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Komakech A, Whitmer S, Izudi J, Kizito C, Ninsiima M, Ahirirwe SR, Kabami Z, Ario AR, Kadobera D, Kwesiga B, Gidudu S, Migisha R, Makumbi I, Eurien D, Kayiwa J, Bulage L, Gonahasa DN, Kyamwine I, Okello PE, Nansikombi HT, Atuhaire I, Asio A, Elayeete S, Nsubuga EJ, Masanja V, Migamba SM, Mwine P, Nakamya P, Nampeera R, Kwiringira A, Akunzirwe R, Naiga HN, Namubiru SK, Agaba B, Zalwango JF, Zalwango MG, King P, Simbwa BN, Zavuga R, Wanyana MW, Kiggundu T, Oonyu L, Ndyabakira A, Komugisha M, Kibwika B, Ssemanda I, Nuwamanya Y, Kamukama A, Aanyu D, Kizza D, Ayen DO, Mulei S, Balinandi S, Nyakarahuka L, Baluku J, Kyondo J, Tumusiime A, Aliddeki D, Masiira B, Muwanguzi E, Kimuli I, Bulwadda D, Isabirye H, Aujo D, Kasambula A, Okware S, Ochien E, Komakech I, Okot C, Choi M, Cossaboom CM, Eggers C, Klena JD, Osinubi MO, Sadigh KS, Worrell MC, Boore AL, Shoemaker T, Montgomery JM, Nabadda SN, Mwanga M, Muruta AN, Harris JR. Sudan virus disease super-spreading, Uganda, 2022. BMC Infect Dis 2024; 24:520. [PMID: 38783244 PMCID: PMC11112911 DOI: 10.1186/s12879-024-09391-0] [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: 12/05/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND On 20 September 2022, Uganda declared its fifth Sudan virus disease (SVD) outbreak, culminating in 142 confirmed and 22 probable cases. The reproductive rate (R) of this outbreak was 1.25. We described persons who were exposed to the virus, became infected, and they led to the infection of an unusually high number of cases during the outbreak. METHODS In this descriptive cross-sectional study, we defined a super-spreader person (SSP) as any person with real-time polymerase chain reaction (RT-PCR) confirmed SVD linked to the infection of ≥ 13 other persons (10-fold the outbreak R). We reviewed illness narratives for SSPs collected through interviews. Whole-genome sequencing was used to support epidemiologic linkages between cases. RESULTS Two SSPs (Patient A, a 33-year-old male, and Patient B, a 26-year-old male) were identified, and linked to the infection of one probable and 50 confirmed secondary cases. Both SSPs lived in the same parish and were likely infected by a single ill healthcare worker in early October while receiving healthcare. Both sought treatment at multiple health facilities, but neither was ever isolated at an Ebola Treatment Unit (ETU). In total, 18 secondary cases (17 confirmed, one probable), including three deaths (17%), were linked to Patient A; 33 secondary cases (all confirmed), including 14 (42%) deaths, were linked to Patient B. Secondary cases linked to Patient A included family members, neighbours, and contacts at health facilities, including healthcare workers. Those linked to Patient B included healthcare workers, friends, and family members who interacted with him throughout his illness, prayed over him while he was nearing death, or exhumed his body. Intensive community engagement and awareness-building were initiated based on narratives collected about patients A and B; 49 (96%) of the secondary cases were isolated in an ETU, a median of three days after onset. Only nine tertiary cases were linked to the 51 secondary cases. Sequencing suggested plausible direct transmission from the SSPs to 37 of 39 secondary cases with sequence data. CONCLUSION Extended time in the community while ill, social interactions, cross-district travel for treatment, and religious practices contributed to SVD super-spreading. Intensive community engagement and awareness may have reduced the number of tertiary infections. Intensive follow-up of contacts of case-patients may help reduce the impact of super-spreading events.
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Affiliation(s)
- Allan Komakech
- Uganda National Institute of Public Health, Kampala, Uganda.
- Clarke International University, Kampala, Uganda.
| | - Shannon Whitmer
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jonathan Izudi
- Department of Community Health, Faculty of Medicine, Mbarara University of Science and Technology (MUST), Mbarara, Uganda
- Data Science and Evaluations Unit, African Population and Health Research Center, Nairobi, Kenya
| | | | | | | | - Zainah Kabami
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Alex R Ario
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Benon Kwesiga
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Samuel Gidudu
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Issa Makumbi
- National Public Health Emergency Operations Center, Kampala, Uganda
| | | | - Joshua Kayiwa
- National Public Health Emergency Operations Center, Kampala, Uganda
| | - Lilian Bulage
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Irene Kyamwine
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Paul E Okello
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | - Alice Asio
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Sarah Elayeete
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | | | - Patience Mwine
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Rose Nampeera
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | | | | | - Brian Agaba
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | - Patrick King
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Robert Zavuga
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | - Lawrence Oonyu
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | - Brian Kibwika
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | | | - Adams Kamukama
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Dorothy Aanyu
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Dominic Kizza
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Sophia Mulei
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Luke Nyakarahuka
- Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems, and Veterinary Public Health, Makerere University, Kampala, Uganda
| | - Jimmy Baluku
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | - Dativa Aliddeki
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Ben Masiira
- , African Field Epidemiology Network, Kampala, Uganda
| | | | - Ivan Kimuli
- World Health Organization, Geneva, Switzerland
| | | | | | | | | | | | | | | | | | - Mary Choi
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Carrie Eggers
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John D Klena
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Modupe O Osinubi
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Katrin S Sadigh
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mary C Worrell
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Amy L Boore
- United States Centers for Disease Control and Prevention, Kampala, Uganda
| | - Trevor Shoemaker
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M Montgomery
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan N Nabadda
- National Health Laboratory and Diagnostic Services, Kampala, Uganda
| | | | | | - Julie R Harris
- United States Centers for Disease Control and Prevention, Kampala, Uganda
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Marpaung DSS, Sinaga AOY, Damayanti D, Taharuddin T. Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation. ANAL SCI 2024:10.1007/s44211-024-00566-y. [PMID: 38607600 DOI: 10.1007/s44211-024-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.
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Affiliation(s)
- David Septian Sumanto Marpaung
- Department of Biosystems Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia.
| | - Ayu Oshin Yap Sinaga
- Department of Biology, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Damayanti Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Taharuddin Taharuddin
- Department of Chemical Engineering, University of Lampung, Jl. Prof. Dr. Ir. Sumantri Brojonegoro No.1, Gedong Meneng, Kec. Rajabasa, Kota Bandar Lampung, Lampung, 35141, Indonesia
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Pretelli I, Crittenden AN, Dounias E, Friant S, Koster J, Kramer KL, Mangola SM, Saez AM, Lew-Levy S. Child and adolescent foraging: New directions in evolutionary research. Evol Anthropol 2024; 33:e22020. [PMID: 38214699 DOI: 10.1002/evan.22020] [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: 05/22/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/13/2024]
Abstract
Young children and adolescents in subsistence societies forage for a wide range of resources. They often target child-specific foods, they can be very successful foragers, and they share their produce widely within and outside of their nuclear family. At the same time, while foraging, they face risky situations and are exposed to diseases that can influence their immune development. However, children's foraging has largely been explained in light of their future (adult) behavior. Here, we reinterpret findings from human behavioral ecology, evolutionary medicine and cultural evolution to center foraging children's contributions to life history evolution, community resilience and immune development. We highlight the need to foreground immediate alongside delayed benefits and costs of foraging, including inclusive fitness benefits, when discussing children's food production from an evolutionary perspective. We conclude by recommending that researchers carefully consider children's social and ecological context, develop cross-cultural perspectives, and incorporate children's foraging into Indigenous sovereignty discourse.
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Affiliation(s)
- Ilaria Pretelli
- Institute for Advanced Study in Toulouse, Toulouse School of Economics, and University of Toulouse Capitole, Toulouse, France
- Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Edmond Dounias
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Sagan Friant
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jeremy Koster
- Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Karen L Kramer
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Shani M Mangola
- The Law School of Tanzania, Dar es Salaam, Tanzania
- Olanakwe Community Fund, Mang'ola, Tanzania
| | - Almudena Mari Saez
- TransVHIMI Unit, French National Institute for Sustainable Development, IRD, Montpellier, France
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Grayo S, Camara A, Doukouré B, Ellis I, Troupin C, Fischer K, Vanhomwegen J, White M, Groschup MH, Diederich S, Tordo N. Geographic Disparities in Domestic Pig Population Exposure to Ebola Viruses, Guinea, 2017-2019. Emerg Infect Dis 2024; 30:681-690. [PMID: 38526081 PMCID: PMC10977825 DOI: 10.3201/eid3004.231034] [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] [Indexed: 03/26/2024] Open
Abstract
Although pigs are naturally susceptible to Reston virus and experimentally to Ebola virus (EBOV), their role in Orthoebolavirus ecology remains unknown. We tested 888 serum samples collected from pigs in Guinea during 2017-2019 (between the 2013-16 epidemic and its resurgence in 2021) by indirect ELISA against the EBOV nucleoprotein. We identified 2 hotspots of possible pig exposure by IgG titer levels: the northern coast had 48.7% of positive serum samples (37/76), and Forest Guinea, bordering Sierra Leone and Liberia, where the virus emerged and reemerged, had 50% of positive serum samples (98/196). The multitarget Luminex approach confirms ELISA results against Ebola nucleoprotein and highlights cross-reactivities to glycoprotein of EBOV, Reston virus, and Bundibugyo virus. Those results are consistent with previous observations of the circulation of Orthoebolavirus species in pig farming regions in Sierra Leone and Ghana, suggesting potential risk for Ebola virus disease in humans, especially in Forest Guinea.
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Knox MA, Bromhead C, Hayman DTS. Development of a non-infectious control for viral hemorrhagic fever PCR assays. PLoS Negl Trop Dis 2024; 18:e0011390. [PMID: 38648254 PMCID: PMC11065202 DOI: 10.1371/journal.pntd.0011390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/02/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024] Open
Abstract
Assay validation is an essential component of disease surveillance testing, but can be problematic in settings where access to positive control material is limited and a safety risk for handlers. Here we describe a single non-infectious synthetic control that can help develop and validate the PCR based detection of the viral causes of Crimean-Congo hemorrhagic fever, Ebola virus disease, Lassa fever, Marburg virus disease and Rift Valley fever. We designed non-infectious synthetic DNA oligonucleotide sequences incorporating primer binding sites suitable for five assays, and a T7 promotor site which was used to transcribe the sequence. Transcribed RNA was used as template in a dilution series, extracted and amplified with RT-PCR and RT-qPCR to demonstrate successful recovery and determine limits of detection in a range of laboratory settings. Our results show this approach is adaptable to any diagnostic assay requiring validation of nucleic acid extraction and/or amplification, particularly where sourcing reliable, safe material for positive controls is infeasible.
