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Grassly NC, Shaw AG, Owusu M. Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges. THE LANCET. MICROBE 2024:100939. [PMID: 39222653 DOI: 10.1016/j.lanmic.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 09/04/2024]
Abstract
Wastewater surveillance holds great promise as a sensitive method to detect spillover of zoonotic infections and early pandemic emergence, thereby informing risk mitigation and public health response. Known viruses with pandemic potential are shed in human stool or urine, or both, and the experiences with SARS-CoV-2, monkeypox virus, and Zika virus highlight the feasibility of community-based wastewater surveillance for pandemic viruses that have different transmission routes. We reviewed human shedding and wastewater surveillance data for prototype viruses representing viral families of concern to estimate the likely sensitivity of wastewater surveillance compared with that of clinical surveillance. We examined how data on wastewater surveillance detection, together with viral genetic sequences and animal faecal biomarkers, could be used to identify spillover infections or early human transmission and adaptation. The opportunities and challenges associated with global wastewater surveillance for the prevention of pandemics are described in this Personal View, focusing on low-income and middle-income countries, where the risk of pandemic emergence is the highest. We propose a research and public health agenda to ensure an equitable and sustainable solution to these challenges.
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Affiliation(s)
- Nicholas C Grassly
- Department of Infectious Disease Epidemiology & MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - Alexander G Shaw
- Department of Infectious Disease Epidemiology & MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Michael Owusu
- Department of Medical Diagnostics, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Adlhoch C, Alm E, Enkirch T, Lamb F, Melidou A, Willgert K, Marangon S, Monne I, Stegeman JA, Delacourt R, Baldinelli F, Broglia A. Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. EFSA J 2024; 22:e8735. [PMID: 38576537 PMCID: PMC10988447 DOI: 10.2903/j.efsa.2024.8735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Avian influenza viruses (AIV) remain prevalent among wild bird populations in the European Union and European Economic Area (EU/EEA), leading to significant illness in and death of birds. Transmission between bird and mammal species has been observed, particularly in fur animal farms, where outbreaks have been reported. While transmission from infected birds to humans is rare, there have been instances of exposure to these viruses since 2020 without any symptomatic infections reported in the EU/EEA. However, these viruses continue to evolve globally, and with the migration of wild birds, new strains carrying potential mutations for mammalian adaptation could be selected. If avian A(H5N1) influenza viruses acquire the ability to spread efficiently among humans, large-scale transmission could occur due to the lack of immune defences against H5 viruses in humans. The emergence of AIV capable of infecting mammals, including humans, can be facilitated by various drivers. Some intrinsic drivers are related to virus characteristics or host susceptibility. Other drivers are extrinsic and may increase exposure of mammals and humans to AIV thereby stimulating mutation and adaptation to mammals. Extrinsic drivers include the ecology of host species, such as including wildlife, human activities like farming practices and the use of natural resources, climatic and environmental factors. One Health measures to mitigate the risk of AIV adapting to mammals and humans focus on limiting exposure and preventing spread. Key options for actions include enhancing surveillance targeting humans and animals, ensuring access to rapid diagnostics, promoting collaboration between animal and human sectors, and implementing preventive measures such as vaccination. Effective communication to different involved target audiences should be emphasised, as well as strengthening veterinary infrastructure, enforcing biosecurity measures at farms, and reducing wildlife contact with domestic animals. Careful planning of poultry and fur animal farming, especially in areas with high waterfowl density, is highlighted for effective risk reduction.
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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [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: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Lehmann T, Kouam C, Woo J, Diallo M, Wilkerson R, Linton YM. The African mosquito-borne diseasosome: geographical patterns, range expansion and future disease emergence. Proc Biol Sci 2023; 290:20231581. [PMID: 38018102 PMCID: PMC10685135 DOI: 10.1098/rspb.2023.1581] [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: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Mosquito-borne diseases (MBDs) threaten public health and food security globally. We provide the first biogeographic description of the African mosquito fauna (677 species) and the 151 mosquito-borne pathogens (MBPs) they transmit. While mosquito species richness agrees with expectations based on Africa's land surface, African arboviruses and mammalian plasmodia are more speciose than expected. Species assemblages of mosquitoes and MBPs similarly separate sub-Saharan Africa from North Africa, and those in West and Central Africa from eastern and southern Africa. Similarities between mosquitoes and MBPs in diversity and range size suggest that mosquitoes are key in delimiting the range of MBPs. With approximately 25% endemicity, approximately 50% occupying one to three countries and less than 5% occupying greater than 25 countries, the ranges of mosquitoes and MBPs are surprisingly small, suggesting that most MBPs are transmitted by a single mosquito species. Exceptionally widespread mosquito species feed on people and livestock, and most are high-altitude-windborne migrants. Likewise, widespread MBPs are transmitted among people or livestock by widespread mosquitoes, suggesting that adapting to people or livestock and to widespread mosquito species promote range expansion in MBPs. Range size may predict range expansion and emergence risk. We highlight key knowledge gaps that impede prediction and mitigation of future emergence of local and global MBDs.
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Affiliation(s)
- Tovi Lehmann
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Cedric Kouam
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Joshua Woo
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Mawlouth Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Richard Wilkerson
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History, Washington, DC, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History, Washington, DC, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
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Ojeda-Porras AC, Roy V, Bourzikat O, Favetta P, Agrofoglio LA. Cobalt-assisted route to rare carbocyclic C-ribonucleosides. RSC Adv 2023; 13:30777-30786. [PMID: 37869399 PMCID: PMC10587889 DOI: 10.1039/d3ra04937j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023] Open
Abstract
(Re)emerging RNA viruses have been major threats to public health in the past years, and from the few drugs available, nucleoside analogues are still at the cornerstone of the antiviral therapy. Among them, the synthesis of carbocyclic C-nucleosides is suffering from long syntheses and poor yields. Herein we report a concise stereoselective synthesis of rare carbocyclic C-nucleosides (11a-l) bearing non-canonical nucleobases through a cobalt-assisted-route as key step starting from the optically pure (-)-cyclopentenone 1. This approach paves the route for novel carbocyclic C-nucleoside discovery.
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Affiliation(s)
- A C Ojeda-Porras
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - V Roy
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - O Bourzikat
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - P Favetta
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - L A Agrofoglio
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
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Williams SMT, Ansumana R, Johnny J, Bakarr IA, Osborne A. Knowledge, Attitudes and Practices Assessment on Bat-Borne Zoonotic Diseases Among the People of Moyamba District, Sierra Leone. Risk Manag Healthc Policy 2023; 16:1331-1342. [PMID: 37489233 PMCID: PMC10363381 DOI: 10.2147/rmhp.s413802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Background Bats are considered wildlife species of public health concern, as they are known to host various pathogenic agents, and their interactions with humans are potential routes of pathogen spillover. A high level of knowledge on Bat-borne Zoonotic Diseases (BZD), their causative agents, signs, symptoms, mode and pattern of transmission, health attitudes, and practices towards the disorders are vital parameters in handling them. This study aimed to look into BZD knowledge, public attitudes, and behaviour. Methods We surveyed the 14 chiefdoms of Moyamba district. A total of 421 participants were randomly sampled using closed-ended questionnaire. Simple linear regression analysis was used to determine the effects of gender, age, education, and livelihood opportunities on BZD knowledge (at 95% confidence interval and alpha value = 0.05). The findings were analysed and correlated with a scientific and public health perspective to assess the breadth of knowledge and awareness of BZD among the people of Moyamba district. Results The findings from the study show a low level of knowledge on BZD among the people of the Moyamba district, with only 119 (28.3%) individuals that had some knowledge about BZD. Of those that knew about BZD, 94 (79.0%) had very little knowledge, 24 (20.2%) had a fair amount, and 1 (0.8%) had a great deal of knowledge about BZD. The primary mode of knowledge dissemination was through social media platforms. Conclusion The level of knowledge about BZD is also very low. As a result of these findings, policymakers, health professionals, and environmental educators will be compelled to develop strategies to reduce the risk of BZD transmission in Sierra Leone's population.
