic and antigenic characterization of major causative enteroviruses will provide information for rational vaccine design. Compared with molecular studies on EV-A71, that for non-EV-A71 enteroviruses remain few and limited in Vietnam. Therefore, we conducted a 10-year study on the circulation and genetic characterization of coxsackievirus A16 (CV-A16) and CV-A6 isolated from patients with HFMD in Northern Vietnam between 2008 and 2017. Enteroviruses were detected in 2228 of 3212 enrolled patients. Of the 42 serotypes assigned, 28.4% and 22.4% accounted for CV-A6 and CV-A16, being the second and the third dominant serotypes after EV-A71 (31.7%), respectively. The circulation of CV-A16 and CV-A6 showed a wide geographic distribution and distinct periodicity. Phylogenetic analyses revealed that the majority of Vietnamese CV-A6 and CV-A16 strains were located within the largest sub-genotypes or sub-genogroups. These comprised strains isolated from patients with HFMD worldwide during the past decade and the Vietnamese strains have been evolving in a manner similar to the strains circulating worldwide. Amino acid sequences of the putative functional loops on VP1 and other VPs among Vietnamese CV-A6 and CV-A16 isolates were highly conserved. Moreover, the functional loop patterns of VP1 were similar to the dominant patterns found worldwide, except for the T164K substitution on the EF loop in Vietnamese CV-A16. The findings suggest that the development of a universal HFMD vaccine, at least in Vietnam, must target CV-A6 and CV-A16 as two of the three major HFMD-causing serotypes. Vietnamese isolates or their genome sequences can be considered for rational vaccine design.
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Affiliation(s)
| | - Anh Thi Hai Dao
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Anh The Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Chikako Kataoka
- The Research Foundation for Microbial Diseases of Osaka University, Japan
| | - Taichiro Takemura
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Chau Ha Pham
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hung Manh Vu
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Ta Thi Thu Hong
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Nguyen Thi Viet Ha
- Hanoi Medical University, Hanoi, Viet Nam; National Children's Hospital, Hanoi, Viet Nam
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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16
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Puenpa J, Chansaenroj J, Auphimai C, Srimuan D, Thatsanathorn T, Poovorawan Y, Wanlapakorn N. Neutralizing antibody against Enterovirus-A71 in Thai children: A longitudinal study from birth to age 4 years. Vaccine 2020; 38:7638-7644. [PMID: 33067033 DOI: 10.1016/j.vaccine.2020.10.002] [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: 08/21/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 11/19/2022]
Abstract
Thailand is one of the countries in the Asia-pacific region that has been most affected by the Enterovirus-A71 (EV-A71) epidemic. An individual who is susceptible to EV-A71 may also be infected asymptomatically, thus, a serological assay is a useful tool to estimate the cumulative incidence of infection in the community and to provide guidance for vaccination scheduling. There have been several candidate EV-A71 vaccines, of which three have been approved and licensed in China. The population target for EV-A71 vaccine is children younger than three years of age. In Thailand, there are limited data available on the seroprevalence of EV-A71 neutralizing (NT) antibodies and the timing of seroconversion in children. This study aims to investigate the seroprevalence and seroconversion rate of EV-A71 NT antibody in a cohort of Thai children. Sera were collected at the King Chulalongkorn Memorial Hospital in Bangkok, Thailand from 100 children between 2015 and 2020. Maternal sera were collected on the day of delivery. Serum samples from children were collected at birth (month 0) and at 2, 7, 18, 24, 36, and 48 months of age to test for EV-A71 NT antibody titers using an enzyme-linked immunosorbent assay (ELISA)-based microneutralization test. The seroprotection rate (NT antibody ≥1:16) in children at months 0, 2, 7, 18, 24, 36, and 48 was 81.0%, 60.0%, 9.0%, 10.0%, 13.0%, 17.0%, and 37.1%, respectively. The seroprotection rate was lowest at month 7 due to waning of the maternal antibody and the immunity of children increased with increasing age. At 48 months of age, less than 40% of children were seroprotected. Children at the age of 6 months should be considered a primary target for vaccination.
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Affiliation(s)
- Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chompoonut Auphimai
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Donchida Srimuan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thaksaporn Thatsanathorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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17
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Haddad C, Davila-Calderon J, Tolbert BS. Integrated approaches to reveal mechanisms by which RNA viruses reprogram the cellular environment. Methods 2020; 183:50-56. [PMID: 32622045 PMCID: PMC7329689 DOI: 10.1016/j.ymeth.2020.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
RNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets.