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Affiliation(s)
- Matthew A. Knox
- Massey University, School of Veterinary Science, Palmerston North, Manawatu-Wanganui, New Zealand
| | - Collette Bromhead
- Massey University, School of Health Sciences, Wellington, New Zealand
| | - David TS Hayman
- Massey University, School of Veterinary Science, Palmerston North, Manawatu-Wanganui, New Zealand
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6
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Ma Y, Zhao Y, Ma Y. Kernel Bayesian nonlinear matrix factorization based on variational inference for human-virus protein-protein interaction prediction. Sci Rep 2024; 14:5693. [PMID: 38454139 PMCID: PMC10920681 DOI: 10.1038/s41598-024-56208-w] [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: 09/16/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
Identification of potential human-virus protein-protein interactions (PPIs) contributes to the understanding of the mechanisms of viral infection and to the development of antiviral drugs. Existing computational models often have more hyperparameters that need to be adjusted manually, which limits their computational efficiency and generalization ability. Based on this, this study proposes a kernel Bayesian logistic matrix decomposition model with automatic rank determination, VKBNMF, for the prediction of human-virus PPIs. VKBNMF introduces auxiliary information into the logistic matrix decomposition and sets the prior probabilities of the latent variables to build a Bayesian framework for automatic parameter search. In addition, we construct the variational inference framework of VKBNMF to ensure the solution efficiency. The experimental results show that for the scenarios of paired PPIs, VKBNMF achieves an average AUPR of 0.9101, 0.9316, 0.8727, and 0.9517 on the four benchmark datasets, respectively, and for the scenarios of new human (viral) proteins, VKBNMF still achieves a higher hit rate. The case study also further demonstrated that VKBNMF can be used as an effective tool for the prediction of human-virus PPIs.
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Affiliation(s)
- Yingjun Ma
- School of Mathematics and Statistics, Xiamen University of Technology, Xiamen, China
| | - Yongbiao Zhao
- School of Computer, Central China Normal University, Wuhan, China
| | - Yuanyuan Ma
- School of Computer Engineering, Hubei University of Arts and Science, Xiangyang, China.
- Hubei Key Laboratory of Power System Design and Test for Electrical Vehicle, Hubei University of Arts and Science, Xiangyang, China.
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Eskew EA, Olival KJ, Mazet JAK, Daszak P. A global-scale dataset of bat viral detection suggests that pregnancy reduces viral shedding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581969. [PMID: 38464184 PMCID: PMC10925100 DOI: 10.1101/2024.02.25.581969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding viral infection dynamics in wildlife hosts can help forecast zoonotic pathogen spillover and human disease risk. Bats are particularly important reservoirs of zoonotic viruses, including some of major public health concern such as Nipah virus, Hendra virus, and SARS-related coronaviruses. Previous work has suggested that metapopulation dynamics, seasonal reproductive patterns, and other bat life history characteristics might explain temporal variation in spillover of bat-associated viruses into people. Here, we analyze viral dynamics in free-ranging bat hosts, leveraging a multi-year, global-scale viral detection dataset that spans eight viral families and 96 bat species from 14 countries. We fit hierarchical Bayesian models that explicitly control for important sources of variation, including geographic region, specimen type, and testing protocols, while estimating the influence of reproductive status on viral detection in female bats. Our models revealed that late pregnancy had a negative effect on viral shedding across multiple data subsets, while lactation had a weaker influence that was inconsistent across data subsets. These results are unusual for mammalian hosts, but given recent findings that bats may have high individual viral loads and population-level prevalence due to dampening of antiviral immunity, we propose that it would be evolutionarily advantageous for pregnancy to either not further reduce immunity or actually increase the immune response, reducing viral load, shedding, and risk of fetal infection. This novel hypothesis would be valuable to test given its potential to help monitor, predict, and manage viral spillover risk from bats.
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Affiliation(s)
- Evan A. Eskew
- EcoHealth Alliance, New York, NY 10018, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
| | | | - Jonna A. K. Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | | | - PREDICT Consortium
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Obeng-Kusi M, Martin J, Abraham I. The economic burden of Ebola virus disease: a review and recommendations for analysis. J Med Econ 2024; 27:309-323. [PMID: 38299454 DOI: 10.1080/13696998.2024.2313358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/30/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Ebola virus disease (EVD) continues to be a major public health threat globally, particularly in the low-and-middle-income countries (LMICs) of Africa. The social and economic burdens of EVD are substantial and have triggered extensive research into prevention and control. We aim to highlight the impact and economic implications, identify research gaps, and offer recommendations for future economic studies pertaining to EVD. METHOD We conducted a comprehensive librarian-led search in PubMed/Medline, Embase, Google Scholar, EconLit and Scopus for economic evaluations of EVD. After study selection and data extraction, findings on the impact and economics of EVD were synthesized using a narrative approach, while identifying gaps, and recommending critical areas for future EVD economic studies. RESULTS The economic evaluations focused on the burden of illness, vaccine cost-effectiveness, willingness-to-pay for a vaccine, EVD funding, and preparedness costs. The estimated economic impact of the 2014 EVD outbreak in Guinea, Liberia, and Sierra Leone across studies ranged from $30 billion to $50 billion. Facility construction and modification emerged as significant cost drivers for preparedness. The EVD vaccine demonstrated cost-effectiveness in a dynamic transmission model; resulting in an incremental cost-effectiveness ratio of about $96 per additional disability adjusted life year averted. Individuals exhibited greater willingness to be vaccinated if it incurred no personal cost, with a minority willing to pay about $1 for the vaccine. CONCLUSIONS The severe impact of EVD puts pressure on governments and the international community for better resource utilization and re-allocation. Several technical and methodological issues related to economic evaluation of EVD remain to be addressed, especially for LMICs. We recommend conducting cost-of-sequelae and cost-of-distribution analyses in addition to adapting existing economic analytical methods to EVD. Characteristics of the affected regions should be considered to provide evidence-based economic plans and economic-evaluation of mitigations that enhance resource allocation for prevention and treatment.
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Affiliation(s)
- Mavis Obeng-Kusi
- Center for Health Outcomes and PharmacoEconomic Research, University of Arizona, Tucson, AZ, USA
| | - Jennifer Martin
- Arizona Health Sciences Library, University of Arizona, Tucson, AZ, USA
| | - Ivo Abraham
- Center for Health Outcomes and PharmacoEconomic Research, University of Arizona, Tucson, AZ, USA
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Wang TY, Meng FD, Sang GJ, Zhang HL, Tian ZJ, Zheng H, Cai XH, Tang YD. A novel viral vaccine platform based on engineered transfer RNA. Emerg Microbes Infect 2023; 12:2157339. [PMID: 36482724 PMCID: PMC9769134 DOI: 10.1080/22221751.2022.2157339] [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] [Indexed: 12/14/2022]
Abstract
In recent years, an increasing number of emerging and remerging virus outbreaks have occurred and the rapid development of vaccines against these viruses has been crucial. Controlling the replication of premature termination codon (PTC)-containing viruses is a promising approach to generate live but replication-defective viruses that can be used for potent vaccines. Here, we used anticodon-engineered transfer RNAs (ACE-tRNAs) as powerful precision switches to control the replication of PTC-containing viruses. We showed that ACE-tRNAs display higher potency of reading through PTCs than genetic code expansion (GCE) technology. Interestingly, ACE-tRNA has a site preference that may influence its read-through efficacy. We further attempted to use ACE-tRNAs as a novel viral vaccine platform. Using a human immunodeficiency virus type 1 (HIV-1) pseudotyped virus as an RNA virus model, we found that ACE-tRNAs display high potency for read-through viral PTCs and precisely control their production. Pseudorabies virus (PRV), a herpesvirus, was used as a DNA virus model. We found that ACE-tRNAs display high potency for reading through viral PTCs and precisely controlling PTC-containing virus replication. In addition, PTC-engineered PRV completely attenuated and lost virulence in mice in vivo, and immunization with PRV containing a PTC elicited a robust immune response and provided complete protection against wild-type PRV challenge. Overall, replication-controllable PTC-containing viruses based on ACE-tRNAs provide a new strategy to rapidly attenuate virus infection and prime robust immune responses. This technology can be used as a platform for rapidly developing viral vaccines in the future.
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Affiliation(s)
- Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Fan-Dan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Guo-Ju Sang
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Hong-Liang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Hao Zheng
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China,Hao Zheng Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai150001, People’s Republic of China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China,Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, People's Republic of China,Xue-Hui Cai State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, People’s Republic of China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin150001, People’s Republic of China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China, Yan-Dong Tang
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10
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Koehler JW, Stefan CP, Hall AT, Delp KL, O'Hearn AE, Taylor-Howell CL, Wauquier N, Schoepp RJ, Minogue TD. Sequence optimized diagnostic assay for Ebola virus detection. Sci Rep 2023; 13:18840. [PMID: 37914767 PMCID: PMC10620139 DOI: 10.1038/s41598-023-29390-6] [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: 08/23/2021] [Accepted: 12/17/2021] [Indexed: 11/03/2023] Open
Abstract
Rapid pathogen identification is a critical first step in patient isolation, treatment, and controlling an outbreak. Real-time PCR is a highly sensitive and specific approach commonly used for infectious disease diagnostics. However, mismatches in the primer or probe sequence and the target organism can cause decreased sensitivity, assay failure, and false negative results. Limited genomic sequences for rare pathogens such as Ebola virus (EBOV) can negatively impact assay performance due to undiscovered genetic diversity. We previously developed and validated several EBOV assays prior to the 2013-2016 EBOV outbreak in West Africa, and sequencing EBOV Makona identified sequence variants that could impact assay performance. Here, we assessed the impact sequence mismatches have on EBOV assay performance, finding one or two primer or probe mismatches resulted in a range of impact from minimal to almost two log sensitivity reduction. Redesigning this assay improved detection of all EBOV variants tested. Comparing the performance of the new assay with the previous assays across a panel of human EBOV samples confirmed increased assay sensitivity as reflected in decreased Cq values with detection of three positive that tested negative with the original assay.
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Affiliation(s)
- Jeffrey W Koehler
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | - Christopher P Stefan
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | - Adrienne T Hall
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | - Korey L Delp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | - Aileen E O'Hearn
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | - Cheryl L Taylor-Howell
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | | | - Randal J Schoepp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, MD, 20102, USA.