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Affiliation(s)
- Samuel Maxwell Tom Williams
- Department of Biological Sciences, School of Environmental Sciences, Njala University, Freetown, Sierra Leone
| | - Rashid Ansumana
- Department of Public Health, School of Community Health Sciences, Njala University, Freetown, Sierra Leone
| | - Jonathan Johnny
- Department of Wildlife Management and Conservation, School of Natural Resources Management, Njala University, Freetown, Sierra Leone
| | - Ibrahim A Bakarr
- Department of Wildlife Management and Conservation, School of Natural Resources Management, Njala University, Freetown, Sierra Leone
| | - Augustus Osborne
- Department of Biological Sciences, School of Environmental Sciences, Njala University, Freetown, Sierra Leone
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Jensen GS, Yu L, Iloba I, Cruickshank D, Matos JR, Newman RA. Differential Activities of the Botanical Extract PBI-05204 and Oleandrin on Innate Immune Functions under Viral Challenge Versus Inflammatory Culture Conditions. Molecules 2023; 28:4799. [PMID: 37375354 DOI: 10.3390/molecules28124799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The Nerium oleander extract PBI 05204 (PBI) and its cardiac glycoside constituent oleandrin have direct anti-viral properties. Their effect on the immune system, however, is largely unknown. We used an in vitro model of human peripheral blood mononuclear cells to document effects under three different culture conditions: normal, challenged with the viral mimetic polyinosinic:polycytidylic acid Poly I:C, and inflamed by lipopolysaccharide (LPS). Cells were evaluated for immune activation marks CD69, CD25, and CD107a, and culture supernatants were tested for cytokines. Both PBI and oleandrin directly activated Natural Killer (NK) cells and monocytes and triggered increased production of cytokines. Under viral mimetic challenge, PBI and oleandrin enhanced the Poly I:C-mediated immune activation of monocytes and NK cells and enhanced production of IFN-γ. Under inflammatory conditions, many cytokines were controlled at similar levels as in cultures treated with PBI and oleandrin without inflammation. PBI triggered higher levels of some cytokines than oleandrin. Both products increased T cell cytotoxic attack on malignant target cells, strongest by PBI. The results show that PBI and oleandrin directly activate innate immune cells, enhance anti-viral immune responses through NK cell activation and IFN-γ levels, and modulate immune responses under inflamed conditions. The potential clinical impact of these activities is discussed.
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Affiliation(s)
| | - Liu Yu
- NIS Labs, 807 St. George St., Port Dover, ON N0A 1N0, Canada
| | - Ifeanyi Iloba
- NIS Labs, 1437 Esplanade, Klamath Falls, OR 97601, USA
| | | | - Jose R Matos
- Phoenix Biotechnology, 8626 Tesoro Drive, Suite 801, San Antonio, TX 78217, USA
| | - Robert A Newman
- Phoenix Biotechnology, 8626 Tesoro Drive, Suite 801, San Antonio, TX 78217, USA
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da Paz TYB, Hernández LHA, Silva SPD, Silva FSD, Barros BCVD, Casseb LMN, Guimarães RJDPSE, Vasconcelos PFDC, Cruz ACR. Novel Rodent Arterivirus Detected in the Brazilian Amazon. Viruses 2023; 15:v15051150. [PMID: 37243236 DOI: 10.3390/v15051150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
As part of a continuous effort to investigate the viral communities associated with wild mammals at the human-animal interface in an Amazonian metropolitan region, this study describes the detection of a novel rodent-borne arterivirus. A sample containing pooled organs of Oecomys paricola was submitted to RNA sequencing, and four sequences taxonomically assigned as related to the Arteriviridae family were recovered, corresponding to an almost complete genome of nearly 13 kb summed. In the phylogenetic analysis with the standard domains used for taxa demarcation in the family, the tentatively named Oecomys arterivirus 1 (OAV-1) was placed within the clade of rodent- and porcine-associated viruses, corresponding to the Variarterivirinae subfamily. The divergence analysis, based on the same amino acid alignment, corroborated the hypothesis that the virus may represent a new genus within the subfamily. These findings contribute to the expansion of the current knowledge about the diversity, host and geographical range of the viral family. Arterivirids are non-human pathogens and are usually species-specific, but the susceptibility of cell lines derived from different organisms should be conducted to confirm these statements for this proposed new genus in an initial attempt to assess its spillover potential.
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Affiliation(s)
- Thito Y Bezerra da Paz
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Leonardo H Almeida Hernández
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Fábio Silva da Silva
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Bruno C Veloso de Barros
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Livia M Neves Casseb
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Ricardo J de Paula Souza E Guimarães
- Geoprocessing Laboratory, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Pedro F da Costa Vasconcelos
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Ana C Ribeiro Cruz
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
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Paul A, Chakraborty N, Sarkar A, Acharya K, Ranjan A, Chauhan A, Srivastava S, Singh AK, Rai AK, Mubeen I, Prasad R. Ethnopharmacological Potential of Phytochemicals and Phytogenic Products against Human RNA Viral Diseases as Preventive Therapeutics. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1977602. [PMID: 36860811 PMCID: PMC9970710 DOI: 10.1155/2023/1977602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 02/22/2023]
Abstract
RNA viruses have been the most destructive due to their transmissibility and lack of control measures. Developments of vaccines for RNA viruses are very tough or almost impossible as viruses are highly mutable. For the last few decades, most of the epidemic and pandemic viral diseases have wreaked huge devastation with innumerable fatalities. To combat this threat to mankind, plant-derived novel antiviral products may contribute as reliable alternatives. They are assumed to be nontoxic, less hazardous, and safe compounds that have been in uses in the beginning of human civilization. In this growing COVID-19 pandemic, the present review amalgamates and depicts the role of various plant products in curing viral diseases in humans.
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Affiliation(s)
- Anamika Paul
- Department of Botany, Scottish Church College, Kolkata 700006, India
| | | | - Anik Sarkar
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Krishnendu Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, 344090 Rostov-on-Don, Russia
| | - Abhishek Chauhan
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, U.P., India
| | - Shilpi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Akhilesh Kumar Singh
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401 Bihar, India
| | - Ashutosh Kumar Rai
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Iqra Mubeen
- State Key Laboratory of Rice Biology, and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, 845401 Bihar, India
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Dixit H, Kulharia M, Verma SK. Metalloproteome of human-infective RNA viruses: a study towards understanding the role of metal ions in virology. Pathog Dis 2023; 81:ftad020. [PMID: 37653445 DOI: 10.1093/femspd/ftad020] [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: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Metalloproteins and metal-based inhibitors have been shown to effectively combat infectious diseases, particularly those caused by RNA viruses. In this study, a diverse set of bioinformatics methods was employed to identify metal-binding proteins of human RNA viruses. Seventy-three viral proteins with a high probability of being metal-binding proteins were identified. These proteins included 40 zinc-, 47 magnesium- and 14 manganese-binding proteins belonging to 29 viral species and eight significant viral families, including Coronaviridae, Flaviviridae and Retroviridae. Further functional characterization has revealed that these proteins play a critical role in several viral processes, including viral replication, fusion and host viral entry. They fall under the essential categories of viral proteins, including polymerase and protease enzymes. Magnesium ion is abundantly predicted to interact with these viral enzymes, followed by zinc. In addition, this study also examined the evolutionary aspects of predicted viral metalloproteins, offering essential insights into the metal utilization patterns among different viral species. The analysis indicates that the metal utilization patterns are conserved within the functional classes of the proteins. In conclusion, the findings of this study provide significant knowledge on viral metalloproteins that can serve as a valuable foundation for future research in this area.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi 110007, Delhi, India
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Walser M, Mayor J, Rothenberger S. Designed Ankyrin Repeat Proteins: A New Class of Viral Entry Inhibitors. Viruses 2022; 14:2242. [PMID: 36298797 PMCID: PMC9611651 DOI: 10.3390/v14102242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 08/08/2023] Open
Abstract
Designed ankyrin repeat proteins (DARPins) are engineered proteins comprising consensus designed ankyrin repeats as scaffold. Tightly packed repeats form a continuous hydrophobic core and a large groove-like solvent-accessible surface that creates a binding surface. DARPin domains recognizing a target of interest with high specificity and affinity can be generated using a synthetic combinatorial library and in vitro selection methods. They can be linked together in a single molecule to build multispecific and multifunctional proteins without affecting expression or function. The modular architecture of DARPins offers unprecedented possibilities of design and opens avenues for innovative antiviral strategies.