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18
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Huang K, Zhang Y, Han Z, Zhou X, Song Y, Wang D, Zhu S, Yan D, Xu W, Xu W. Global Spread of the B5 Subgenotype EV-A71 and the Phylogeographical Analysis of Chinese Migration Events. Front Cell Infect Microbiol 2020; 10:475. [PMID: 33102246 PMCID: PMC7546772 DOI: 10.3389/fcimb.2020.00475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/03/2020] [Indexed: 11/30/2022] Open
Abstract
The subgenotype B5 of EV-A71 is a widely circulating subgenotype that frequently spreads across the globe. Several outbreaks have occurred in nations, such as Malaysia, Thailand, Vietnam, and Japan. Appearing first in Taiwan, China, the subgenotype has been frequently reported in mainland of China even though no outbreaks have been reported so far. The current study reconstructed the migration of the B5 subgenotype of EV-A71 in China via phylogeographical analysis. Furthermore, we investigated its population dynamics in order to draw more credible inferences. Following a dataset cleanup of B5 subgenotype of EV-A71, we detected earlier B5 subgenotypes of EV-A71 sequences that had been circulating in Malaysia and Singapore since the year 2000, which was before the 2003 outbreak that occurred in Sarawak. The Bayesian inference indicated that the most recent common ancestor of B5 subgenotype EV-A71 appeared in September, 1994 (1994.75). With respect to the overall prevalence, geographical reconstruction revealed that the B5 subgenotype EV-A71 originated singly from single-source cluster and subsequently developed several active lineages. Based on a large amount of data that was accumulated, we conclude that the appearance of the B5 subgenotype of EV-A71 in mainland of China was mainly due to multiple migrations from different origins.
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Affiliation(s)
- Keqiang Huang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaofang Zhou
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongyan Wang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen Xu
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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19
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Huang KYA, Zhou D, Fry EE, Kotecha A, Huang PN, Yang SL, Tsao KC, Huang YC, Lin TY, Ren J, Stuart DI. Structural and functional analysis of protective antibodies targeting the threefold plateau of enterovirus 71. Nat Commun 2020; 11:5253. [PMID: 33067459 PMCID: PMC7567869 DOI: 10.1038/s41467-020-19013-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Enterovirus 71 (EV71)-neutralizing antibodies correlate with protection and have potential as therapeutic agents. We isolate and characterize a panel of plasmablast-derived monoclonal antibodies from an infected child whose antibody response focuses on the plateau epitope near the icosahedral 3-fold axes. Eight of a total of 19 antibodies target this epitope and three of these potently neutralize the virus. Representative neutralizing antibodies 38-1-10A and 38-3-11A both confer effective protection against lethal EV71 challenge in hSCARB2-transgenic mice. The cryo-electron microscopy structures of the EV71 virion in complex with Fab fragments of these potent and protective antibodies reveal the details of a conserved epitope formed by residues in the BC and HI loops of VP2 and the BC and HI loops of VP3 spanning the region around the 3-fold axis. Remarkably, the two antibodies interact with the epitope in quite distinct ways. These plateau-binding antibodies provide templates for promising candidate therapeutics.
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MESH Headings
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Capsid Proteins/chemistry
- Capsid Proteins/genetics
- Capsid Proteins/immunology
- Enterovirus A, Human/chemistry
- Enterovirus A, Human/genetics
- Enterovirus A, Human/immunology
- Enterovirus Infections/immunology
- Enterovirus Infections/virology
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Female
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Neutralization Tests
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Affiliation(s)
- Kuan-Ying A Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Daming Zhou
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, OX3 7BN, UK
| | - Elizabeth E Fry
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, OX3 7BN, UK
| | - Abhay Kotecha
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, OX3 7BN, UK
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shu-Li Yang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yhu-Chering Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tzou-Yien Lin
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jingshan Ren
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, OX3 7BN, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK.
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20
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Davila-Calderon J, Patwardhan NN, Chiu LY, Sugarman A, Cai Z, Penutmutchu SR, Li ML, Brewer G, Hargrove AE, Tolbert BS. IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex. Nat Commun 2020; 11:4775. [PMID: 32963221 PMCID: PMC7508794 DOI: 10.1038/s41467-020-18594-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
Enterovirus 71 (EV71) poses serious threats to human health, particularly in Southeast Asia, and no drugs or vaccines are available. Previous work identified the stem loop II structure of the EV71 internal ribosomal entry site as vital to viral translation and a potential target. After screening an RNA-biased library using a peptide-displacement assay, we identify DMA-135 as a dose-dependent inhibitor of viral translation and replication with no significant toxicity in cell-based studies. Structural, biophysical, and biochemical characterization support an allosteric mechanism in which DMA-135 induces a conformational change in the RNA structure that stabilizes a ternary complex with the AUF1 protein, thus repressing translation. This mechanism is supported by pull-down experiments in cell culture. These detailed studies establish enterovirus RNA structures as promising drug targets while revealing an approach and mechanism of action that should be broadly applicable to functional RNA targeting. Human enterovirus 71 (EV71) contains an internal ribosome entry site (IRES) that promotes translation of viral RNA. Here the authors show that an antiviral small molecule DMA-135 binds to the EV71 IRES RNA, inducing conformational change and stabilizing a ternary complex to repress translation.