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11
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Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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12
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Hampton LM, Luquero F, Costa A, Legand A, Formenty P. Ebola outbreak detection and response since 2013. THE LANCET. MICROBE 2023; 4:e661-e662. [PMID: 37354912 PMCID: PMC10469237 DOI: 10.1016/s2666-5247(23)00136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 06/26/2023]
Affiliation(s)
- Lee M Hampton
- Gavi, the Vaccine Alliance, Global Health Campus, Grand-Saconnex, Switzerland.
| | - Francisco Luquero
- Gavi, the Vaccine Alliance, Global Health Campus, Grand-Saconnex, Switzerland
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13
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Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023; 21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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14
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Isibor PO, Onwaeze OO, Kayode-Edwards II, Agbontaen DO, Ifebem-Ezima IAM, Bilewu O, Onuselogu C, Akinniyi AP, Obafemi YD, Oniha MI. Investigating and combatting the key drivers of viral zoonoses in Africa: an analysis of eight epidemics. BRAZ J BIOL 2023; 84:e270857. [PMID: 37531478 DOI: 10.1590/1519-6984.270857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/02/2023] [Indexed: 08/04/2023] Open
Abstract
Investigating the interplay of factors that result in a viral zoonotic outbreak is difficult, though it is increasingly important. As anthropogenic influences shift the delicate balance of ecosystems, new zoonoses emerge in humans. Sub-Saharan Africa is a notable hotspot for zoonotic disease due to abundant competent mammalian reservoir hosts. Furthermore, poverty, corruption, and an overreliance on natural resources play considerable roles in depleting biological resources, exacerbating the population's susceptibility. Unsurprisingly, viral zoonoses have emerged in Africa, including HIV/AIDS, Ebola, Avian influenza, Lassa fever, Zika, and Monkeypox. These diseases are among the principal causes of death in endemic areas. Though typically distinct in their manifestations, viral zoonoses are connected by underlying, definitive factors. This review summarises vital findings on viral zoonoses in Africa using nine notable case studies as a benchmark for future studies. We discuss the importance of ecological recuperation and protection as a central strategy to control zoonotic diseases. Emphasis was made on moderating key drivers of zoonotic diseases to forestall future pandemics. This is in conjunction with attempts to redirect efforts from reactive to pre-emptive through a multidisciplinary "one health" approach.
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Affiliation(s)
- P O Isibor
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O O Onwaeze
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - I I Kayode-Edwards
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - D O Agbontaen
- University of South Wales, Department of Public Health, Pontypridd, United Kingdom
| | - I-A M Ifebem-Ezima
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O Bilewu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - C Onuselogu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - A P Akinniyi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - Y D Obafemi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - M I Oniha
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
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15
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Escudero-Pérez B, Lalande A, Mathieu C, Lawrence P. Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans. Viruses 2023; 15:v15030599. [PMID: 36992308 PMCID: PMC10060007 DOI: 10.3390/v15030599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Emerging infectious diseases of zoonotic origin are an ever-increasing public health risk and economic burden. The factors that determine if and when an animal virus is able to spill over into the human population with sufficient success to achieve ongoing transmission in humans are complex and dynamic. We are currently unable to fully predict which pathogens may appear in humans, where and with what impact. In this review, we highlight current knowledge of the key host–pathogen interactions known to influence zoonotic spillover potential and transmission in humans, with a particular focus on two important human viruses of zoonotic origin, the Nipah virus and the Ebola virus. Namely, key factors determining spillover potential include cellular and tissue tropism, as well as the virulence and pathogenic characteristics of the pathogen and the capacity of the pathogen to adapt and evolve within a novel host environment. We also detail our emerging understanding of the importance of steric hindrance of host cell factors by viral proteins using a “flytrap”-type mechanism of protein amyloidogenesis that could be crucial in developing future antiviral therapies against emerging pathogens. Finally, we discuss strategies to prepare for and to reduce the frequency of zoonotic spillover occurrences in order to minimize the risk of new outbreaks.
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Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Alexandre Lalande
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Cyrille Mathieu
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
- Correspondence:
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16
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Jain S, Khaiboullina S, Martynova E, Morzunov S, Baranwal M. Epidemiology of Ebolaviruses from an Etiological Perspective. Pathogens 2023; 12:pathogens12020248. [PMID: 36839520 PMCID: PMC9963726 DOI: 10.3390/pathogens12020248] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/21/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Since the inception of the ebolavirus in 1976, 32 outbreaks have resulted in nearly 15,350 deaths in more than ten countries of the African continent. In the last decade, the largest (2013-2016) and second largest (2018-2020) ebolavirus outbreaks have occurred in West Africa (mainly Guinea, Liberia, and Sierra Leone) and the Democratic Republic of the Congo, respectively. The 2013-2016 outbreak indicated an alarming geographical spread of the virus and was the first to qualify as an epidemic. Hence, it is imperative to halt ebolavirus progression and develop effective countermeasures. Despite several research efforts, ebolaviruses' natural hosts and secondary reservoirs still elude the scientific world. The primary source responsible for infecting the index case is also unknown for most outbreaks. In this review, we summarize the history of ebolavirus outbreaks with a focus on etiology, natural hosts, zoonotic reservoirs, and transmission mechanisms. We also discuss the reasons why the African continent is the most affected region and identify steps to contain this virus.
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Affiliation(s)
- Sahil Jain
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Svetlana Khaiboullina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tatarstan, Russia
| | - Ekaterina Martynova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tatarstan, Russia
| | - Sergey Morzunov
- Department of Pathology, School of Medicine, University of Nevada, Reno, NV 89557, USA
- Correspondence: (S.M.); or (M.B.); Tel.: +1-775-682-6230 (S.M.); +91-175-2393118 (M.B.); Fax: +91-175-2364498 (M.B.)
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
- Correspondence: (S.M.); or (M.B.); Tel.: +1-775-682-6230 (S.M.); +91-175-2393118 (M.B.); Fax: +91-175-2364498 (M.B.)
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17
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Gruber MF, Rubin S, Krause PR. Approaches to demonstrating the effectiveness of filovirus vaccines: Lessons from Ebola and COVID-19. Front Immunol 2023; 14:1109486. [PMID: 36817425 PMCID: PMC9932497 DOI: 10.3389/fimmu.2023.1109486] [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: 11/27/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Zaire ebolavirus (EBOV), Sudan ebolavirus (SUDV) and Marburg virus (MARV), are members of the Filoviridae family that can cause severe disease and death in humans and animals. The reemergence of Ebola, Sudan and Marburg virus disease highlight the need for continued availability of safe and effectives vaccines as well as development of new vaccines. While randomized controlled trials using disease endpoints provide the most robust assessment of vaccine effectiveness, challenges to this approach include the unpredictable size, location, occurrence and duration of filovirus disease outbreaks. Thus, other approaches to demonstrating vaccine effectiveness have been considered. These approaches are discussed using examples of preventive vaccines against other infectious diseases. In addition, this article proposes a clinical immunobridging strategy using licensed EBOV vaccines as comparators for demonstrating the effectiveness of filovirus vaccine candidates that are based on the same licensed vaccine platform technology.
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Affiliation(s)
- Marion F. Gruber
- International AIDS Vaccine Initiative, New York, NY, United States,*Correspondence: Marion F. Gruber,
| | - Steven Rubin
- GlaxoSmithKline (GSk), Rockville, MD, United States
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18
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A Review: The Antiviral Activity of Cyclic Peptides. Int J Pept Res Ther 2023; 29:7. [PMID: 36471676 PMCID: PMC9713128 DOI: 10.1007/s10989-022-10478-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 12/02/2022]
Abstract
In the design and development of therapeutic agents, macromolecules with restricted structures have stronger competitive edges than linear biological entities since cyclization can overcome the limitations of linear structures. The common issues of linear peptides include susceptibility to degradation of the peptidase enzyme, off-target effects, and necessity of routine dosing, leading to instability and ineffectiveness. The unique conformational constraint of cyclic peptides provides a larger surface area to interact with the target at the same time, improving the membrane permeability and in vivo stability compared to their linear counterparts. Currently, cyclic peptides have been reported to possess various activities, such as antifungal, antiviral and antimicrobial activities. To date, there is emerging interest in cyclic peptide therapeutics, and increasing numbers of clinically approved cyclic peptide drugs are available on the market. In this review, the medical significance of cyclic peptides in the defence against viral infections will be highlighted. Except for chikungunya virus, which lacks specific antiviral treatment, all the viral diseases targeted in this review are those with effective treatments yet with certain limitations to date. Thus, strategies and approaches to optimise the antiviral effect of cyclic peptides will be discussed along with their respective outcomes. Apart from isolated naturally occurring cyclic peptides, chemically synthesized or modified cyclic peptides with antiviral activities targeting coronavirus, herpes simplex viruses, human immunodeficiency virus, Ebola virus, influenza virus, dengue virus, five main hepatitis viruses, termed as type A, B, C, D and E and chikungunya virus will be reviewed herein. Graphical Abstract
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19
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Christofferson RC, Cormier SA. Beyond the Unknown: A Broad Framing for Preparedness for Emerging Infectious Threats. Am J Trop Med Hyg 2022; 107:1159-1161. [PMID: 36191876 PMCID: PMC9768276 DOI: 10.4269/ajtmh.22-0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/05/2022] [Indexed: 12/30/2022] Open
Abstract
There have been multiple instances of novel pathogen emergence that have affected the health and security of the global community. To highlight that these novel pathogens presented a clear danger to public health, the WHO included "Disease X" on their list of priority pathogens in 2018. Indeed, since the emergence of SARS-CoV-2, Disease X has been pointed to as the looming threat of "the next big thing." However, developing surveillance and preparedness plans with Disease X as the linchpin is too narrow and ignores a large swath of potential threats from already identified, often neglected diseases. We propose instead the idea of "Disease f(x)" as a preferred call to arms with which to prioritize research and programmatic development. The common mathematical notation f(x) represents the knowledge that outbreaks are a function of many variables that define the transmission trajectory of that pathogen. Disease f(x) exploits commonalities across pathogen groupings while recognizing that emergences and outbreaks are fluid and that responses need to be agile and progressively tailored to specific pathogens with cultural and regional context. Adoption of this mindset across sectors, including biotechnology, disaster management, and epidemiology, will allow us to develop more efficient and effective responses to address the next major infectious threat.
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Affiliation(s)
- Rebecca C. Christofferson
- School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana;,Address correspondence to Rebecca C. Christofferson, LSU School of Veterinary Medicine, Skip Bertman Drive, Baton Rouge, LA 70803. E-mail:
| | - Stephania A. Cormier
- College of Science, Louisiana State University and Pennington Biomedical Research Center, Baton Rouge, Louisiana
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20
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Schuettenberg A, Piña A, Metrailer M, Peláez-Sánchez RG, Agudelo-Flórez P, Lopez JÁ, Ryle L, Monroy FP, Altin JA, Ladner JT. Highly Multiplexed Serology for Nonhuman Mammals. Microbiol Spectr 2022; 10:e0287322. [PMID: 36125316 PMCID: PMC9602771 DOI: 10.1128/spectrum.02873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023] Open
Abstract
Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.