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Affiliation(s)
- Marcel Walser
- Molecular Partners AG, Wagistrasse 14, 8952 Zurich-Schlieren, Switzerland
| | - Jennifer Mayor
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
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12
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UBR5 Acts as an Antiviral Host Factor against MERS-CoV via Promoting Ubiquitination and Degradation of ORF4b. J Virol 2022; 96:e0074122. [PMID: 35980206 PMCID: PMC9472757 DOI: 10.1128/jvi.00741-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within the past 2 decades, three highly pathogenic human coronaviruses have emerged, namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The health threats and economic burden posed by these tremendously severe coronaviruses have paved the way for research on their etiology, pathogenesis, and treatment. Compared to SARS-CoV and SARS-CoV-2, MERS-CoV genome encoded fewer accessory proteins, among which the ORF4b protein had anti-immunity ability in both the cytoplasm and nucleus. Our work for the first time revealed that ORF4b protein was unstable in the host cells and could be degraded by the ubiquitin proteasome system. After extensive screenings, it was found that UBR5 (ubiquitin protein ligase E3 component N-recognin 5), a member of the HECT E3 ubiquitin ligases, specifically regulated the ubiquitination and degradation of ORF4b. Similar to ORF4b, UBR5 can also translocate into the nucleus through its nuclear localization signal, enabling it to regulate ORF4b stability in both the cytoplasm and nucleus. Through further experiments, lysine 36 was identified as the ubiquitination site on the ORF4b protein, and this residue was highly conserved in various MERS-CoV strains isolated from different regions. When UBR5 was knocked down, the ability of ORF4b to suppress innate immunity was enhanced and MERS-CoV replication was stronger. As an anti-MERS-CoV host protein, UBR5 targets and degrades ORF4b protein through the ubiquitin proteasome system, thereby attenuating the anti-immunity ability of ORF4b and ultimately inhibiting MERS-CoV immune escape, which is a novel antagonistic mechanism of the host against MERS-CoV infection. IMPORTANCE ORF4b was an accessory protein unique to MERS-CoV and was not present in SARS-CoV and SARS-CoV-2 which can also cause severe respiratory disease. Moreover, ORF4b inhibited the production of antiviral cytokines in both the cytoplasm and the nucleus, which was likely to be associated with the high lethality of MERS-CoV. However, whether the host proteins regulate the function of ORF4b is unknown. Our study first determined that UBR5, a host E3 ligase, was a potential host anti-MERS-CoV protein that could reduce the protein level of ORF4b and diminish its anti-immunity ability by inducing ubiquitination and degradation. Based on the discovery of ORF4b-UBR5, a critical molecular target, further increasing the degradation of ORF4b caused by UBR5 could provide a new strategy for the clinical development of drugs for MERS-CoV.
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Sepúlveda CS, García CC, Damonte EB. Inhibitors of Nucleotide Biosynthesis as Candidates for a Wide Spectrum of Antiviral Chemotherapy. Microorganisms 2022; 10:1631. [PMID: 36014049 PMCID: PMC9413629 DOI: 10.3390/microorganisms10081631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Emerging and re-emerging viruses have been a challenge in public health in recent decades. Host-targeted antivirals (HTA) directed at cellular molecules or pathways involved in virus multiplication represent an interesting strategy to combat viruses presently lacking effective chemotherapy. HTA could provide a wide range of agents with inhibitory activity against current and future viruses that share similar host requirements and reduce the possible selection of antiviral-resistant variants. Nucleotide metabolism is one of the more exploited host metabolic pathways as a potential antiviral target for several human viruses. This review focuses on the antiviral properties of the inhibitors of pyrimidine and purine nucleotide biosynthesis, with an emphasis on the rate-limiting enzymes dihydroorotate dehydrogenase (DHODH) and inosine monophosphate dehydrogenase (IMPDH) for which there are old and new drugs active against a broad spectrum of pathogenic viruses.
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Affiliation(s)
- Claudia Soledad Sepúlveda
- Laboratory of Virology, Biochemistry Department, School of Sciences, University of Buenos Aires (UBA), Ciudad Universitaria, Buenos Aires 1428, Argentina
- Institute of Biochemistry of the School of Sciences (IQUIBICEN), CONICET-UBA, Ciudad Universitaria, Buenos Aires 1428, Argentina
| | - Cybele Carina García
- Laboratory of Virology, Biochemistry Department, School of Sciences, University of Buenos Aires (UBA), Ciudad Universitaria, Buenos Aires 1428, Argentina
- Institute of Biochemistry of the School of Sciences (IQUIBICEN), CONICET-UBA, Ciudad Universitaria, Buenos Aires 1428, Argentina
| | - Elsa Beatriz Damonte
- Laboratory of Virology, Biochemistry Department, School of Sciences, University of Buenos Aires (UBA), Ciudad Universitaria, Buenos Aires 1428, Argentina
- Institute of Biochemistry of the School of Sciences (IQUIBICEN), CONICET-UBA, Ciudad Universitaria, Buenos Aires 1428, Argentina
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14
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Roy V, Agrofoglio LA. Nucleosides and emerging viruses: A new story. Drug Discov Today 2022; 27:1945-1953. [PMID: 35189369 PMCID: PMC8856764 DOI: 10.1016/j.drudis.2022.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/13/2022] [Accepted: 02/16/2022] [Indexed: 12/24/2022]
Abstract
With several US Food and Drug Administration (FDA)-approved drugs and high barriers to resistance, nucleoside and nucleotide analogs remain the cornerstone of antiviral therapies for not only herpesviruses, but also HIV and hepatitis viruses (B and C); however, with the exception of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which vaccines have been developed at unprecedented speed, there are no vaccines or small antivirals yet available for (re)emerging viruses, which are primarily RNA viruses. Thus, herein, we present an overview of ribonucleoside analogs recently developed and acting as inhibitors of the viral RNA-dependent RNA polymerase (RdRp). They are new lead structures that will be exploited for the discovery of new antiviral nucleosides.
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Affiliation(s)
- Vincent Roy
- ICOA, University of Orléans, CNRS UMR 7311, Rue de Chartres, 45067 Orléans, France
| | - Luigi A Agrofoglio
- ICOA, University of Orléans, CNRS UMR 7311, Rue de Chartres, 45067 Orléans, France.
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15
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Chakrabartty I, Khan M, Mahanta S, Chopra H, Dhawan M, Choudhary OP, Bibi S, Mohanta YK, Emran TB. Comparative overview of emerging RNA viruses: Epidemiology, pathogenesis, diagnosis and current treatment. Ann Med Surg (Lond) 2022; 79:103985. [PMID: 35721786 PMCID: PMC9188442 DOI: 10.1016/j.amsu.2022.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
From many decades, emerging infections have threatened humanity. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. The SARS, Ebola, MERS epidemics and the most recent emergence of COVID-19 pandemic have threatened populations across borders. Since a highly pathogenic CoV has been evolved into the human population in the twenty-first century known as SARS, scientific advancements and innovative methods to tackle these viruses have increased in order to improve response preparedness towards the unpredictable threat posed by these rapidly emerging pathogens. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. However, in this review, we have done a systematic comparison of all three CoVs i.e., SARS, MERS and SARS-CoV-2 along with Ebola and Zika in terms of their epidemiology, virology, clinical features and current treatment strategies. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Each of these viruses has been elaborated on the basis of their epidemiology, virulence, transmission and treatment. However, special attention has been given to SARS-CoV-2 and the disease caused by it i.e., COVID-19 due to current havoc caused worldwide. At the end, insights into the current understanding of the lessons learned from previous epidemics to combat emerging CoVs have been described. The travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates associated with these highly transmissible and pathogenic viruses highlight the need for new prophylactic and therapeutic actions which include but are not limited to clinical indicators, contact tracing, and laboratory investigations as important factors that need to be taken into account in order to arrive at the final conclusion. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Globally, numerous studies and researchers have recently started fighting this virus.