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Affiliation(s)
| | | | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Zhengguo Cai
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA.
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA.
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21
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Nguyen TTK, Ngo TT, Tran PM, Pham TTT, Vu HTT, Nguyen NTH, Thwaites G, Virtala AK, Vapalahti O, Baker S, Le Van T. Respiratory viruses in individuals with a high frequency of animal exposure in southern and highland Vietnam. J Med Virol 2020; 92:971-981. [PMID: 31769525 PMCID: PMC7228379 DOI: 10.1002/jmv.25640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022]
Abstract
Active surveillance for zoonotic respiratory viruses is essential to inform the development of appropriate interventions and outbreak responses. Here we target individuals with a high frequency of animal exposure in Vietnam. Three-year community-based surveillance was conducted in Vietnam during 2013-2016. We enrolled a total of 581 individuals (animal-raising farmers, slaughterers, animal-health workers, and rat traders), and utilized reverse transcription-polymerase chain reaction to detect 15 common respiratory viruses in pooled nasal-throat swabs collected at baseline or acute respiratory disease episodes. A respiratory virus was detected in 7.9% (58 of 732) of baseline samples, and 17.7% (136 of 770) of disease episode samples (P < .001), with enteroviruses (EVs), rhinoviruses and influenza A virus being the predominant viruses detected. There were temporal and spatial fluctuations in the frequencies of the detected viruses over the study period, for example, EVs and influenza A viruses were more often detected during rainy seasons. We reported the detection of common respiratory viruses in individuals with a high frequency of animal exposure in Vietnam, an emerging infectious disease hotspot. The results show the value of baseline/control sampling in delineating the causative relationships and have revealed important insights into the ecological aspects of EVs, rhinoviruses and influenza A and their contributions to the burden posed by respiratory infections in Vietnam.
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Affiliation(s)
- Tu Thi Kha Nguyen
- Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
- Dong Thap Provincial Center for Disease ControlDong Thap ProvinceVietnam
| | - Tue Tri Ngo
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
| | - Phuc My Tran
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
| | | | - Hang Thi Ty Vu
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
| | | | - Guy Thwaites
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthOxford UniversityOxfordUnited Kingdom
| | - Anna‐Maija K. Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Olli Vapalahti
- Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Veterinary Biosciences, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Virology and ImmunologyHUSLAB, Helsinki University HospitalHelsinkiFinland
| | - Stephen Baker
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthOxford UniversityOxfordUnited Kingdom
- Department of MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Tan Le Van
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
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22
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Nhan LNT, Khanh TH, Hong NTT, Van HMT, Nhu LNT, Ny NTH, Nguyet LA, Thanh TT, Anh NT, Hang VTT, Qui PT, Viet HL, Tung TH, Ha DQ, Tuan HM, Thwaites G, Chau NVV, Thwaites L, Hung NT, van Doorn HR, Tan LV. Clinical, etiological and epidemiological investigations of hand, foot and mouth disease in southern Vietnam during 2015 - 2018. PLoS Negl Trop Dis 2020; 14:e0008544. [PMID: 32804980 PMCID: PMC7451980 DOI: 10.1371/journal.pntd.0008544] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 08/27/2020] [Accepted: 06/30/2020] [Indexed: 11/19/2022] Open
Abstract
Hand, foot and mouth disease (HFMD) continues to challenge Asia with pandemic potential. In Vietnam, there have been two major outbreaks occurring during 2011-2012 (>200,000 hospitalizations and >200 deaths) and more recently in 2018 (>130,000 hospitalizations and 17 deaths). Given the high burden and the complex epidemic dynamics of HFMD, synthesizing its clinical and epidemiological data remains essential to inform the development of appropriate interventions and design public health measures. We report the results of a hospital-based study conducted during 2015-2018, covering the severe HFMD outbreak recently documented in Vietnam in 2018. The study was conducted at three major hospitals responsible for receiving HFMD patients from southern Vietnam with a population of over 40 million. A total of 19 enterovirus serotypes were detected in 1196 HFMD patients enrolled in the clinical study during 2015-2018, with enterovirus A71 (EV-A71), coxsackievirus A6 (CV-A6), CV-A10 and CV-A16 being the major causes. Despite the emergence of coxsackieviruses, EV-A71 remains the leading cause of severe HFMD in Vietnam. EV-A71 was consistently detected at a higher frequency during the second half of the years. The emergence of EV-A71 subgenogroup C4 in late 2018 was preceded by its low activity during 2017-early 2018. Compared with EV-A71 subgenogroup B5, C4 was more likely to be associated with severe HFMD, representing the first report demonstrating the difference in clinical severity between subgenogroup C4 and B5, the two predominant EV-A71 subgenogroups causing HFMD worldwide. Our data have provided significant insights into important aspects of HFMD over four years (2015-2018) in Vietnam, and emphasize active surveillance for pathogen circulation remains essential to inform the local public health authorities in the development of appropriate intervention strategies to reduce the burden of this emerging infections. Multivalent vaccines are urgently needed to control HFMD.