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Affiliation(s)
- Alexa Schuettenberg
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alejandra Piña
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Morgan Metrailer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | | | - Juan Álvaro Lopez
- Microbiology School, Primary Immunodeficiencies Group, University of Antioquia, Medellín, Colombia
| | - Luke Ryle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Fernando P. Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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21
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Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nat Microbiol 2022; 7:1736-1743. [PMID: 36266338 DOI: 10.1038/s41564-022-01233-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost. Alongside this, the use of models that can forecast emergence and size of infectious disease outbreaks has risen, highlighted by the coronavirus disease 2019 pandemic but also due to modelling advances that allow for rapid estimates in emerging outbreaks to inform monitoring, coordination and resource deployment. However, genomics studies have remained largely retrospective. While they contain high-resolution views of pathogen diversification and evolution in the context of selection, they are often not aligned with designing interventions. This is a missed opportunity because pathogen diversification is at the core of the most pressing infectious public health challenges, and interventions need to take the mechanisms of virulence and understanding of pathogen diversification into account. In this Perspective, we assess these converging fields, discuss current challenges facing both surveillance specialists and modellers who want to harness genomic data, and propose next steps for integrating longitudinally sampled genomic data with statistical learning and interpretable modelling to make reliable predictions into the future.
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Affiliation(s)
- Jessica E Stockdale
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.
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22
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Alfson KJ, Goez-Gazi Y, Gazi M, Chou YL, Niemuth NA, Mattix ME, Staples H, Klaffke B, Rodriguez GF, Escareno P, Bartley C, Ticer A, Clemmons EA, Dutton III JW, Griffiths A, Meister GT, Sanford DC, Cirimotich CM, Carrion R. Development of a Well-Characterized Cynomolgus Macaque Model of Sudan Virus Disease for Support of Product Development. Vaccines (Basel) 2022; 10:1723. [PMID: 36298588 PMCID: PMC9611481 DOI: 10.3390/vaccines10101723] [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: 07/31/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/30/2022] Open
Abstract
The primary objective of this study was to characterize the disease course in cynomolgus macaques exposed to Sudan virus (SUDV), to determine if infection in this species is an appropriate model for the evaluation of filovirus countermeasures under the FDA Animal Rule. Sudan virus causes Sudan virus disease (SVD), with an average case fatality rate of approximately 50%, and while research is ongoing, presently there are no approved SUDV vaccines or therapies. Well characterized animal models are crucial for further developing and evaluating countermeasures for SUDV. Twenty (20) cynomolgus macaques were exposed intramuscularly to either SUDV or sterile phosphate-buffered saline; 10 SUDV-exposed animals were euthanized on schedule to characterize pathology at defined durations post-exposure and 8 SUDV-exposed animals were not part of the scheduled euthanasia cohort. Survival was assessed, along with clinical observations, body weights, body temperatures, hematology, clinical chemistry, coagulation, viral load (serum and tissues), macroscopic observations, and histopathology. There were statistically significant differences between SUDV-exposed animals and mock-exposed animals for 26 parameters, including telemetry body temperature, clinical chemistry parameters, hematology parameters, activated partial thromboplastin time, serum viremia, and biomarkers that characterize the disease course of SUDV in cynomolgus macaques.
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Affiliation(s)
- Kendra J. Alfson
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Yenny Goez-Gazi
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Michal Gazi
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Ying-Liang Chou
- Battelle Biomedical Research Center (BBRC), 1425 Plain City Georgesville Road, West Jefferson, OH 43162, USA
| | - Nancy A. Niemuth
- Battelle Biomedical Research Center (BBRC), 1425 Plain City Georgesville Road, West Jefferson, OH 43162, USA
| | - Marc E. Mattix
- Nonclinical Pathology Services, LLC, 5920 Clubhouse Pointe Dr., Medina, OH 44256, USA
| | - Hilary Staples
- Current affiliation: National Emerging Infectious Diseases Laboratory, Department of Microbiology, Boston University School of Medicine, 620 Albany St, Boston, MA 02118, USA
| | - Benjamin Klaffke
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Gloria F. Rodriguez
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Priscilla Escareno
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Carmen Bartley
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Anysha Ticer
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Elizabeth A. Clemmons
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - John W. Dutton III
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
| | - Anthony Griffiths
- Current affiliation: National Emerging Infectious Diseases Laboratory, Department of Microbiology, Boston University School of Medicine, 620 Albany St, Boston, MA 02118, USA
| | - Gabe T. Meister
- Battelle Biomedical Research Center (BBRC), 1425 Plain City Georgesville Road, West Jefferson, OH 43162, USA
| | - Daniel C. Sanford
- Battelle Biomedical Research Center (BBRC), 1425 Plain City Georgesville Road, West Jefferson, OH 43162, USA
| | - Chris M. Cirimotich
- Battelle Biomedical Research Center (BBRC), 1425 Plain City Georgesville Road, West Jefferson, OH 43162, USA
| | - Ricardo Carrion
- Texas Biomedical Research Institute, 8715 W. Military Dr., San Antonio, TX 78227, USA
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23
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Warren CJ, Yu S, Peters DK, Barbachano-Guerrero A, Yang Q, Burris BL, Worwa G, Huang IC, Wilkerson GK, Goldberg TL, Kuhn JH, Sawyer SL. Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans. Cell 2022; 185:3980-3991.e18. [PMID: 36182704 PMCID: PMC9588614 DOI: 10.1016/j.cell.2022.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/22/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023]
Abstract
Simian arteriviruses are endemic in some African primates and can cause fatal hemorrhagic fevers when they cross into primate hosts of new species. We find that CD163 acts as an intracellular receptor for simian hemorrhagic fever virus (SHFV; a simian arterivirus), a rare mode of virus entry that is shared with other hemorrhagic fever-causing viruses (e.g., Ebola and Lassa viruses). Further, SHFV enters and replicates in human monocytes, indicating full functionality of all of the human cellular proteins required for viral replication. Thus, simian arteriviruses in nature may not require major adaptations to the human host. Given that at least three distinct simian arteriviruses have caused fatal infections in captive macaques after host-switching, and that humans are immunologically naive to this family of viruses, development of serology tests for human surveillance should be a priority.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Shuiqing Yu
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Douglas K Peters
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Bridget L Burris
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Gabriella Worwa
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - I-Chueh Huang
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Gregory K Wilkerson
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA.
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Lebeau G, El Safadi D, Paulo-Ramos A, Hoareau M, Desprès P, Krejbich-Trotot P, Chouchou F, Roche M, Viranaicken W. The Efficient Antiviral Response of A549 Cells Is Enhanced When Mitochondrial Respiration Is Promoted. Pathogens 2022; 11:pathogens11101168. [PMID: 36297225 PMCID: PMC9611969 DOI: 10.3390/pathogens11101168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/19/2022] Open
Abstract
When exposed to a viral infection, the attacked cells promptly set up defense mechanisms. As part of the antiviral responses, the innate immune interferon pathway and associated interferon-stimulated genes notably allow the production of proteins bearing antiviral activity. Numerous viruses are able to evade the interferon response, highlighting the importance of controlling this pathway to ensure their efficient replication. Several viruses are also known to manipulate the metabolism of infected cells to optimize the availability of amino acids, nucleotides, and lipids. They then benefit from a reprogramming of the metabolism that favors glycolysis instead of mitochondrial respiration. Given the increasingly discussed crosstalk between metabolism and innate immunity, we wondered whether this switch from glycolysis to mitochondrial respiration would be beneficial or deleterious for an efficient antiviral response. We used a cell-based model of metabolic reprogramming. Interestingly, we showed that increased mitochondrial respiration was associated with an enhanced interferon response following polyriboinosinic:polyribocytidylic acid (poly:IC) stimulation. This suggests that during viral infection, the metabolic reprogramming towards glycolysis is also part of the virus’ strategies to inhibit the antiviral response.
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Affiliation(s)
- Grégorie Lebeau
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
- Correspondence:
| | - Daed El Safadi
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
| | - Aurélie Paulo-Ramos
- INSERM, UMR 1188 Diabète Athérothombose Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Saint-Denis, La Réunion, France
| | - Mathilde Hoareau
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
| | - Philippe Desprès
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
| | - Pascale Krejbich-Trotot
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
| | - Florian Chouchou
- IRISSE Laboratory (EA4075), UFR SHE, University of La Réunion, 97430 Le Tampon, La Réunion, France
| | - Marjolaine Roche
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
| | - Wildriss Viranaicken
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Plateforme Technologique CYROI, Université de La Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, 94791 Sainte Clotilde, La Réunion, France
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25
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Lin M, Chen H, Jia L, Yang M, Qiu S, Song H, Wang L, Zheng T. Using a grey relational analysis in an improved Grunow-Finke assessment tool to detect unnatural epidemics. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2022; 43:1508-1517. [PMID: 36100578 DOI: 10.1111/risa.14016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Grunow-Finke epidemiological assessment tool (GFT) has several limitations in its ability to differentiate between natural and man-made epidemics. Our study aimed to improve the GFT and analyze historical epidemics to validate the model. Using a gray relational analysis (GRA), we improved the GFT by revising the existing standards and adding five new standards. We then removed the artificial weights and final decision threshold. Finally, by using typically unnatural epidemic events as references, we used the GRA to calculate the unnatural probability and obtain assessment results. Using the advanced tool, we conducted retrospective and case analyses to test its performance. In the validation set of 13 historical epidemics, unnatural and natural epidemics were divided into two categories near the unnatural probability of 45%, showing evident differences (p < 0.01) and an assessment accuracy close to 100%. The unnatural probabilities of the Ebola virus disease of 2013 and Middle East Respiratory Syndrome of 2012 were 30.6% and 36.1%, respectively. Our advanced epidemic assessment tool improved the accuracy of the original GFT from approximately 55% to approximately 100% and reduced the impact of human factors on these outcomes effectively.