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Affiliation(s)
- Ishani Chakrabartty
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre Guwahati, 781008, Assam, India
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.,Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, India
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Yugal Kishore Mohanta
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
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16
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [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: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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17
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Simple and Economical Extraction of Viral RNA and Storage at Ambient Temperature. Microbiol Spectr 2022; 10:e0085922. [PMID: 35647876 PMCID: PMC9241768 DOI: 10.1128/spectrum.00859-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA extraction is essential for the molecular detection of common viral pathogens. However, available extraction methods and the need for ultra-cold storage limit molecular testing in resource-constrained settings. Herein, we describe the development of an economical RNAExtraction and Storage (RNAES) protocol that eliminates requirements for instrumentation, expensive materials, and preserved cold chain. Through an iterative process, we optimized viral lysis and RNA binding to and elution from glass fiber membranes included in simple RNAES packets. Efficient viral lysis was achieved with a nontoxic buffer containing sucrose, KCl, proteinase K, and carrier RNA. Viral RNA binding to glass fiber membranes was concentration dependent across seven orders of magnitude (4.0–10.0 log10 copies/μL) and significantly increased with an acidic arginine binding buffer. For the clinical evaluation, 36 dengue virus (DENV)-positive serum samples were extracted in duplicate with the optimized RNAES protocol and once in an EMAG instrument (bioMérieux). DENV RNA was successfully extracted from 71/72 replicates (98.6%) in the RNAES protocol, and real-time RT-PCR cycle threshold (CT) values correlated between extraction methods. DENV RNA, extracted from clinical samples, was stable when stored on dried RNAES membranes at ambient temperature for up to 35 days, with median eluate RNA concentration decreasing by 0.18 and 0.29 log10 copies/μL between day 0 and days 7 and 35, respectively. At a cost of $0.08/sample, RNAES packets address key limitations to available protocols and may increase capacity for molecular detection of RNA viruses. IMPORTANCE RNA extraction methods and ultra-cold storage requirements limit molecular testing for common viruses. We developed a simple, flexible, and economical method that simultaneously addresses these limitations. At $0.08/sample, the new RNAExtraction and Storage (RNAES) protocol successfully extracted viral RNA from acute-phase sera and provided stable, ambient-temperature RNA storage for 35 days. Using this approach, we expect to improve RNA virus detection and outbreak response in resource-constrained settings.
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18
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Islam E. Development of epitope-based chimeric protein as a vaccine against Lujo virus by utilizing immunoinformatic tools. Future Virol 2022. [DOI: 10.2217/fvl-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Lujo is a modern zoonotic virus that is potentially fatal and spreads by bodily fluids. In this research, immunoinformatic tools are used to build a vaccine. Methodology: The epitopes of cytotoxic T-lymphocytes, helper T-lymphocytes and linear B-lymphocytes were predicted from the most antigenic protein. The designed vaccine's physiochemical properties and 3D structure have been forecasted. Low free energy and strong binding affinity estimated in molecular docking against toll-like receptor 4 (TLR4) and dynamic simulation. Furthermore, in silico cloning in the Escherichia coli K12 host system was performed for high level of expression. Conclusion: Finally, immune simulation was used to determine immune responses to the vaccine that was formulated confirming the developed vaccine as a good candidate against Lujo virus.
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Affiliation(s)
- Enayetul Islam
- Department of Genetic Engineering & Biotechnology, University of Chittagong, Chittagong, Bangladesh
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19
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Shaik FB, Swarnalatha K, Mohan M, Thomas A, Chikati R, Sandeep G, Maddu N. Novel antiviral effects of chloroquine, hydroxychloroquine, and green tea catechins against SARS CoV-2 main protease (Mpro) and 3C-like protease for COVID-19 treatment. CLINICAL NUTRITION OPEN SCIENCE 2022; 42:62-72. [PMID: 35106518 PMCID: PMC8795779 DOI: 10.1016/j.nutos.2021.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Coronaviruses are globally emerging viruses that threaten our health care systems and have become a popular pandemic around the world. This causes a sudden rise in positive coronavirus cases and related deaths to occur worldwide, representing a significant health hazard to humans and the economy. METHODS We examined predominantly catechins of green tea include epigallocatechin-3-gallate (EGCG), epicatechin-3-gallate (ECG), and drugs of chloroquine (CQ), and hydroxychloroquine (HCQ) appearing to reveal anti-viral activities. Data were collected from PubMed, Google Scholar, and Science Direct databases. To investigate the role of antiviral effects (CQ and HCQ), green tea catechins, beneficial use of convalescent plasma; covaxin in COVID-19 patients faced a dangerous healthiness issue. Computational docking analysis has been used for this purpose. RESULTS The lead compounds are EGCG and ECG act as potential inhibitors bind to the active site region of the HKU4-CoV 3CL protease and M-Pro protease enzymes of coronavirus. Conclusions: SARS-COV-2 is a pathogen of substantial vigour concern and the review unveils the role of catechins associated with many viral diseases. We suggested that the function of green tea catechins, novel drugs of CQ, and HCQ exhibit antiviral activities against positive-sense single-stranded RNA viruses (CoVs).
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Affiliation(s)
- Fareeda Begum Shaik
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, 515003, A.P. India
| | - K. Swarnalatha
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, 515003, A.P. India
| | | | - Anu Thomas
- Department of Nursing, Banaswadi College of Nursing, Bangalore, Karnataka, India
| | - Rajasekhar Chikati
- Department of Biochemistry, Yogivemana University, Kadapa, 516005, A.P. India
| | - G. Sandeep
- Division of Molecular Biology, Department of Zoology, Sri Venkateswara University, Tirupati, 517502, A.P, India
| | - Narendra Maddu
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, 515003, A.P. India,Corresponding author. Department of Biochemistry, Sri Krishnadevaraya University, Ananthapuramu, 515003, Andhra Pradesh, India. Tel.: +91 9441983797
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20
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Pérez‐Umphrey AA, Jonsson CB, Bonisoli‐Alquati A, Snider AM, Stouffer PC, Taylor SS. Sex and habitat drive hantavirus prevalence in marsh rice rat populations impacted by the Deepwater Horizon oil spill. Ecosphere 2022. [DOI: 10.1002/ecs2.3929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Anna A. Pérez‐Umphrey
- School of Renewable Natural Resources Louisiana State University and AgCenter Baton Rouge Louisiana USA
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry College of Medicine, University of Tennessee Health Science Center, University of Tennessee Memphis Tennessee USA
| | - Andrea Bonisoli‐Alquati
- School of Renewable Natural Resources Louisiana State University and AgCenter Baton Rouge Louisiana USA
- Department of Biological Sciences California State Polytechnic University, Pomona Pomona California USA
| | - Allison M. Snider
- School of Renewable Natural Resources Louisiana State University and AgCenter Baton Rouge Louisiana USA
| | - Philip C. Stouffer
- School of Renewable Natural Resources Louisiana State University and AgCenter Baton Rouge Louisiana USA
| | - Sabrina S. Taylor
- School of Renewable Natural Resources Louisiana State University and AgCenter Baton Rouge Louisiana USA
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21
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Subudhi BB, Chattopadhyay S, Chattopadhyay S. Targeting host factors of virus-induced inflammation: a strategy for tackling future epidemics by RNA viruses. Future Virol 2022. [DOI: 10.2217/fvl-2021-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Bharat Bhusan Subudhi
- Drug Development & Analysis Lab, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Subhasis Chattopadhyay
- Department of Atomic Energy, School of Biological Sciences, National Institute of Science Education & Research Bhubaneswar, Homi Bhabha National Institute, Khurda, 752050, India
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22
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Public health and management. HEALTHCARE STRATEGIES AND PLANNING FOR SOCIAL INCLUSION AND DEVELOPMENT 2022. [PMCID: PMC8607884 DOI: 10.1016/b978-0-323-90446-9.00001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This chapter explains how hospital community health centers and nurseries home provide preventive curative, rehabilitation care for public health management. In this connection, it is explained how security professions, fire, ambulance providers and emergency medical services can be closely coordinated to increase the efficacy of health services. The authors want to develop awareness among doctors to mobilize other health service processions to manage the system under extreme climatic and disaster conditions to save life and social health stability. The last part of the chapter gives insight on systemic management of disease classification and under what circumstance a disease outbreak becomes epidemic and pandemic at the global level if inadequate management is taken. In this connection, the authors try to explain it with the example of the COVID-19 challenge and bring to the attention of the public to either eradicate or bring stability with the passing of time. So, it is necessary to develop a well-organized health-care system either temporarily or upgrade the existing health-care system to meet the demand in an emergency.