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Affiliation(s)
- Le Nguyen Thanh Nhan
- Children’s Hospital 1, Ho Chi Minh City, Vietnam
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ty Hang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phan Tu Qui
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ho Lu Viet
- Children’s Hospital 2, Ho Chi Minh City, Vietnam
| | | | - Do Quang Ha
- Children’s Hospital 1, Ho Chi Minh City, Vietnam
| | - Ha Manh Tuan
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Louise Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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23
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Antiviral Activity of a Llama-Derived Single-Domain Antibody against Enterovirus A71. Antimicrob Agents Chemother 2020; 64:AAC.01922-19. [PMID: 32152074 DOI: 10.1128/aac.01922-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/19/2020] [Indexed: 12/28/2022] Open
Abstract
In the past few decades, enterovirus A71 (EVA71) has caused devastating outbreaks in the Asia-Pacific region, resulting in serious sequelae in infected young children. No preventive or therapeutic interventions are currently available for curing EVA71 infection, highlighting a great unmet medical need for this disease. Here, we showed that one novel single-domain antibody (sdAb), F1, isolated from an immunized llama, could alleviate EVA71 infection both in vitro and in vivo We also confirmed that the sdAb clone F1 recognizes EVA71 through a novel conformational epitope comprising the highly conserved region of VP3 capsid protein by using competitive-binding and overlapping-peptide enzyme-linked immunosorbent assays (ELISAs). Because of the virion's icosahedral structure, we reasoned that adjacent epitopes must be clustered within molecular ranges that may be simultaneously bound by an engineered antibody with multiple valency. Therefore, two single-domain binding modules (F1) were fused to generate an sdAb-in-tandem design so that the capture of viral antigens could be further increased by valency effects. We showed that the tetravalent construct F1×F1-hFc, containing two sdAb-in-tandem on a fragment crystallizable (Fc) scaffold, exhibits more potent neutralization activity against EVA71 than does the bivalent sdAb F1-hFc by at least 5.8-fold. We also demonstrated that, using a human scavenger receptor class B member 2 (hSCARB2) transgenic mouse model, a half dose of the F1×F1-hFc provided better protection against EVA71 infection than did the F1-hFc. Thus, our study furnishes important insights into multivalent sdAb engineering against viral infection and provides a novel strategic deployment approach for preparedness of emerging infectious diseases such as EVA71.
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24
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Tadesse GA, Zhu T, Le Nguyen Thanh N, Hung NT, Duong HTH, Khanh TH, Quang PV, Tran DD, Yen LM, Doorn RV, Hao NV, Prince J, Javed H, Kiyasseh D, Tan LV, Thwaites L, Clifton DA. Severity detection tool for patients with infectious disease. Healthc Technol Lett 2020; 7:45-50. [PMID: 32431851 PMCID: PMC7199289 DOI: 10.1049/htl.2019.0030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 11/12/2019] [Accepted: 01/16/2020] [Indexed: 01/22/2023] Open
Abstract
Hand foot and mouth disease (HFMD) and tetanus are serious infectious diseases in low- and middle-income countries. Tetanus, in particular, has a high mortality rate and its treatment is resource-demanding. Furthermore, HFMD often affects a large number of infants and young children. As a result, its treatment consumes enormous healthcare resources, especially when outbreaks occur. Autonomic nervous system dysfunction (ANSD) is the main cause of death for both HFMD and tetanus patients. However, early detection of ANSD is a difficult and challenging problem. The authors aim to provide a proof-of-principle to detect the ANSD level automatically by applying machine learning techniques to physiological patient data, such as electrocardiogram waveforms, which can be collected using low-cost wearable sensors. Efficient features are extracted that encode variations in the waveforms in the time and frequency domains. The proposed approach is validated on multiple datasets of HFMD and tetanus patients in Vietnam. Results show that encouraging performance is achieved. Moreover, the proposed features are simple, more generalisable and outperformed the standard heart rate variability analysis. The proposed approach would facilitate both the diagnosis and treatment of infectious diseases in low- and middle-income countries, and thereby improve patient care.