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Affiliation(s)
- Mengxuan Lin
- Academy of Military Medical Sciences, Academy of Military Science of Chinese PLA, Beijing, China
| | - Hui Chen
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Leili Jia
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Mingjuan Yang
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Shaofu Qiu
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Hongbin Song
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Ligui Wang
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Tao Zheng
- Academy of Military Medical Sciences, Academy of Military Science of Chinese PLA, Beijing, China
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26
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Chen J, Liu Y, Yue J, Duan X, Tang M. Coevolving spreading dynamics of negative information and epidemic on multiplex networks. NONLINEAR DYNAMICS 2022; 110:3881-3891. [PMID: 36035014 PMCID: PMC9395805 DOI: 10.1007/s11071-022-07776-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
The widespread dissemination of negative information on vaccine may arise people's concern on the safety of vaccine and increase their hesitancy in vaccination, which can seriously impede the progress of epidemic control. Existing works on information-epidemic coupled dynamics focus on the suppression effects of information on epidemic. Here we propose a negative information and epidemic coupled propagation model on two-layer multiplex networks to study the effects of negative information of vaccination on epidemic spreading, where the negative information propagates on the virtual communication layer and the disease spreads on the physical contact layer. In our model, an individual getting an adverse event after vaccination will spread negative information and an individual affected by the negative information will reduce his/her willingness to get vaccinated and spread the negative information. By using the microscopic Markov chain method, we analytically predict the epidemic threshold and final infection density, which agree well with simulation results. We find that the spread of negative information leads to a lower epidemic outbreak threshold and a higher final infection density. However, the individuals' vaccination activities, but not the negative information spreading, has a leading impact on epidemic spreading. Only when the individuals obviously reduce their vaccination willingness due to negative information, the negative information can impact the epidemic spreading significantly.
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Affiliation(s)
- Jiaxing Chen
- School of Computer Science, Southwest Petroleum University, Chengdu, 610500 China
- Tianjin Key Lab of Intelligence Computing and Novel Software Technology, Tianjin University of Technology, Tianjin, 300384 China
| | - Ying Liu
- School of Computer Science, Southwest Petroleum University, Chengdu, 610500 China
| | - Jing Yue
- School of Computer Science, Southwest Petroleum University, Chengdu, 610500 China
| | - Xi Duan
- School of Science, Southwest Petroleum University, Chengdu, 610500 China
| | - Ming Tang
- School of Physics and Electronic Science, East China Normal University, Shanghai, 200241 China
- Shanghai Key Laboratory of Multidimensional Information Processing, East China Normal University, Shanghai, 200241 China
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27
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Tiemessen MM, Solforosi L, Dekking L, Czapska-Casey D, Serroyen J, Sullivan NJ, Volkmann A, Pau MG, Callendret B, Schuitemaker H, Luhn K, Zahn R, Roozendaal R. Protection against Marburg Virus and Sudan Virus in NHP by an Adenovector-Based Trivalent Vaccine Regimen Is Correlated to Humoral Immune Response Levels. Vaccines (Basel) 2022; 10:1263. [PMID: 36016151 PMCID: PMC9412258 DOI: 10.3390/vaccines10081263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
The Marburg virus (MARV) and Sudan virus (SUDV) belong to the filovirus family. The sporadic human outbreaks occur mostly in Africa and are characterized by an aggressive disease course with high mortality. The first case of Marburg virus disease in Guinea in 2021, together with the increased frequency of outbreaks of Ebola virus (EBOV), which is also a filovirus, accelerated the interest in potential prophylactic vaccine solutions against multiple filoviruses. We previously tested a two-dose heterologous vaccine regimen (Ad26.Filo, MVA-BN-Filo) in non-human primates (NHP) and showed a fully protective immune response against both SUDV and MARV in addition to the already-reported protective effect against EBOV. The vaccine-induced glycoprotein (GP)-binding antibody levels appear to be good predictors of the NHP challenge outcome as indicated by the correlation between antibody levels and survival outcome as well as the high discriminatory capacity of the logistic model. Moreover, the elicited GP-specific binding antibody response against EBOV, SUDV, and MARV remains stable for more than 1 year. Overall, the NHP data indicate that the Ad26.Filo, MVA-BN-Filo regimen may be a good candidate for a prophylactic vaccination strategy in regions at high risk of filovirus outbreaks.
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Affiliation(s)
- Machteld M. Tiemessen
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Laura Solforosi
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Liesbeth Dekking
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | | | - Jan Serroyen
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ariane Volkmann
- Bavarian Nordic GmbH, Fraunhoferstrasse 13, D-82152 Martinsried, Germany
| | - Maria Grazia Pau
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Benoit Callendret
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Hanneke Schuitemaker
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Kerstin Luhn
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Roland Zahn
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
| | - Ramon Roozendaal
- Janssen Vaccines & Prevention B.V., Archimedesweg 6, 2333 CN Leiden, The Netherlands
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28
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Mokhtary P, Pourhashem Z, Mehrizi AA, Sala C, Rappuoli R. Recent Progress in the Discovery and Development of Monoclonal Antibodies against Viral Infections. Biomedicines 2022; 10:biomedicines10081861. [PMID: 36009408 PMCID: PMC9405509 DOI: 10.3390/biomedicines10081861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 07/29/2022] [Indexed: 01/09/2023] Open
Abstract
Monoclonal antibodies (mAbs), the new revolutionary class of medications, are fast becoming tools against various diseases thanks to a unique structure and function that allow them to bind highly specific targets or receptors. These specialized proteins can be produced in large quantities via the hybridoma technique introduced in 1975 or by means of modern technologies. Additional methods have been developed to generate mAbs with new biological properties such as humanized, chimeric, or murine. The inclusion of mAbs in therapeutic regimens is a major medical advance and will hopefully lead to significant improvements in infectious disease management. Since the first therapeutic mAb, muromonab-CD3, was approved by the U.S. Food and Drug Administration (FDA) in 1986, the list of approved mAbs and their clinical indications and applications have been proliferating. New technologies have been developed to modify the structure of mAbs, thereby increasing efficacy and improving delivery routes. Gene delivery technologies, such as non-viral synthetic plasmid DNA and messenger RNA vectors (DMabs or mRNA-encoded mAbs), built to express tailored mAb genes, might help overcome some of the challenges of mAb therapy, including production restrictions, cold-chain storage, transportation requirements, and expensive manufacturing and distribution processes. This paper reviews some of the recent developments in mAb discovery against viral infections and illustrates how mAbs can help to combat viral diseases and outbreaks.
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Affiliation(s)
- Pardis Mokhtary
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy;
- Department of Biochemistry and Molecular Biology, University of Siena, 53100 Siena, Italy
| | - Zeinab Pourhashem
- Student Research Committee, Pasteur Institute of Iran, Tehran 1316943551, Iran;
- Malaria and Vector Research Group, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Akram Abouei Mehrizi
- Malaria and Vector Research Group, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Claudia Sala
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy;
- Correspondence: (C.S.); (R.R.)
| | - Rino Rappuoli
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy;
- Correspondence: (C.S.); (R.R.)
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29
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Lo VT, Yoon SW, Noh JY, Jang SS, Na W, Song D, Jeong DG, Kim HK. Characterization of replication and variations in genome segments of a bat reovirus, BatMRV/B19-02, by RNA-seq in infected Vero-E6 cells. Arch Virol 2022; 167:2133-2142. [PMID: 35821149 DOI: 10.1007/s00705-022-05534-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/26/2022] [Indexed: 11/26/2022]
Abstract
Mammalian orthoreoviruses (MEVs) that can cause enteric, respiratory, and encephalitic infections have been identified in a wide variety of mammalian species. Here, we report a novel MRV type 1 strain detected in Miniopterus schreibersii that may have resulted from reassortment events. Using next-generation RNA sequencing (RNA-seq), we found that the ratios of the RNA levels of the 10 reovirus segments in infected cells were constant during the late stages of infection. We also discovered that the relative abundance of each segment differed. Notably, the relative abundance of M2 (encoding the µ1 protein) and S4 (encoding the σ3 protein) RNAs was higher than that of the others throughout the infection. Additionally, massive junctions were identified. These results support the hypothesis that defective genome segments are generated and that cross-family recombination occurs. These data may further the study of gene function, viral replication, and virus evolution.
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Affiliation(s)
- Van Thi Lo
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Sun-Woo Yoon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Ji Yeong Noh
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Korea
| | - Seong Sik Jang
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Korea
| | - Woonsung Na
- College of Veterinary Medicine, Chonnam National University, Gwangju, Korea
| | - Daesub Song
- College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Dae Gwin Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
- Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Korea.
| | - Hye Kwon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Korea.
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30
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Muzembo BA, Kitahara K, Ohno A, Ntontolo NP, Ngatu NR, Okamoto K, Miyoshi SI. Rapid diagnostic tests versus RT-PCR for Ebola virus infections: a systematic review and meta-analysis. Bull World Health Organ 2022; 100:447-458. [PMID: 35813519 PMCID: PMC9243686 DOI: 10.2471/blt.21.287496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/08/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022] Open
Abstract
Objective To evaluate the clinical accuracy of rapid diagnostic tests for the detection of Ebola virus. Methods We searched MEDLINE®, Embase® and Web of Science for articles published between 1976 and October 2021 reporting on clinical studies assessing the performance of Ebola virus rapid diagnostic tests compared with reverse transcription polymerase chain reaction (RT-PCR). We assessed study quality using the QUADAS-2 criteria. To estimate the pooled sensitivity and specificity of these rapid diagnostic tests, we used a bivariate random-effects meta-analysis. Findings Our search identified 113 unique studies, of which nine met the inclusion criteria. The studies were conducted in the Democratic Republic of the Congo, Guinea, Liberia and Sierra Leone and they evaluated 12 rapid diagnostic tests. We included eight studies in the meta-analysis. The pooled sensitivity and specificity of the rapid tests were 86% (95% confidence interval, CI: 80-91) and 95% (95% CI: 91-97), respectively. However, pooled sensitivity decreased to 83% (95% CI: 77-88) after removing outliers. Pooled sensitivity increased to 90% (95% CI: 82-94) when analysis was restricted to studies using the RT-PCR from altona Diagnostics as gold standard. Pooled sensitivity increased to 99% (95% CI: 67-100) when the analysis was restricted to studies using whole or capillary blood specimens. Conclusion The included rapid diagnostic tests did not detect all the Ebola virus disease cases. While the sensitivity and specificity of these tests are moderate, they are still valuable tools, especially useful for triage and detecting Ebola virus in remote areas.