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23
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Nieto-Claudin A, Esperón F, Apakupakul K, Peña I, Deem SL. Health assessments uncover novel viral sequences in five species of Galapagos tortoises. Transbound Emerg Dis 2021; 69:e1079-e1089. [PMID: 34784447 DOI: 10.1111/tbed.14391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/27/2021] [Accepted: 11/07/2021] [Indexed: 01/06/2023]
Abstract
Emerging infectious diseases (EIDs) have been reported as causes of morbidity and mortality in free-living animal populations, including turtles and tortoises, and they have even resulted in species extinctions, with human activities contributing to the spread of many of these diseases. In the Galapagos, giant tortoises are endangered due to habitat change, invasive species, and other human impacts; however, the impact of EIDs on Galapagos tortoise conservation remains understudied. To fill this gap, we conducted health assessments of five tortoise species from the islands of Santa Cruz, Isabela and Española. We performed health evaluations of 454 animals and PCR testing for pathogens known to be relevant in other tortoise species. We identified two novel sequences of adenoviruses and four of herpesviruses. Based on alignments of the DNA polymerase gene and maximum likelihood phylogenetic analyses, we found both novel adenoviruses to be most closely related to red footed tortoise adenovirus 2, by nucleotide sequence and red footed tortoise adenovirus 1, based on amino acid sequence. Three of the herpesvirus sequences translated into the same deduced amino acid sequence; therefore, they may be considered the same viral species, closely related to terrapene herpesvirus 2. The fourth herpesvirus sequence was highly divergent from any sequence previously detected and is related to an eagle owl herpesvirus based on nucleotide sequence and to loggerhead oro-cutaneous herpesvirus based on amino acids. These novel viruses may be pathogenic for giant tortoises under specific conditions (e.g., stress). Continued screening is crucial to determine if these viruses play a role in tortoise fitness, morbidity and survival. This information allows us to provide recommendations to the Galapagos National Park Directorate and other institutions to improve the management of these unique species both in Galapagos and globally, and for tortoise reintroduction plans throughout the archipelago.
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Affiliation(s)
- Ainoa Nieto-Claudin
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador.,Veterinary Faculty, Complutense University of Madrid, Puerta de Hierro Av, Madrid, Spain.,Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, Missouri
| | - Fernando Esperón
- Veterinary Faculty, Complutense University of Madrid, Puerta de Hierro Av, Madrid, Spain.,INIA, CISA, Algete-El Casar Road, Valdeolmos, Spain.,Veterinary Department, School of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Kathleen Apakupakul
- Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, Missouri
| | - Irene Peña
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador
| | - Sharon L Deem
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador.,Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, Missouri
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24
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Waris A, Din M, Iqbal N, Yar L, Khalid A, Nawaz M, Baset A, Ali M. Evaluation of serum procalcitonin level as a biomarker for disease severity in COVID-19 patients. New Microbes New Infect 2021; 43:100922. [PMID: 34336223 PMCID: PMC8302477 DOI: 10.1016/j.nmni.2021.100922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) has infected millions of individuals around the globe. Forecasting the COVID-19 severity is essential, and various biomarkers could be used to evaluate it. The current study was therefore aimed to evaluate the serum pro-calcitonin (PCT) level as a biomarker for bacterial co-infection and disease severity in COVID-19 patients. A total of 430 COVID-19 positive individuals were examined, in which 332 (77.2%) were male individuals while 98 (22.8%) were female individuals. Among the examined samples, 281 were classified as moderate (PCT value 0.07 ± 0.06 ng/mL), 95 were severe (PCT value 0.5 ± 0.4 ng/mL), and 54 were classified as critical (PCT value > 1 ng/mL) individuals. The increase in the total serum level of PCT was observed with the severity of the disease (p < 0.05). The statistical analysis represented no association of PCT value with gender (p 0.9650) while revealed a significant association (p < 0.001) with the age and PCT value in COVID-19 patients. It can be concluded that the serial PCT measurement could determine the prognosis of the disease and the presence of bacterial co-infection in COVID-19 patients. Further exploration of the topic is needed to evaluate the effect of different therapies on the PCT level and to prescribe specific treatment options for coinfection.
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Affiliation(s)
- A. Waris
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - M. Din
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - N. Iqbal
- Department of Statistics, Quaid-i-Azam University, Islamabad, Pakistan
| | - L. Yar
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - A. Khalid
- Sahiwal Medical College, University of Health Sciences, Lahore, Pakistan
| | - M. Nawaz
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - A. Baset
- Department of Zoology, Bacha Khan University, Charsadda, Pakistan
| | - M. Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
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Näslund J, Ahlm C, Islam K, Evander M, Bucht G, Lwande OW. Emerging Mosquito-Borne Viruses Linked to Aedes aegypti and Aedes albopictus: Global Status and Preventive Strategies. Vector Borne Zoonotic Dis 2021; 21:731-746. [PMID: 34424778 DOI: 10.1089/vbz.2020.2762] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Emerging mosquito-borne viruses continue to cause serious health problems and economic burden among billions of people living in and near the tropical belt of the world. The highly invasive mosquito species Aedes aegypti and Aedes albopictus have successively invaded and expanded their presence as key vectors of Chikungunya virus, dengue virus, yellow fever virus, and Zika virus, and that has consecutively led to frequent outbreaks of the corresponding viral diseases. Of note, these two mosquito species have gradually adapted to the changing weather and environmental conditions leading to a shift in the epidemiology of the viral diseases, and facilitated their establishment in new ecozones inhabited by immunologically naive human populations. Many abilities of Ae. aegypti and Ae. albopictus, as vectors of significant arbovirus pathogens, may affect the infection and transmission rates after a bloodmeal, and may influence the vector competence for either virus. We highlight that many collaborating risk factors, for example, the global transportation systems may result in sporadic and more local outbreaks caused by mosquito-borne viruses related to Ae. aegypti and/or Ae. albopictus. Those local outbreaks could in synergy grow and produce larger epidemics with pandemic characters. There is an urgent need for improved surveillance of vector populations, human cases, and reliable prediction models. In summary, we recommend new and innovative strategies for the prevention of these types of infections.
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Affiliation(s)
- Jonas Näslund
- Swedish Defence Research Agency, CBRN, Defence and Security, Umeå, Sweden
| | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umea, Sweden.,Arctic Research Centre at Umeå University, Umea, Sweden
| | - Koushikul Islam
- Department of Clinical Microbiology, Umeå University, Umea, Sweden
| | - Magnus Evander
- Department of Clinical Microbiology, Umeå University, Umea, Sweden.,Arctic Research Centre at Umeå University, Umea, Sweden
| | - Göran Bucht
- Department of Clinical Microbiology, Umeå University, Umea, Sweden
| | - Olivia Wesula Lwande
- Department of Clinical Microbiology, Umeå University, Umea, Sweden.,Arctic Research Centre at Umeå University, Umea, Sweden
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Yi H, Wang J, Wang J, Lu Y, Zhang Y, Peng R, Lu J, Chen Z. The Emergence and Spread of Novel SARS-CoV-2 Variants. Front Public Health 2021; 9:696664. [PMID: 34409009 PMCID: PMC8364952 DOI: 10.3389/fpubh.2021.696664] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.
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Affiliation(s)
- Huaimin Yi
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jin Wang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiong Wang
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuying Lu
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yali Zhang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruihao Peng
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiahai Lu
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zeliang Chen
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
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27
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Vale FF, Vítor JMB, Marques AT, Azevedo-Pereira JM, Anes E, Goncalves J. Origin, phylogeny, variability and epitope conservation of SARS-CoV-2 worldwide. Virus Res 2021; 304:198526. [PMID: 34339772 PMCID: PMC8323504 DOI: 10.1016/j.virusres.2021.198526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses innumerous challenges, like understanding what triggered the emergence of this new human virus, how this RNA virus is evolving or how the variability of viral genome may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at GenBank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Additionally, we analyzed 199,984 spike glycoprotein sequences. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide variants (SNVs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNVs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. Additionally, all predicted epitopes for the structural E, M and N proteins are highly conserved. The amino acid changes present in the spike glycoprotein of variables of concern (VOCs) comprise between 3.4% and 20.7% of the predicted epitopes of this protein. These results favors the continuous efficacy of the available vaccines targeting the spike protein, and other structural proteins. Multiple epitopes vaccines should sustain vaccine efficacy since at least some of the epitopes present in variability regions of VOCs are conserved and thus recognizable by antibodies.