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Affiliation(s)
- Girmaw Abebe Tadesse
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK.,IBM Research
- Africa, Nairobi, Kenya
| | - Tingting Zhu
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Duc Duong Tran
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Lam Minh Yen
- Oxford Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Rogier Van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, UK
| | - Nguyen Van Hao
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - John Prince
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Hamza Javed
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Dani Kiyasseh
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Le Van Tan
- Oxford Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Louise Thwaites
- Oxford Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, UK
| | - David A Clifton
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
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25
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Kuo FL, Khanh TH, Chung WY, Hung NT, Luo ST, Chang WC, Nhan LNT, Thinh LQ, Lee MS. Seroprevalence of EV-A71 neutralizing antibodies following the 2011 epidemic in HCMC, Vietnam. PLoS Negl Trop Dis 2020; 14:e0008124. [PMID: 32126083 PMCID: PMC7077839 DOI: 10.1371/journal.pntd.0008124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 03/17/2020] [Accepted: 02/08/2020] [Indexed: 01/04/2023] Open
Abstract
Enterovirus-A71 (EV-A71) cyclically causes hand-foot-mouth disease (HFMD) epidemics in Asian children. An EV-A71 epidemic occurred in Southern Vietnam in 2011, but its scale is not clear. We collected residual sera from non-HFMD Vietnamese inpatients in 2012–2013 to determine seroprevalence of EV-A71 neutralizing antibodies, and measured cross-reactive neutralizing antibody titers against three EV-A71 genogroups. About 23.5% of 1-year-old children in Southern Vietnam has been infected by EV-A71, and the median age of infection was estimated to be 3 years. No significant antigenic variation could be detected among the three EV-A71 genogroups. The high seroprevalence of EV-A71 neutralizing antibody in children living in southern Vietnam indicates the necessity of introducing EV-A71 vaccines in southern Vietnam, particularly for children under 6 months of age. Moreover, it is critical to understand EV-A71 disease burden for formulating national vaccination policy. Enterovirus-A71 (EV-A71), a member of the enterovirus genus, is a virulent pathogen causing neurological complications. EV-A71 mainly spreads through oral-fecal or oral-oral transmission, as well as respiratory droplets. EV-A71 outbreaks have cyclically occurred throughout some Asian countries since 1997, with millions of people affected. The presence of serum neutralizing antibodies to EV-A71 can represent the prevalence of previous EV-A71 infections and seroprevalence studies are widely used to understand prevalence of infectious diseases. The results of our study demonstrate that about 50% of young children under 3 years of age were infected during the 2011 epidemic in southern Vietnam. The high seroprevalence of EV-A71 neutralizing antibody in children living in southern Vietnam indicates the necessity of introducing EV-A71 vaccines, particularly for children under 6 months of age. Moreover, it is critical to understand EV-A71 disease burden for formulating national vaccination policy in the future.
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Affiliation(s)
- Fang-Lin Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | | | - Wan-Yu Chung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | | | - Shu-Ting Luo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Wen-Chiung Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | | | - Le Quoc Thinh
- Children’s Hospital No. 1, Ho Chi Minh City, Vietnam
| | - Min-Shi Lee
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
- * E-mail: ,
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26
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Functional analyses of mammalian virus 5'UTR-derived, small RNAs that regulate virus translation. Methods 2020; 183:13-20. [PMID: 32081746 DOI: 10.1016/j.ymeth.2020.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 11/21/2022] Open
Abstract
Enterovirus A71 (EV-A711) RNA contains an internal ribosomal entry site (IRES) to direct cap-independent translation. IRES-dependent translation requires the host's translation initiation factors and IRES-associated trans-acting factors (ITAFs). We previously showed that hnRNP A1, the mRNA stability factor HuR, and the RISC subunit Argonaute 2 (Ago2) are ITAFs that associate with stem loop II (SL-II) of the IRES and promote IRES-dependent translation. By contrast, the mRNA decay factor AUF1 is a negative-acting ITAF that also binds SL-II. Moreover, the small RNA-processing enzyme Dicer produces at least four virus-derived, small RNAs (vsRNAs 1-4) from the EV-A71 5'UTR in infected cells. One of these, vsRNA1, derived from SL-II, inhibits IRES activity via an unknown mechanism. In vitro RNA-binding assays revealed that vsRNA1 can alter association of Ago2, HuR, and AUF1 with SL-II. This presents a possible mechanism by which vsRNA1 could control association of ITAFs with the IRES and modulate viral translation. Here, we describe methods for functional analyses of vsRNA1-mediated regulation of IRES activity. These methods should be applicable to other virus-derived, small RNAs as well.