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Affiliation(s)
- Basilua Andre Muzembo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita Ward, Okayama, 700-8530, Japan
| | - Kei Kitahara
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Kolkata, India
| | - Ayumu Ohno
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Kolkata, India
| | | | - Nlandu Roger Ngatu
- Department of Public Health, Kagawa University Faculty of Medicine, Miki, Japan
| | - Keinosuke Okamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita Ward, Okayama, 700-8530, Japan
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita Ward, Okayama, 700-8530, Japan
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31
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Koundouno FR, Kafetzopoulou LE, Faye M, Renevey A, Soropogui B, Ifono K, Nelson EV, Kamano AA, Tolno C, Annibaldis G, Millimono SL, Camara J, Kourouma K, Doré A, Millimouno TE, Tolno FMB, Hinzmann J, Soubrier H, Hinrichs M, Thielebein A, Herzer G, Pahlmann M, Ki-Zerbo GA, Formenty P, Legand A, Wiley MR, Faye O, Diagne MM, Sall AA, Lemey P, Bah A, Günther S, Keita S, Duraffour S, Magassouba N. Detection of Marburg Virus Disease in Guinea. N Engl J Med 2022; 386:2528-2530. [PMID: 35767445 PMCID: PMC7613962 DOI: 10.1056/nejmc2120183] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Fara R Koundouno
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Annick Renevey
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Kékoura Ifono
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Emily V Nelson
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Aly A Kamano
- World Health Organization Guinea, Conakry, Guinea
| | | | | | - Saa L Millimono
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Karifa Kourouma
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | - Julia Hinzmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hugo Soubrier
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Mette Hinrichs
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anke Thielebein
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Glaucia Herzer
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Meike Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | | | | | | | | | | | | | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sakoba Keita
- Agence Nationale de Sécurité Sanitaire, Conakry, Guinea
| | - Sophie Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - N'Faly Magassouba
- Laboratoire des Fièvres Hémorragiques Virales de Guinée, Conakry, Guinea
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32
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Zhang Z, Li D, Wang X, Wang Y, Lin J, Jiang S, Wu Z, He Y, Gao X, Zhu Z, Xiao Y, Qu Z, Li Y. Rapid detection of viruses: Based on silver nanoparticles modified with bromine ions and acetonitrile. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2022; 438:135589. [PMID: 35261557 PMCID: PMC8890791 DOI: 10.1016/j.cej.2022.135589] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 05/02/2023]
Abstract
Nearly 200 million people have been diagnosed with COVID-19 since the outbreak in 2019, and this disease has claimed more than 5 million lives worldwide. Currently, researchers are focusing on vaccine development and the search for an effective strategy to control the infection source. This work designed a detection platform based on Surface-Enhanced Raman Spectroscopy (SERS) by introducing acetonitrile and calcium ions into the silver nanoparticle reinforced substrate system to realize the rapid detection of novel coronavirus. Acetonitrile may amplify the calcium-induced hot spots of silver nanoparticles and significantly enhanced the stability of silver nanoparticles. It also elicited highly sensitive SERS signals of the virus. This approach allowed us to capture the characteristic SERS signals of SARS-CoV-2, Human Adenovirus 3, and H1N1 influenza virus molecules at a concentration of 100 copies/test (PFU/test) with upstanding reproduction and signal-to-noise ratio. Machine learning recognition technology was employed to qualitatively distinguish the three virus molecules with 1000 groups of spectra of each virus. Acetonitrile is a potent internal marker in regulating the signal intensity of virus molecules in saliva and serum. Thus, we used the SERS peak intensity to quantify the virus content in saliva and serum. The results demonstrated a satisfactory linear relationship between peak intensity and protein concentration. Collectively, this rapid detection method has a broad application prospect in clinical diagnosis of viruses, management of emergent viral infectious diseases, and exploration of the interaction between viruses and host cells.
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Affiliation(s)
- Zhe Zhang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Dan Li
- Institute of Physics, Guizhou University, Guiyang City, Guizhou Province 550025, PR China
| | - Xiaotong Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Yunpeng Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Jingyi Lin
- The Fourth Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
| | - Shen Jiang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Zheng Wu
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Yingying He
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Xin Gao
- Institute of Physics, Guizhou University, Guiyang City, Guizhou Province 550025, PR China
| | - Zhuo Zhu
- The Second Hospital of Jilin University, Jilin University, Changchun City, Jilin Province 130041, PR China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun City, Jilin Province 130041, PR China
| | - Zhangyi Qu
- College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
| | - Yang Li
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
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Njukeng PA, Njumkeng C, Ntongowa C, Abdulaziz M. Strengthening laboratory networks in the Central Africa region: A milestone for epidemic preparedness and response. Afr J Lab Med 2022; 11:1492. [PMID: 35747554 PMCID: PMC9210186 DOI: 10.4102/ajlm.v11i1.1492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/11/2022] [Indexed: 11/14/2022] Open
Abstract
Background Health systems in the Central Africa region are among the weakest and least funded in the world. The lack of laboratory networks and adequately trained personnel with clearly defined responsibilities has hampered the implementation of laboratory quality improvement programmes. Global Health Systems Solutions (GHSS) obtained a grant from the Africa Centres for Disease Control and Prevention to develop laboratory networks for disease surveillance and strengthen the quality of laboratory testing in the Central Africa region. Intervention One year after the grant was awarded on 01 October 2018, GHSS has launched a Regional Integrated Surveillance and Laboratory Network (RISLNET) for Central Africa and developed National Laboratory Strategic Plans and Policies for member states, eight frameworks and guideline documents, as well as a website for RISLNET Central Africa. GHSS has also launched an Extension for Community Health Outcomes platform to supervise laboratories enrolled for accreditation, installed a Basic Laboratory Information System (BLIS) in four laboratories in four member states, and trained 247 laboratory personnel and laboratory experts on BLIS, quality assurance, external quality assurance, Strengthening Laboratory Management Towards Accreditation (SLMTA), quality management systems, and equipment maintenance and calibration. Lessons learnt Participating laboratories now serve as reference laboratories for COVID-19 testing in various countries. Point-of-care testing, using the GeneXpert platform, has been the central strategy for the scale-up of COVID-19 testing in the Central Africa region. Recommendations Expanding SLMTA to other laboratories within Central Africa will significantly improve the quality management of laboratories for a better healthcare system.
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Affiliation(s)
| | | | | | - Mohammed Abdulaziz
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
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Collins D, Diallo BI, Bah MB, Bah M, Standley CJ, Corvil S, Martel LD, MacDonald PDM. Evaluation of the first two Frontline cohorts of the field epidemiology training program in Guinea, West Africa. HUMAN RESOURCES FOR HEALTH 2022; 20:40. [PMID: 35549712 PMCID: PMC9097411 DOI: 10.1186/s12960-022-00729-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/25/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND The 2014-2016 Ebola virus disease outbreak in West Africa revealed weaknesses in the health systems of the three most heavily affected countries, including a shortage of public health professionals at the local level trained in surveillance and outbreak investigation. In response, the Frontline Field Epidemiology Training Program (FETP) was created by CDC in 2015 as a 3-month, accelerated training program in field epidemiology that specifically targets the district level. In Guinea, the first two FETP-Frontline cohorts were held from January to May, and from June to September 2017. Here, we report the results of a cross-sectional evaluation of these first two cohorts of FETP-Frontline in Guinea. METHODS The evaluation was conducted in April 2018 and consisted of interviews with graduates, their supervisors, and directors of nearby health facilities, as well as direct observation of data reports and surveillance tools at health facilities. Interviews and site visits were conducted using standardized questionnaires and checklists. Qualitative data were coded under common themes and analyzed using descriptive statistics. RESULTS The evaluation revealed a significant perception of improvement in all assessed skills by the graduates, as well as high levels of self-reported involvement in key activities related to data collection, analysis, and reporting. Supervisors highlighted improvements to systematic and quality case and summary reporting as key benefits of the FETP-Frontline program. At the health facility level, staff reported the training had resulted in improvements to information sharing and case notifications. Reported barriers included lack of transportation, available support personnel, and other resources. Graduates and supervisors both emphasized the importance of continued and additional training to solidify and retain skills. CONCLUSIONS The evaluation demonstrated a strongly positive perceived benefit of the FETP-Frontline training on the professional activities of graduates as well as the overall surveillance system. However, efforts are needed to ensure greater gender equity and to recruit more junior trainee candidates for future cohorts. Moreover, although improvements to the surveillance system were observed concurrent with the completion of the two cohorts, the evaluation was not designed to directly measure impact on surveillance or response functions. Combined with the rapid implementation of FETP-Frontline around the world, this suggests an opportunity to develop standardized evaluation toolkits, which could incorporate metrics that would directly assess the impact of equitable field epidemiology workforce development on countries' abilities to prevent, detect, and respond to public health threats.
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Affiliation(s)
| | | | | | | | - Claire J Standley
- Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
| | | | - Lise D Martel
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
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Ma Y, He T, Tan Y, Jiang X. Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1322-1333. [PMID: 32750886 DOI: 10.1109/tcbb.2020.3008157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Infectious diseases are currently the most important and widespread health problem, and identifying viral infection mechanisms is critical for controlling diseases caused by highly infectious viruses. Because of the lack of non-interactive protein pairs and serious imbalance between positive and negative sample ratios, the supervised learning algorithm is not suitable for prediction. At the same time, due to the lack of information on viral proteins and significant dissimilarity in sequence, some ensemble learning models have poor generalization ability. In this paper, we propose a Sequence-Based Ensemble Learning (Seq-BEL) method to predict the potential virus-human PPIs. Specifically, based on the amino acid sequence of proteins and the currently known virus-human PPI network, Seq-BEL calculates various features and similarities of human proteins and viral proteins, and then combines these similarities and features to score the potential of virus-human PPIs. The computational results show that Seq-BEL achieves success in predicting potential virus-human PPIs and outperforms other state-of-the-art methods. More importantly, Seq-BEL also has good predictive performance for new human proteins and new viral proteins. In addition, the model has the advantages of strong robustness and good generalization ability, and can be used as an effective tool for virus-human PPI prediction.
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Kaundal R, Loaiza CD, Duhan N, Flann N. deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions. Brief Bioinform 2022; 23:6576450. [PMID: 35511057 DOI: 10.1093/bib/bbac125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 02/07/2022] [Accepted: 03/15/2022] [Indexed: 01/06/2023] Open
Abstract
Host-pathogen protein interactions (HPPIs) play vital roles in many biological processes and are directly involved in infectious diseases. With the outbreak of more frequent pandemics in the last couple of decades, such as the recent outburst of Covid-19 causing millions of deaths, it has become more critical to develop advanced methods to accurately predict pathogen interactions with their respective hosts. During the last decade, experimental methods to identify HPIs have been used to decipher host-pathogen systems with the caveat that those techniques are labor-intensive, expensive and time-consuming. Alternatively, accurate prediction of HPIs can be performed by the use of data-driven machine learning. To provide a more robust and accurate solution for the HPI prediction problem, we have developed a deepHPI tool based on deep learning. The web server delivers four host-pathogen model types: plant-pathogen, human-bacteria, human-virus and animal-pathogen, leveraging its operability to a wide range of analyses and cases of use. The deepHPI web tool is the first to use convolutional neural network models for HPI prediction. These models have been selected based on a comprehensive evaluation of protein features and neural network architectures. The best prediction models have been tested on independent validation datasets, which achieved an overall Matthews correlation coefficient value of 0.87 for animal-pathogen using the combined pseudo-amino acid composition and conjoint triad (PAAC_CT) features, 0.75 for human-bacteria using the combined pseudo-amino acid composition, conjoint triad and normalized Moreau-Broto feature (PAAC_CT_NMBroto), 0.96 for human-virus using PAAC_CT_NMBroto and 0.94 values for plant-pathogen interactions using the combined pseudo-amino acid composition, composition and transition feature (PAAC_CTDC_CTDT). Our server running deepHPI is deployed on a high-performance computing cluster that enables large and multiple user requests, and it provides more information about interactions discovered. It presents an enriched visualization of the resulting host-pathogen networks that is augmented with external links to various protein annotation resources. We believe that the deepHPI web server will be very useful to researchers, particularly those working on infectious diseases. Additionally, many novel and known host-pathogen systems can be further investigated to significantly advance our understanding of complex disease-causing agents. The developed models are established on a web server, which is freely accessible at http://bioinfo.usu.edu/deepHPI/.