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Affiliation(s)
- Filipa F Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal.
| | - Jorge M B Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal; Pharmacy, Pharmacology and Health Technologies Department, Faculty of Pharmacy, Universidade de Lisboa, Lisbon 1649-003, Portugal
| | - Andreia T Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Joao Goncalves
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
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High-Throughput Fluorescent Assay for Inhibitor Screening of Proteases from RNA Viruses. Molecules 2021; 26:molecules26133792. [PMID: 34206406 PMCID: PMC8270262 DOI: 10.3390/molecules26133792] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/07/2023] Open
Abstract
Spanish flu, polio epidemics, and the ongoing COVID-19 pandemic are the most profound examples of severe widespread diseases caused by RNA viruses. The coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands affordable and reliable assays for testing antivirals. To test inhibitors of viral proteases, we have developed an inexpensive high-throughput assay based on fluorescent energy transfer (FRET). We assayed an array of inhibitors for papain-like protease from SARS-CoV-2 and validated it on protease from the tick-borne encephalitis virus to emphasize its versatility. The reaction progress is monitored as loss of FRET signal of the substrate. This robust and reproducible assay can be used for testing the inhibitors in 96- or 384-well plates.
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29
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Sethi K, Dailey GP, Zahid OK, Taylor EW, Ruzicka JA, Hall AR. Direct Detection of Conserved Viral Sequences and Other Nucleic Acid Motifs with Solid-State Nanopores. ACS NANO 2021; 15:8474-8483. [PMID: 33914524 PMCID: PMC8801185 DOI: 10.1021/acsnano.0c10887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The rapid and reliable recognition of nucleic acid sequences is essential to a broad range of fields including genotyping, gene expression analysis, and pathogen screening. For viral detection in particular, the capability is critical for optimal therapeutic response and preventing disease transmission. Here, we report an approach for detecting identifying sequence motifs within genome-scale single-strand DNA and RNA based on solid-state nanopores. By designing DNA oligonucleotide probes with complementarity to target sequences within a target genome, we establish a protocol to yield affinity-tagged duplex molecules the same length as the probe only if the target is present. The product can subsequently be bound to a protein chaperone and analyzed quantitatively with a selective solid-state nanopore assay. We first use a model DNA genome (M13mp18) to validate the approach, showing the successful isolation and detection of multiple target sequences simultaneously. We then demonstrate the protocol for the detection of RNA viruses by identifying and targeting a highly conserved sequence within human immunodeficiency virus (HIV-1B).
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Affiliation(s)
- Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Gabrielle P. Dailey
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Osama K. Zahid
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Ethan W. Taylor
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jan A. Ruzicka
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC 27268, USA
| | - Adam R. Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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30
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Kumar M, Bharti R, Ranjan T. The Evolutionary Significance of Generalist Viruses with Special Emphasis on Plant Viruses and their Hosts. Open Virol J 2020. [DOI: 10.2174/1874357902014010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The host range of a virus is defined as the number of species a virus potentially infects. The specialist virus infects one or few related species while the generalist virus infects several different species, possibly in different families. Origin of generalist viruses from their specialist nature and the expansion of the host range of the generalist virus occur with the host shift event in which the virus encounters and adapts to a new host. Host shift events have resulted in the majority of the newly emerging viral diseases. This review discusses the advantages and disadvantages of generalist over specialist viruses and the unique features of plant viruses and their hosts that result in a higher incidence of generalist viruses in plants.
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31
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Menshawey R, Menshawey E, Alserr AHK, Abdelmassih AF. Low iron mitigates viral survival: insights from evolution, genetics, and pandemics-a review of current hypothesis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020; 21:75. [PMID: 38624521 PMCID: PMC7738201 DOI: 10.1186/s43042-020-00114-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
Background Upon re-examination of our human history, evolutionary perspectives, and genetics, a prevailing iron deficiency phenotype appears to have evolved to protect the human race from extinction. Body In this review, we summarize the evolutionary and genetic perspectives pointing towards the hypothesis that low iron mitigates infection. The presence of infection promotes the generation of resistance alleles, and there are some evolutionary and genetic clues that suggest the presence of an iron deficiency phenotype that may have developed to protect against infection. Examples include the relative paucity of iron overload genes given the essential role of iron, as well as the persistence of iron deficiency among populations in spite of public health efforts to treat it. Additional examination of geographic areas with severe iron deficiency in the setting of pandemics including H1N1, SARS, and COVID-19 reveals that areas with higher prevalence of iron deficiency are less affected. RNA viruses have several evolutionary adaptations which suggest their absolute need for iron, and this dependency may be exploited during treatment. Conclusion RNA viruses pose a unique challenge to modern healthcare, with an average of 2-3 new pathogens being discovered yearly. Their overarching requirements for iron, along with human evolutionary and genetic adaptations which favored an iron deficiency phenotype, ultimately suggest the potential need for iron control in these infections.
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Affiliation(s)
- Rahma Menshawey
- Faculty of Medicine, Kasr al Ainy, Cairo University, Geziret Elroda, Manial, Cairo, 11562 Egypt
| | - Esraa Menshawey
- Faculty of Medicine, Kasr al Ainy, Cairo University, Geziret Elroda, Manial, Cairo, 11562 Egypt
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32
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Navare AT, Mast FD, Olivier JP, Bertomeu T, Neal M, Carpp LN, Kaushansky A, Coulombe-Huntington J, Tyers M, Aitchison JD. Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020; 221:2020.10.12.336487. [PMID: 33173868 PMCID: PMC7654857 DOI: 10.1101/2020.10.12.336487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses co-opt host proteins to carry out their lifecycle. Repurposed host proteins may thus become functionally compromised; a situation analogous to a loss-of-function mutation. We term such host proteins viral-induced hypomorphs. Cells bearing cancer driver loss-of-function mutations have successfully been targeted with drugs perturbing proteins encoded by the synthetic lethal partners of cancer-specific mutations. Synthetic lethal interactions of viral-induced hypomorphs have the potential to be similarly targeted for the development of host-based antiviral therapeutics. Here, we use GBF1, which supports the infection of many RNA viruses, as a proof-of-concept. GBF1 becomes a hypomorph upon interaction with the poliovirus protein 3A. Screening for synthetic lethal partners of GBF1 revealed ARF1 as the top hit, disruption of which, selectively killed cells that synthesize poliovirus 3A. Thus, viral protein interactions can induce hypomorphs that render host cells vulnerable to perturbations that leave uninfected cells intact. Exploiting viral-induced vulnerabilities could lead to broad-spectrum antivirals for many viruses, including SARS-CoV-2. SUMMARY Using a viral-induced hypomorph of GBF1, Navare et al., demonstrate that the principle of synthetic lethality is a mechanism to selectively kill virus-infected cells.
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Affiliation(s)
- Arti T Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Maxwell Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Lindsay N Carpp
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | | | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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33
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Affiliation(s)
- Samuel Cibulski
- Centro de Biotecnologia–CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba–UFPB, João Pessoa, Paraíba, Brazil
- * E-mail:
| | | | - Paulo Michel Roehe
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul–UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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34
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Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon 2020; 6:e04743. [PMID: 32835122 PMCID: PMC7430346 DOI: 10.1016/j.heliyon.2020.e04743] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.
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Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680, Indonesia
| | - Aghnianditya Kresno Dewantari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
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35
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Porras-Villamil JF, Olivera MJ, Ríos-Camargo NK. The First Few Hundred Cases for Coronavirus Disease 2019 (COVID-19) in Colombia. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:48-56. [PMID: 34268205 PMCID: PMC8266000 DOI: 10.18502/ijph.v49is1.3669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022]
Abstract
Background: SARS-CoV-2 virus is the causative agent of COVID-19 disease. It is essential to understand the epidemiological characteristics of the first few cases in each country. This study aimed to describe the geographical distribution, and temporal appearance of the first few hundred cases in Colombia. Methods: This observational study was conducted to review the literature and key documentary information from public health institutions, websites and news reports were examined. Results: The first few 100 cases for COVID-19 were confirmed in Colombia. According to sex, men with 54% predominate, the most affected age group was 20 to 29 yr old (26%), 9% of the cases required hospitalization and no deaths were reported. Most of the confirmed subjects were from the departments of Cundinamarca. To date, most cases are imported (63%), especially from Spain. Conclusion: The COVID-19 pandemic puts in evidence the lack of understanding, prevention and contention power of the different countries around the world is not as good as it could be. Politics must not affect the different proposed measures.