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27
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Wang C, Chen Y, Xu T, Tian X, Zheng J, Liu W, Xia Y, Li Y, Zhu B, Zhou R. A novel method to diagnose the infection of enterovirus A71 in children by detecting IgA from saliva. J Med Virol 2020; 92:1059-1064. [PMID: 31944333 DOI: 10.1002/jmv.25672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/21/2019] [Indexed: 01/19/2023]
Abstract
Enterovirus A71 (EV-A71) is one of the main pathogens causing hand, foot, and mouth disease, and often causes diseases of the central nervous system. Early diagnosis is important to prevent EV-A71 outbreaks. The detection of serum immunoglobulin M (IgM) is widely used for the early diagnosis of EV-A71 in clinics, especially in rural areas. However, this technique requires the extraction of blood from children who have thin blood vessels and who might fear the use of needles. Therefore, difficulties in the detection process are often encountered. This study developed a noninvasive method to detect EV-A71-specific immunoglobulin A (IgA) in saliva for the diagnosis of EV-A71 infection. The sensitivity and specificity of IgA detection did not differ significantly compared with IgM detection. IgA antibodies were present in saliva for a relatively shorter period than IgM antibodies were present in serum. The sensitivity of IgA detection was higher than that of IgM detection for secondary EV-A71 infections. These results suggest that the detection of EV-A71-specific IgA in the saliva allows the effective early diagnosis of EV-A71 and may be suitable for detecting EV-A71 infections in children.
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Affiliation(s)
- Changbing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The Affiliated First Hospital of Guangzhou Medical University, Guangzhou, China.,Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yi Chen
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Tiantian Xu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The Affiliated First Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianbin Zheng
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The Affiliated First Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Xia
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yinghua Li
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Bing Zhu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The Affiliated First Hospital of Guangzhou Medical University, Guangzhou, China
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28
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Gonzalez G, Carr MJ, Kobayashi M, Hanaoka N, Fujimoto T. Enterovirus-Associated Hand-Foot and Mouth Disease and Neurological Complications in Japan and the Rest of the World. Int J Mol Sci 2019; 20:ijms20205201. [PMID: 31635198 PMCID: PMC6834195 DOI: 10.3390/ijms20205201] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Enteroviruses (EVs) are responsible for extremely large-scale, periodic epidemics in pediatric cohorts, particularly in East and Southeast Asia. Clinical presentation includes a diverse disease spectrum, including hand-foot and mouth disease (HFMD), aseptic meningitis, encephalitis, acute flaccid paralysis, and acute flaccid myelitis. HFMD is predominantly attributable to EV-A types, including the major pathogen EV-A71, and coxsackieviruses, particularly CV-A6, CV-A16, and CV-A10. There have been multiple EV-A71 outbreaks associated with a profound burden of neurological disease and fatal outcomes in Asia since the early 1980s. Efficacious vaccines against EV-A71 have been developed in China but widespread pediatric vaccination programs have not been introduced in other countries. Encephalitis, as a consequence of complications arising from HFMD infection, leads to damage to the thalamus and medulla oblongata. Studies in Vietnam suggest that myoclonus is a significant indicator of central nervous system (CNS) complications in EV-A71-associated HFMD cases. Rapid response in HFMD cases in children is imperative to prevent the progression to a CNS infection; however, prophylactic and therapeutic agents have not been well established internationally, therefore surveillance and functional studies including development of antivirals and multivalent vaccines is critically important to reduce disease burden in pediatric populations.
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Affiliation(s)
- Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan.
- National Advanced Computing Collaboratory, National Center for High Technology, San Jose 1174-1200, Costa Rica.
| | - Michael J Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan.
| | | | - Nozomu Hanaoka
- Division 4, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Tsuguto Fujimoto
- Division 4, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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29
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Puenpa J, Wanlapakorn N, Vongpunsawad S, Poovorawan Y. The History of Enterovirus A71 Outbreaks and Molecular Epidemiology in the Asia-Pacific Region. J Biomed Sci 2019; 26:75. [PMID: 31627753 PMCID: PMC6798416 DOI: 10.1186/s12929-019-0573-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/01/2019] [Indexed: 01/01/2023] Open
Abstract
Enterovirus A71 (EV-A71) is one of the common causative pathogens for hand foot and mouth disease (HFMD) affecting young children. HFMD outbreak can result in a substantial pediatric hospitalization and burden the healthcare services, especially in less-developed countries. Since the initial epidemic of predominantly EV-A71 in California in 1969, the high prevalence of HFMD in the Asia-pacific region and elsewhere around the world represents a significant morbidity in this age group. With the advent of rapid and accurate diagnostic tools, there has been a dramatic increase in the number of laboratory-confirmed EV-A71 infection over the past two decades. The population, cultural, and socioeconomic diversity among countries in the Asia-Pacific region all influence the transmission and morbidity associated with HFMD. This review summarizes the current state of epidemiology of EV-A71 in Asia-Pacific countries based on the most recent epidemiological data and available information on the prevalence and disease burden. This knowledge is important in guiding the prevention, control and future research on vaccine development of this highly contagious disease of significant socioeconomic implications in public health.