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Affiliation(s)
- Rakesh Kaundal
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences.,Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences.,Department of Computer Science, College of Science; Utah State University, Logan, 84322 USA
| | - Cristian D Loaiza
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences.,Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences
| | - Naveen Duhan
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences.,Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences
| | - Nicholas Flann
- Department of Computer Science, College of Science; Utah State University, Logan, 84322 USA
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Rugarabamu S, Rumisha SF, Mwanyika GO, Sindato C, Lim HY, Misinzo G, Mboera LEG. Viral haemorrhagic fevers and malaria co-infections among febrile patients seeking health care in Tanzania. Infect Dis Poverty 2022; 11:33. [PMID: 35462550 PMCID: PMC9036688 DOI: 10.1186/s40249-022-00959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background In recent years there have been reports of viral haemorrhagic fever (VHF) epidemics in sub-Saharan Africa where malaria is endemic. VHF and malaria have overlapping clinical presentations making differential diagnosis a challenge. The objective of this study was to determine the prevalence of selected zoonotic VHFs and malaria co-infections among febrile patients seeking health care in Tanzania. Methods This facility-based cross-sectional study was carried out between June and November 2018 in Buhigwe, Kalambo, Kyela, Kilindi, Kinondoni, Kondoa, Mvomero, and Ukerewe districts in Tanzania. The study involved febrile patients seeking health care from primary healthcare facilities. Blood samples were collected and tested for infections due to malaria, Crimean-Congo haemorrhagic fever (CCHF), Ebola virus disease (EVD), Marburg virus disease (MVD), Rift Valley fever (RVF) and yellow fever (YF). Malaria infections were tested using rapid diagnostics tests while exposure to VHFs was determined by screening for immunoglobulin M antibodies using commercial enzyme-linked immunosorbent assays. The Chi-square test was used to compare the proportions. Results A total of 308 participants (mean age = 35 ± 19 years) were involved in the study. Of these, 54 (17.5%) had malaria infection and 15 (4.8%) were positive for IgM antibodies against VHFs (RVF = 8; CCHF = 2; EBV = 3; MBV = 1; YF = 1). Six (1.9%) individuals had both VHF (RVF = 2; CCHF = 1; EVD = 2; MVD = 1) and malaria infections. The highest co-infection prevalence (0.6%) was observed among individuals aged 46‒60 years (P < 0.05). District was significantly associated with co-infection (P < 0.05) with the highest prevalence recorded in Buhigwe (1.2%) followed by Kinondoni (0.9%) districts. Headache (100%) and muscle, bone, back and joint pains (83.3%) were the most significant complaints among those infected with both VHFs and malaria (P = 0.001). Conclusions Co-infections of VHF and malaria are prevalent in Tanzania and affect more the older than the younger population. Since the overlapping symptoms in co-infected individuals may challenge accurate diagnosis, adequate laboratory diagnosis should be emphasized in the management of febrile illnesses.
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Holbrook AJ, Ji X, Suchard MA. From viral evolution to spatial contagion: a biologically modulated Hawkes model. Bioinformatics 2022; 38:1846-1856. [PMID: 35040956 PMCID: PMC8963291 DOI: 10.1093/bioinformatics/btac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/11/2021] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
SUMMARY Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly relates a pathogen's evolution to its spatial contagion dynamics-effectively combining the two epidemiological paradigms of phylogenetic inference and self-exciting process modeling-and apply this phylogenetic Hawkes process to a Bayesian analysis of 23 421 viral cases from the 2014 to 2016 Ebola outbreak in West Africa. The proposed model is able to detect individual viruses with significantly elevated rates of spatiotemporal propagation for a subset of 1610 samples that provide genome data. Finally, to facilitate model application in big data settings, we develop massively parallel implementations for the gradient and Hessian of the log-likelihood and apply our high-performance computing framework within an adaptively pre-conditioned Hamiltonian Monte Carlo routine. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew J Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Marc A Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
- Department of Biomathematics
- Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
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Cihlar T, Mackman RL. Journey of remdesivir from the inhibition of hepatitis C virus to the treatment of COVID-19. Antivir Ther 2022; 27:13596535221082773. [DOI: 10.1177/13596535221082773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
If a planned path reaches a dead-end, one can simply stop. Or one can turn around, walk back to the last intersection and take another path, or one can consider taking few paths in parallel. The last scenario is reflective of the journey of remdesivir, the first antiviral for the treatment of COVID-19, that was approved by FDA less than 10 months after the isolation of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. As of January 2022, 10 million COVID-19 patients have been treated with remdesivir worldwide, but the journey of this molecule started more than a decade earlier with the search for a cure of hepatitis C virus. The development path of remdesivir before the emergence of COVID-19 represents a valuable example of a preemptive pandemic preparedness, but the pursuit of this path would not have been possible without sustaining support of John C. Martin, whom we will sorely miss for his piercing vision, uncompromising leadership, and genuine compassion for patients suffering around the world.
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Abstract
Epidemics of infectious diseases, such as the one caused by the rapid spread of the coronavirus disease 2019 (COVID-19), have tested the world's more advanced health systems and have caused an enormous societal and economic damage. The mechanism of contagion is well understood. As people move around, over time, they regularly engage in social interactions. The spatiotemporal network representing these interactions constitutes the backbone on which an epidemic spreads, causing outbreaks. At the same time, advanced technological responses have claimed some success in controlling the epidemic based on digital contact tracing technologies. Motivated by these observations, we design, develop and evaluate a stochastic agent-basedSEIRmodel of epidemic spreading in spatiotemporal networks informed by mobility data of individuals (trajectories). The model focuses on individual variation in mobility patterns that affects the degree of exposure to the disease. Understanding the role that individual nodes play in the process of disease spreading through network effects is fundamental as it allows to (i) assess the risk of infection of individuals, (ii) assess the size of a disease outbreak due to specific individuals, and (iii) assess targeted intervention strategies that aim to control the epidemic spreading. We perform a comprehensive analysis of the model employing COVID-19 as a use case. The results indicate that simple individual-based intervention strategies that exhibit significant network effects can effectively control the spread of an epidemic. We have also demonstrated that targeted interventions can outperform generic intervention strategies. Overall, our work provides an evidence-based data-driven model to support decision making and inform public policy regarding intervention strategies for containing or mitigating the epidemic spread.
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Ding X, Li Z, Avery L, Ballesteros E, Makol R, Liu C. pH-EVD: A pH-Paper-Based Extraction and Visual Detection System for Instrument-Free SARS-CoV-2 Diagnostics. ADVANCED NANOBIOMED RESEARCH 2022; 2:2100101. [PMID: 35441159 PMCID: PMC9011642 DOI: 10.1002/anbr.202100101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/29/2021] [Indexed: 11/28/2022] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide. However, most SARS-CoV-2 detection methods depend on time-consuming sample preparation and large detection instruments. Herein, a method employing nonbleeding pH paper to achieve both RNA extraction and visual isothermal amplification is proposed, enabling rapid, instrument-free SARS-CoV-2 detection. By taking advantage of capillary forces, pH-paper-based RNA extraction can be accomplished within 1 min without need for any equipment. Further, the pH paper can mediate dye-free visual isothermal amplification detection. In less than a 46-min sample-to-answer time, pH-paper-based extraction and visual detection (termed pH-EVD) can consistently detect 1200 genome equivalents per microliter of SARS-CoV-2 in saliva, which is comparable to TaqMan probe-based quantitative reverse transcription PCR (RT-qPCR). Through coupling with a chemically heated incubator called a smart cup, the instrument-free, pH-EVD-based SARS-CoV-2 detection method on 30 nasopharyngeal swab samples and 33 contrived saliva samples is clinically validated. Thus, the pH-EVD method provides simple, rapid, reliable, low-cost, and instrument-free SARS-CoV-2 detection and has the potential to streamline onsite COVID-19 diagnostics.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
| | - Ziyue Li
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
| | - Lori Avery
- Department of Pathology and Laboratory MedicineUniversity of Connecticut Health CenterFarmingtonCT06030USA
| | - Enrique Ballesteros
- Department of Pathology and Laboratory MedicineUniversity of Connecticut Health CenterFarmingtonCT06030USA
| | - Rohit Makol
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
| | - Changchun Liu
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
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Rapp M, Shapiro L, Frank J. Contributions of single-particle cryoelectron microscopy toward fighting COVID-19. Trends Biochem Sci 2022; 47:117-123. [PMID: 34799235 PMCID: PMC8556535 DOI: 10.1016/j.tibs.2021.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Single-particle cryoelectron microscopy (cryo-EM), whose full capabilities have been realized only within the past decade, has had a pivotal role in the fight against COVID-19. This is due to the technique's intrinsic power to depict both structural and dynamic features of molecules; in this case, of the spike protein of SARS-CoV-2. By now, numerous cryo-EM studies have furthered our understanding of spike protein-angiotensin-converting enzyme 2 (ACE2) receptor interactions, which has informed the design of effective vaccines, and have enabled the characterization of neutralizing antibody binding sites, which will lead to the design of novel therapeutics as the virus evolves.
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Affiliation(s)
- Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA.
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA; Department of Biological Sciences, Columbia University, New York, USA.