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Affiliation(s)
| | - Mario Javier Olivera
- National Institute of Health, Department of Parasitology, Avenida calle 26 No. 51-20 - Zona 6 CAN, Bogotá, D.C., Colombia
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36
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Zhang Z, Cai Z, Tan Z, Lu C, Jiang T, Zhang G, Peng Y. Rapid identification of human-infecting viruses. Transbound Emerg Dis 2019; 66:2517-2522. [PMID: 31373773 PMCID: PMC7168554 DOI: 10.1111/tbed.13314] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/01/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023]
Abstract
Viruses have caused much mortality and morbidity to humans and pose a serious threat to global public health. The virome with the potential of human infection is still far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of methodology for rapidly identifying novel viruses with the potential of human infection. This study built several machine learning models to discriminate human-infecting viruses from other viruses based on the frequency of k-mers in the viral genomic sequences. The k-nearest neighbor (KNN) model can predict the human-infecting viruses with an accuracy of over 90%. The performance of this KNN model built on the short contigs (≥1 kb) is comparable to those built on the viral genomes. We used a reported human blood virome to further validate this KNN model with an accuracy of over 80% based on very short raw reads (150 bp). Our work demonstrates a conceptual and generic protocol for the discovery of novel human-infecting viruses in viral metagenomics studies.
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Affiliation(s)
- Zheng Zhang
- College of BiologyHunan UniversityChangshaChina
| | - Zena Cai
- College of BiologyHunan UniversityChangshaChina
| | - Zhiying Tan
- College of Computer Science and Electronic EngineeringHunan UniversityChangshaChina
| | - Congyu Lu
- College of BiologyHunan UniversityChangshaChina
| | - Taijiao Jiang
- Suzhou Institute of Systems MedicineSuzhouChina
- Center of System Medicine, Institute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Gaihua Zhang
- College of Life SciencesHunan Normal UniversityChangshaChina
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37
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dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA. Viruses 2019; 11:v11100943. [PMID: 31615058 PMCID: PMC6832592 DOI: 10.3390/v11100943] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 12/24/2022] Open
Abstract
RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that RNA viruses produce double-stranded RNA (dsRNA) while replicating. Purifying and sequencing dsRNA from the total RNA isolated from infected tissue allowed us to recover dsRNA virus sequences and replicated sequences from single-stranded RNA (ssRNA) viruses. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length or partial RNA viral genomes of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here, we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don’t have sequenced genomes and/or commercially available rRNA depletion reagents. In addition, a significant advantage of this method is the ability to identify replicated viral sequences of ssRNA viruses, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants.
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38
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Washburne AD, Crowley DE, Becker DJ, Olival KJ, Taylor M, Munster VJ, Plowright RK. Taxonomic patterns in the zoonotic potential of mammalian viruses. PeerJ 2018; 6:e5979. [PMID: 30519509 PMCID: PMC6272030 DOI: 10.7717/peerj.5979] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Predicting and simplifying which pathogens may spill over from animals to humans is a major priority in infectious disease biology. Many efforts to determine which viruses are at risk of spillover use a subset of viral traits to find trait-based associations with spillover. We adapt a new method-phylofactorization-to identify not traits but lineages of viruses at risk of spilling over. Phylofactorization is used to partition the International Committee on Taxonomy of Viruses viral taxonomy based on non-human host range of viruses and whether there exists evidence the viruses have infected humans. We identify clades on a range of taxonomic levels with high or low propensities to spillover, thereby simplifying the classification of zoonotic potential of mammalian viruses. Phylofactorization by whether a virus is zoonotic yields many disjoint clades of viruses containing few to no representatives that have spilled over to humans. Phylofactorization by non-human host breadth yields several clades with significantly higher host breadth. We connect the phylogenetic factors above with life-histories of clades, revisit trait-based analyses, and illustrate how cladistic coarse-graining of zoonotic potential can refine trait-based analyses by illuminating clade-specific determinants of spillover risk.
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Affiliation(s)
- Alex D. Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Daniel E. Crowley
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Daniel J. Becker
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Matthew Taylor
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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39
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Baechlein C, Grundhoff A, Fischer N, Alawi M, Hoeltig D, Waldmann KH, Becher P. Pegivirus Infection in Domestic Pigs, Germany. Emerg Infect Dis 2018; 22:1312-4. [PMID: 27314228 PMCID: PMC4918184 DOI: 10.3201/eid2207.160024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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40
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Abstract
The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.
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Affiliation(s)
- Jennifer L. Gardy
- British Columbia Centre for Disease Control, Vancouver, V5Z 4R4 British Columbia Canada
- School of Population and Public Health, University of British Columbia, Vancouver, V6T 1Z3 British Columbia Canada
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT UK
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41
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Carrasco-Hernandez R, Jácome R, López Vidal Y, Ponce de León S. Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review. ILAR J 2017; 58:343-358. [PMID: 28985316 PMCID: PMC7108571 DOI: 10.1093/ilar/ilx026] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022] Open
Abstract
Pathogenic RNA viruses are potentially the most important group involved in zoonotic disease transmission, and they represent a challenge for global disease control. Their biological diversity and rapid adaptive rates have proved to be difficult to overcome and to anticipate by modern medical technology. Also, the anthropogenic change of natural ecosystems and the continuous population growth are driving increased rates of interspecies contacts and the interchange of pathogens that can develop into global pandemics. The combination of molecular, epidemiological, and ecological knowledge of RNA viruses is therefore essential towards the proper control of these emergent pathogens. This review outlines, throughout different levels of complexity, the problems posed by RNA viral diseases, covering some of the molecular mechanisms allowing them to adapt to new host species-and to novel pharmaceutical developments-up to the known ecological processes involved in zoonotic transmission.
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Affiliation(s)
- R Carrasco-Hernandez
- R. Carrasco-Hernandez, PhD, is a postdoctoral research fellow at the Microbiome Laboratory in the Postgraduate Division of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Rodrigo Jácome
- Rodrigo Jácome, MD, PhD, is a postdoctoral research fellow at the Microbiome Laboratory in the Postgraduate Division of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Yolanda López Vidal
- Yolanda López-Vidal, MD, PhD, is an associate professor “C” and is responsible for the Program of Microbial Molecular Immunology in the Department of Microbiology and Parasitology of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Samuel Ponce de León
- Samuel Ponce-de-León, MD, MSc, is an associate professor “C”, is responsible for the Microbiome Laboratory and Coordinator of the University Program for Health Research of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
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42
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Mossel EC, Crabtree MB, Mutebi JP, Lutwama JJ, Borland EM, Powers AM, Miller BR. Arboviruses Isolated From Mosquitoes Collected in Uganda, 2008-2012. JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:1403-1409. [PMID: 28874015 PMCID: PMC5968633 DOI: 10.1093/jme/tjx120] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 06/07/2023]
Abstract
A large number of arthropod-borne viruses are endemic to East Africa. As a part of the process of undertaking a systematic characterization of the mosquito fauna of Uganda, we examined mosquitoes collected from 2008 through early 2012 for known and novel viruses. In all, 8,288 mosquito pools containing 157,554 mosquitoes were tested. Twenty-nine isolations of 11 different viruses were made from mosquitoes of nine distinct species and from pools identified only to genus Culex. Identified viruses were from family Togaviridae, alphaviruses Sindbis and Babanki viruses; family Rhabdoviridae, hapaviruses Mossuril and Kamese viruses; family Flaviviridae, flaviviruses West Nile and Usutu viruses; family Phenuiviridae, phlebovirus Arumowot virus; and family Peribunyaviridae, orthobunyaviruses Witwatersrand, Pongola, and Germiston viruses. In addition, a novel orthobunyavirus, provisionally named Mburo virus, was isolated from Coquillettidia metallica (Theobald). This is the first report of Babanki, Arumowot, and Mossuril virus isolation from Uganda.
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Affiliation(s)
- Eric C. Mossel
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521 (; ; ; ; ; )
- Corresponding author, e-mail:
| | - Mary B. Crabtree
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521 (; ; ; ; ; )
| | - John-Paul Mutebi
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521 (; ; ; ; ; )
| | - Julius J. Lutwama
- Department of Arbovirology, Uganda Virus Research Institute (UVRI), PO Box 49, Entebbe, Uganda ()
| | - Erin M. Borland
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521 (; ; ; ; ; )
| | - Ann M. Powers
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521 (; ; ; ; ; )
| | - Barry R. Miller
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521 (; ; ; ; ; )
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43
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Manso CF, Bibby DF, Mbisa JL. Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples. Sci Rep 2017. [PMID: 28646219 PMCID: PMC5482852 DOI: 10.1038/s41598-017-02239-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 104 and 103 IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.