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Affiliation(s)
- Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Division of Academic Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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30
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Anh NT, Hong NTT, Nhu LNT, Thanh TT, Lau CY, Limmathurotsakul D, Deng X, Rahman M, Chau NVV, van Doorn HR, Thwaites G, Delwart E, Tan LV. Viruses in Vietnamese Patients Presenting with Community-Acquired Sepsis of Unknown Cause. J Clin Microbiol 2019; 57:e00386-19. [PMID: 31217274 PMCID: PMC6711913 DOI: 10.1128/jcm.00386-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/12/2019] [Indexed: 12/28/2022] Open
Abstract
Community-acquired (CA) sepsis is a major public health problem worldwide, yet the etiology remains unknown for >50% of the patients. Here we applied metagenomic next-generation sequencing (mNGS) to characterize the human virome in 492 clinical samples (384 sera, 92 pooled nasal and throat swabs, 10 stools, and 6 cerebrospinal fluid samples) from 386 patients (213 adults and 173 children) presenting with CA sepsis who were recruited from 6 hospitals across Vietnam between 2013 and 2015. Specific monoplex PCRs were used subsequently to confirm the presence of viral sequences detected by mNGS. We found sequences related to 47 viral species belonging to 21 families in 358 of 386 (93%) patients, including viruses known to cause human infections. After PCR confirmation, human viruses were found in 52 of 386 patients (13.4%); picornavirus (enteroviruses [n = 14], rhinovirus [n = 5], and parechovirus [n = 2]), hepatitis B virus (n = 10), cytomegalovirus (n = 9), Epstein-Barr virus (n = 5), and rotavirus A (n = 3) were the most common viruses detected. Recently discovered viruses were also found (gemycircularvirus [n = 5] and WU polyomavirus, Saffold virus, salivirus, cyclovirus-VN, and human pegivirus 2 [HPgV2] [n, 1 each]), adding to the growing literature about the geographic distribution of these novel viruses. Notably, sequences related to numerous viruses not previously reported in human tissues were also detected. To summarize, we identified 21 viral species known to be infectious to humans in 52 of 386 (13.4%) patients presenting with CA sepsis of unknown cause. The study, however, cannot directly impute sepsis causation to the viruses identified. The results highlight the fact that it remains a challenge to establish the causative agents in CA sepsis patients, especially in tropical settings such as Vietnam.
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Affiliation(s)
- Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Chuen-Yen Lau
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Direk Limmathurotsakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Research Unit, Bangkok, Thailand
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Assessing the efficacy and safety of magnesium sulfate for management of autonomic nervous system dysregulation in Vietnamese children with severe hand foot and mouth disease. BMC Infect Dis 2019; 19:737. [PMID: 31438878 PMCID: PMC6704683 DOI: 10.1186/s12879-019-4356-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/05/2019] [Indexed: 01/21/2023] Open
Abstract
Background Brainstem encephalitis is a serious complication of hand foot and mouth disease (HFMD) in children. Autonomic nervous system (ANS) dysregulation and hypertension may occur, sometimes progressing to cardiopulmonary failure and death. Vietnamese national guidelines recommend use of milrinone if ANS dysregulation with Stage 2 hypertension develops. We wished to investigate whether magnesium sulfate (MgSO4) improved outcomes in children with HFMD if used earlier in the evolution of the ANS dysregulation (Stage 1 hypertension). Methods During a regional epidemic we conducted a randomized, double-blind, placebo-controlled trial of MgSO4 in children with HFMD, ANS dysregulation and Stage 1 hypertension, at the Hospital for Tropical Diseases in Ho Chi Minh city. Study participants received an infusion of MgSO4 or matched placebo for 72 h. We also reviewed data from non-trial HFMD patients in whom milrinone failed to control hypertension, some of whom received MgSO4 as second line therapy. The primary outcome for both analyses was a composite of disease progression within 72 h - addition of milrinone (trial participants only), need for ventilation, shock, or death. Results Between June 2014 and September 2016, 14 and 12 participants received MgSO4 or placebo respectively, before the trial was stopped due to futility. Among 45 non-trial cases with poorly controlled hypertension despite high-dose milrinone, 33 received MgSO4 while 12 did not. There were no statistically significant differences in the composite outcome between the MgSO4 and the placebo/control groups in either study (adjusted relative risk (95%CI) of [6/14 (43%) vs. 6/12 (50%)], 0.84 (0.37, 1.92), p = 0.682 in the trial and [1/33 (3%) vs. 2/12 (17%)], 0.16 (0.01, 1.79), p = 0.132 in the observational cohort). The incidence of adverse events was similar between the groups. Potentially toxic magnesium levels occurred very rarely with the infusion regime used. Conclusion Although we could not demonstrate efficacy in these studies, there were no safety signals associated with use of 30-50 mg/kg/hr. MgSO4 in severe HFMD. Intermittent outbreaks of HFMD are likely to continue across the region, and an adequately powered trial is still needed to evaluate use of MgSO4 in controlling hypertension in severe HFMD, potentially involving a higher dose regimen. Trial registration ClinicalTrials.gov Identifier: NCT01940250 (Registered 22 AUG 2013). Trial sponsor: University of Oxford Electronic supplementary material The online version of this article (10.1186/s12879-019-4356-x) contains supplementary material, which is available to authorized users.