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SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction. BIOCHIP JOURNAL 2022; 16:41-48. [PMID: 35096279 PMCID: PMC8790009 DOI: 10.1007/s13206-021-00044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/02/2022]
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Raab M, Pfadenhauer LM, Doumbouya D, Froeschl G. Clinical presentations, diagnostics, treatments and treatment costs of children and adults with febrile illness in a tertiary referral hospital in south-eastern Guinea: A retrospective longitudinal cohort study. PLoS One 2022; 17:e0262084. [PMID: 35007283 PMCID: PMC8746772 DOI: 10.1371/journal.pone.0262084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Febrile illness is frequent among patients in the tropics. It is caused by a wide variety of common diseases such as malaria or gastrointestinal infections but also by less common but highly contagious pathogens with epidemic potential. This study describes the clinical features of adult and paediatric patients with febrile illness in in the largest tertiary referral hospital in south-eastern Guinea, a region at high risk for viral haemorrhagic fever outbreaks. The study further compares their diagnostic characteristics, treatments and outcomes with non-febrile patients in order to contribute to the local epidemiology of febrile illness. Methods We used retrospective data collection to record demographic and clinical data of all incoming patients during a study period of three months. For the follow-up study of inpatients, we retrospectively reviewed patient charts for diagnostic characteristics, diagnoses and outcomes. Results Of the 4317 incoming patients during the study period, 9.5% had a febrile illness. The most used diagnostic measures to identify causative agents in febrile patients were point-of-care tests and most treatments relied on antibiotics. Most common discharge diagnoses for febrile inpatients were malaria (9.6% adults, 56.7% children), salmonella gastroenteritis/typhoid (10.6% adults, 7.8% children) and respiratory infection/pneumonia (5.3% adults, 18.7% children). Inpatient mortality for children was significantly higher in febrile than non-febrile children (18.5% vs. 5.1%, p<0.001) and considerably higher in febrile than non-febrile adults (29.8% vs. 25.0%, p = 0.404). Conclusions Malaria, respiratory infection and gastroenteritis are considered the main causes for febrile illness. The wide reliance on rapid diagnostic tests to diagnose febrile patients not only risks to over- or under-diagnose certain diseases but also leaves the possibility of highly infectious diseases in febrile patients unexplored. Furthermore, the heavy reliance on antibiotics risks to cause antimicrobial resistance. High mortality rates in febrile patients, especially children, should be of concern to public health authorities.
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Affiliation(s)
- Manuel Raab
- Division of Infectious Diseases and Tropical Medicine, University Hospital (LMU), Munich, Germany
- * E-mail:
| | - Lisa M. Pfadenhauer
- Institute of Medical Informatics, Biometry and Epidemiology, Pettenkofer School of Public Health, Ludwig Maximilian University Munich, Munich, Germany
| | - Dansira Doumbouya
- Paediatric Service, Hôpital Régional de Nzérékoré, Nzérékoré, Guinea
| | - Guenter Froeschl
- Division of Infectious Diseases and Tropical Medicine, University Hospital (LMU), Munich, Germany
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Ito S, Hirobe S, Yamashita R, Sugiyama A, Takeuchi H, Eguchi R, Yoshida J, Oyamada T, Tachibana M, Okada N. Analysis of immune response induction mechanisms implicating the dose-sparing effect of transcutaneous immunization using a self-dissolving microneedle patch. Vaccine 2022; 40:862-872. [PMID: 34998604 DOI: 10.1016/j.vaccine.2021.12.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/19/2021] [Accepted: 12/25/2021] [Indexed: 11/28/2022]
Abstract
Transcutaneous immunization (TCI) is an effective vaccination method that is easier and less painful than the conventional injectable vaccination method. We previously developed self-dissolving microneedle patches (sdMN) and demonstrated that this TCI method has a high vaccination efficacy in mice and humans. To elucidate the mechanism of immune response induction, which is the basis for the efficacy and safety of TCI with sdMN, we examined the local reaction of the skin where sdMN was applied and the kinetics and differentiation status of immune cells in the draining lymph nodes (DLNs). We found that gene expression of the proinflammatory cytokine Il1b and the downstream transcription factor Irf7 was markedly upregulated in skin tissues after sdMN application. Moreover, activation of Langerhans cells and CD207- dermal dendritic cells, which are subsets of antigen-presenting cells (APCs) in the skin, and their migration to the DLNs were promoted. Furthermore, the activated APC subsets promoted CD4+ T cell and B cell differentiation and the formation of germinal centers, which are the sites of high-affinity antibody production. These phenomena associated with sdMN application may contribute to the efficient production of antigen-specific antibodies after TCI using sdMN. These findings provide essential information regarding immune response induction mechanisms for the development and improvement of TCI preparations.
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Affiliation(s)
- Sayami Ito
- Project for Vaccine and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sachiko Hirobe
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory of Clinical Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Molecular Pharmaceutical Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Pharmacy, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryo Yamashita
- Project for Vaccine and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Arisa Sugiyama
- Project for Vaccine and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Honoka Takeuchi
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryosuke Eguchi
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junya Yoshida
- FUJIFILM Advanced Research Laboratories, Fujifilm Holdings Corporation, 577-1 Ushijima, Kaisei Town, Ashigarakami-gun, Kanagawa Prefecture 258-8577, Japan
| | - Takayoshi Oyamada
- FUJIFILM Advanced Research Laboratories, Fujifilm Holdings Corporation, 577-1 Ushijima, Kaisei Town, Ashigarakami-gun, Kanagawa Prefecture 258-8577, Japan
| | - Masashi Tachibana
- Project for Vaccine and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory of Vaccine and Immune Regulation (BIKEN), Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naoki Okada
- Project for Vaccine and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory of Vaccine and Immune Regulation (BIKEN), Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Melnik LI, Guha S, Ghimire J, Smither AR, Beddingfield BJ, Hoffmann AR, Sun L, Ungerleider NA, Baddoo MC, Flemington EK, Gallaher WR, Wimley WC, Garry RF. Ebola virus delta peptide is an enterotoxin. Cell Rep 2022; 38:110172. [PMID: 34986351 DOI: 10.1016/j.celrep.2021.110172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/27/2021] [Accepted: 12/03/2021] [Indexed: 12/21/2022] Open
Abstract
During the 2013-2016 West African (WA) Ebola virus (EBOV) outbreak, severe gastrointestinal symptoms were common in patients and associated with poor outcome. Delta peptide is a conserved product of post-translational processing of the abundant EBOV soluble glycoprotein (sGP). The murine ligated ileal loop model was used to demonstrate that delta peptide is a potent enterotoxin. Dramatic intestinal fluid accumulation follows injection of biologically relevant amounts of delta peptide into ileal loops, along with gross alteration of villous architecture and loss of goblet cells. Transcriptomic analyses show that delta peptide triggers damage response and cell survival pathways and downregulates expression of transporters and exchangers. Induction of diarrhea by delta peptide occurs via cellular damage and regulation of genes that encode proteins involved in fluid secretion. While distinct differences exist between the ileal loop murine model and EBOV infection in humans, these results suggest that delta peptide may contribute to EBOV-induced gastrointestinal pathology.
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Affiliation(s)
- Lilia I Melnik
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Shantanu Guha
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jenisha Ghimire
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Allison R Smither
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Brandon J Beddingfield
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Andrew R Hoffmann
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Leisheng Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Melody C Baddoo
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | | | - William R Gallaher
- Department of Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, LA 70112, USA; Mockingbird Nature Research Group, Pearl River, LA 70452, USA
| | - William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Zalgen Labs, Germantown, MD 20876, USA.
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Ghosh P, Khandekar P. Infectious human diseases: Regions, habitats, threats, and mitigation strategies: The actors—Part I. MGM JOURNAL OF MEDICAL SCIENCES 2022. [DOI: 10.4103/mgmj.mgmj_176_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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48
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Furuyama W, Nanbo A. [Introduction of high containment laboratories in abroad]. Uirusu 2022; 72:139-148. [PMID: 38220158 DOI: 10.2222/jsv.72.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Recently, outbreaks of highly pathogenic viruses, such as those of Ebola and Lassa viruses, have become a global public health issue. Such viruses must be handled in biosafety level 4 (BSL-4) laboratories. Currently, 62 BSL-4 laboratories are in operation, under construction, or planned in 24 counties. In this review, I provide an overview of the current status and characteristics of BSL-4 facilities in abroad and introduce my research on the wild-type Ebola virus at the BSL-4 facility in the USA.
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Affiliation(s)
- Wakako Furuyama
- Department of Virus Infection Dynamics, National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University
| | - Asuka Nanbo
- Department of Virus Infection Dynamics, National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University
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Hussain M, Collier P, Moudgil R. Cardiovascular Complications in Major 21st Century Viral Epidemics and Pandemics: an Insight into COVID-19. Curr Cardiol Rev 2021; 17:e051121192897. [PMID: 33874873 PMCID: PMC8950501 DOI: 10.2174/1573403x17666210419113037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/23/2021] [Accepted: 02/24/2021] [Indexed: 12/30/2022] Open
Abstract
There have many major history-defining epidemics and pandemics in the 21st century. It is well known that acute infections can cause cardiovascular (CV) complications, especially in those with underlying cardiac disease. The variation in rates and types of CVD complications in major 21st century epidemics and pandemics varies greatly. The coronavirus disease 2019 (COVID-19) pandemic has caused the turmoil of the century and has COVID-19 has resulted in substantial human and economic loss. The novelty of COVID-19 and emerging CV effects is a new entity. In this review, we discuss the major epidemics and pandemics of the 21st century and associated CVD complications.
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Affiliation(s)
- Muzna Hussain
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA,Address correspondence to this author at the Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA; Tel: (216) 445-6546, Fax: (216) 445- 6159; E-mail:
| | - Patrick Collier
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rohit Moudgil
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
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Cheng A, Chen T, Jiang G, Han X. Can Major Public Health Emergencies Affect Changes in International Oil Prices? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:12955. [PMID: 34948563 PMCID: PMC8701035 DOI: 10.3390/ijerph182412955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Abstract
In order to deepen the understanding of the impact of major public health emergencies on the oil market and to enhance the risk response capability, this study analyzed the logical relationship between major public health emergencies and international oil price changes, identified the change points, and calculated the probability of abrupt changes to international oil prices. Based on monthly data during six major public health emergencies from 2009 to 2020, this study built a product partition model. The results show that only the influenza A (H1N1) and COVID-19 pandemics were significant reasons for abrupt changes in international oil prices. Furthermore, the wild poliovirus epidemic, the Ebola epidemic, the Zika epidemic, and the Ebola epidemic in the Democratic Republic of the Congo had limited effects. Overall, the outbreak of a Public Health Emergency of International Concern (PHEIC) in major global economies has a more pronounced impact on international oil prices.
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Affiliation(s)
- An Cheng
- Wu Jinglian School of Economics, Changzhou University, Changzhou 213159, China; (A.C.); (G.J.)
- Jiangsu Energy Strategy Research Base, Changzhou University, Changzhou 213159, China
| | - Tonghui Chen
- Institute of Agricultural Economics and Development, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Guogang Jiang
- Wu Jinglian School of Economics, Changzhou University, Changzhou 213159, China; (A.C.); (G.J.)
- Jiangsu Energy Strategy Research Base, Changzhou University, Changzhou 213159, China
| | - Xinru Han
- Institute of Agricultural Economics and Development, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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