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Affiliation(s)
- Carmen F Manso
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom
| | - David F Bibby
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom.
| | - Jean L Mbisa
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom
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44
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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45
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Abstract
Advances in laboratory and information technologies are transforming public health microbiology. High-throughput genome sequencing and bioinformatics are enhancing our ability to investigate and control outbreaks, detect emerging infectious diseases, develop vaccines, and combat antimicrobial resistance, all with increased accuracy, timeliness, and efficiency. The Advanced Molecular Detection (AMD) initiative has allowed the Centers for Disease Control and Prevention (CDC) to provide leadership and coordination in integrating new technologies into routine practice throughout the U.S. public health laboratory system. Collaboration and partnerships are the key to navigating this transition and to leveraging the next generation of methods and tools most effectively for public health.
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46
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Simulundu E, Mweene AS, Changula K, Monze M, Chizema E, Mwaba P, Takada A, Ippolito G, Kasolo F, Zumla A, Bates M. Lujo viral hemorrhagic fever: considering diagnostic capacity and preparedness in the wake of recent Ebola and Zika virus outbreaks. Rev Med Virol 2016; 26:446-454. [PMID: 27593704 PMCID: PMC7169100 DOI: 10.1002/rmv.1903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 12/18/2022]
Abstract
Lujo virus is a novel Old World arenavirus identified in Southern Africa in 2008 as the cause of a viral hemorrhagic fever (VHF) characterized by nosocomial transmission with a high case fatality rate of 80% (4/5 cases). Whereas this outbreak was limited, the unprecedented Ebola virus disease outbreak in West Africa, and recent Zika virus disease epidemic in the Americas, has brought into acute focus the need for preparedness to respond to rare but potentially highly pathogenic outbreaks of zoonotic or arthropod‐borne viral infections. A key determinant for effective control of a VHF outbreak is the time between primary infection and diagnosis of the index case. Here, we review the Lujo VHF outbreak of 2008 and discuss how preparatory measures with respect to developing diagnostic capacity might be effectively embedded into existing national disease control networks, such as those for human immunodeficiency virus, tuberculosis, and malaria.
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Affiliation(s)
- Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Katendi Changula
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Mwaka Monze
- University Teaching Hospital & National Virology Reference Laboratory, Lusaka, Zambia
| | | | | | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Guiseppe Ippolito
- Lazzaro Spallanzani National Institute for Infectious Diseases, IRCCS, Rome, Italy
| | - Francis Kasolo
- World Health Organization, WHO Africa, Brazzaville, Republic of Congo
| | - Alimuddin Zumla
- Department of Infection, Division of Infection and Immunity, University College London, UK.,University of Zambia - University College London Research & Training Programme (www.unza-uclms.org), University Teaching Hospital, Lusaka, Zambia
| | - Matthew Bates
- Department of Infection, Division of Infection and Immunity, University College London, UK.,University of Zambia - University College London Research & Training Programme (www.unza-uclms.org), University Teaching Hospital, Lusaka, Zambia.,HerpeZ (www.herpez.org), University Teaching Hospital, Lusaka, Zambia
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47
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Reguera J, Gerlach P, Rosenthal M, Gaudon S, Coscia F, Günther S, Cusack S. Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases. PLoS Pathog 2016; 12:e1005636. [PMID: 27304209 PMCID: PMC4909276 DOI: 10.1371/journal.ppat.1005636] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/25/2016] [Indexed: 01/15/2023] Open
Abstract
Segmented negative strand RNA viruses of the arena-, bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism. This involves cleavage of host mRNAs close to their capped 5′ end by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. We present the structure of the cap-snatching EN of Hantaan virus, a bunyavirus belonging to hantavirus genus. Hantaan EN has an active site configuration, including a metal co-ordinating histidine, and nuclease activity similar to the previously reported La Crosse virus and Influenza virus ENs (orthobunyavirus and orthomyxovirus respectively), but is more active in cleaving a double stranded RNA substrate. In contrast, Lassa arenavirus EN has only acidic metal co-ordinating residues. We present three high resolution structures of Lassa virus EN with different bound ion configurations and show in comparative biophysical and biochemical experiments with Hantaan, La Crosse and influenza ENs that the isolated Lassa EN is essentially inactive. The results are discussed in the light of EN activation mechanisms revealed by recent structures of full-length influenza virus polymerase. Segmented negative strand viruses (sNSV) such as Influenza, Lassa or Hantaan viruses are responsible for a large number of severe human infectious diseases. Currently, there are vaccines and antiviral treatments available for influenza but none for the infections caused by other sNSV. All carry out transcription by the cap-snatching mechanism, which requires the action of a metal ion dependent endonuclease (EN), a domain within their large viral polymerases. Here we provide the crystal structure of the Hantaan virus (family Bunyaviridae) and Lassa virus (family Arenaviridae) cap-snatching ENs in complex with manganese and a comparative functional study of their catalytic activity. Despite the high structural homology between the two ENs a few changes in the active site, involving a catalytic histidine, cause a different binding of the metal ions with dramatic consequences for their in vitro activity. Hantaan EN binds the metal ions as Influenza A (family Orthomyxoviridae) and LACV (family Bunyaviridae) ENs and all three are active in vitro. In contrast Lassa virus EN is inactive in the same experimental conditions. We can now classify sNSV into two functionally distinct groups (His+ and His- ENs), providing a broad view of the sNSV cap-snatching ENs properties that will be determinant for the comprehensive development of broad-spectrum antiviral drugs. These results also have implications for the viral transcription regulation in the light of recent studies on full-length sNSV polymerases.
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Affiliation(s)
- Juan Reguera
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- * E-mail: (JR); (SC)
| | - Piotr Gerlach
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
| | - Maria Rosenthal
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Stephanie Gaudon
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
| | - Francesca Coscia
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- Unit of Virus-Host Cell Interactions (UMI 3265), Univ. Grenoble-Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9, France
- * E-mail: (JR); (SC)
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48
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Geller R, Estada Ú, Peris JB, Andreu I, Bou JV, Garijo R, Cuevas JM, Sabariegos R, Mas A, Sanjuán R. Highly heterogeneous mutation rates in the hepatitis C virus genome. Nat Microbiol 2016; 1:16045. [PMID: 27572964 DOI: 10.1038/nmicrobiol.2016.45] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/09/2016] [Indexed: 01/10/2023]
Abstract
Spontaneous mutations are the ultimate source of genetic variation and have a prominent role in evolution. RNA viruses such as hepatitis C virus (HCV) have extremely high mutation rates, but these rates have been inferred from a minute fraction of genome sites, limiting our view of how RNA viruses create diversity. Here, by applying high-fidelity ultradeep sequencing to a modified replicon system, we scored >15,000 spontaneous mutations, encompassing more than 90% of the HCV genome. This revealed >1,000-fold differences in mutability across genome sites, with extreme variations even between adjacent nucleotides. We identify base composition, the presence of high- and low-mutation clusters and transition/transversion biases as the main factors driving this heterogeneity. Furthermore, we find that mutability correlates with the ability of HCV to diversify in patients. These data provide a site-wise baseline for interrogating natural selection, genetic load and evolvability in HCV, as well as for evaluating drug resistance and immune evasion risks.
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Affiliation(s)
- Ron Geller
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Úrsula Estada
- Unitat de Genómica, Servei Central de Suport a la Investigació Experimental, Universitat de València, 46100 Burjassot, València, Spain
| | - Joan B Peris
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Iván Andreu
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Juan-Vicente Bou
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Rosario Sabariegos
- Regional Center for Biomedical Research, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Antonio Mas
- Regional Center for Biomedical Research, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain.,Departament de Genètica, Universitat de València, 46100 Burjassot, València, Spain
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49
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Alves JMP, de Oliveira AL, Sandberg TOM, Moreno-Gallego JL, de Toledo MAF, de Moura EMM, Oliveira LS, Durham AM, Mehnert DU, Zanotto PMDA, Reyes A, Gruber A. GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data. Front Microbiol 2016; 7:269. [PMID: 26973638 PMCID: PMC4777721 DOI: 10.3389/fmicb.2016.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.
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Affiliation(s)
- João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - André L de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Tatiana O M Sandberg
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - Marcelo A F de Toledo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Elisabeth M M de Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Liliane S Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São PauloSão Paulo, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São PauloSão Paulo, Brazil
| | - Alan M Durham
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo São Paulo, Brazil
| | - Dolores U Mehnert
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Paolo M de A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los AndesBogotá, Colombia; Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint LouisMO, USA
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
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50
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Affiliation(s)
- R A Stein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Department of Natural Sciences, La Guardia Community College, City University of New York, Queens, NY, USA.
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