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Nhan LNT, Turner HC, Khanh TH, Hung NT, Lien LB, Hong NTT, Nhu LNT, Ny NTH, Nguyet LA, Thanh TT, Van HMT, Viet HL, Tung TH, Phuong TTL, Devine A, Thwaites G, Chau NVV, Thwaites L, van Doorn HR, Tan LV. Economic Burden Attributed to Children Presenting to Hospitals With Hand, Foot, and Mouth Disease in Vietnam. Open Forum Infect Dis 2019; 6:5514500. [PMID: 31363772 PMCID: PMC6657964 DOI: 10.1093/ofid/ofz284] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
Background Hand, foot, and mouth disease (HFMD) has become a major public health concern in the Asia-Pacific region. Knowledge of its economic burden is essential for policy makers in prioritizing the development and implementation of interventions. Methods A multi-hospital-based study was prospectively conducted at 3 major hospitals in Ho Chi Minh City, Vietnam, during 2016–2017. Data on direct and productivity costs were collected alongside clinical information and samples and demographic information from study participants. Results A total of 466 patients were enrolled. Two hundred three of 466 (43.6%) patients lived in Ho Chi Minh City, and 72/466 (15.5%) had severe HFMD. An enterovirus was identified in 74% of 466 patients, with EV-A71, CV-A6, CV-A10, and CV-A16 being the most common viruses identified (236/466, 50.6%). The mean economic burden per case was estimated at US$400.80 (95% confidence interval [CI], $353.80–$448.90), of which the total direct (medical) costs accounted for 69.7%. There were considerable differences in direct medical costs between groups of patients with different clinical severities and pathogens (ie, EV-A71 vs non-EV-A71). In Vietnam, during 2016–2017, the economic burden posed by HFMD was US$90 761 749 (95% CI, $79 033 973–$103 009 756). Conclusions Our findings are of public health significance because for the first time we demonstrate that HFMD causes a substantial economic burden in Vietnam, and although multivalent vaccines are required to control HFMD, effective EV-A71 vaccine could substantially reduce the burden posed by severe HFMD. The results will be helpful for health policy makers in prioritizing resources for the development and implementation of intervention strategies to reduce the burden of HFMD.
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Affiliation(s)
- Le Nguyen Thanh Nhan
- Children's Hospital 1, Ho Chi Minh City, Vietnam.,Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hugo C Turner
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Le Bich Lien
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | | | | | | | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Ho Lu Viet
- Children's Hospital 2, Ho Chi Minh City, Vietnam
| | | | | | - Angela Devine
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol Oxford Tropical Research Unit, Bangkok, Thailand
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Louise Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Kamvar ZN, Cai J, Pulliam JRC, Schumacher J, Jombart T. Epidemic curves made easy using the R package incidence. F1000Res 2019; 8:139. [PMID: 31119031 PMCID: PMC6509961 DOI: 10.12688/f1000research.18002.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 11/20/2022] Open
Abstract
The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling. incidence is available from https://www.repidemicsconsortium.org/incidence.
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Affiliation(s)
- Zhian N Kamvar
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology , School of Public Health, Imperial College London, London, UK
| | - Jun Cai
- Ministry of Education Key Laboratory for Earth System Modelling, Department of Earth System Science, Tsinghua University, Beijing, 100084, China
| | - Juliet R C Pulliam
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA),, Stellenbosch University, Stellenbosch, South Africa
| | | | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology , School of Public Health, Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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Note from the editors: Open access and sound science for rapid public health action. Euro Surveill 2019; 24:1901101. [PMID: 30646980 PMCID: PMC6337059 DOI: 10.2807/1560-7917.es.2019.24.2.1901101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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