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      Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains

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          Abstract

          The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.

          Abstract

          Here, the authors compare seven low passage Zika virus (ZIKV) strains representing the recently circulating viral genetic diversity of African and Asian strains and find that African ZIKV strains have higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice.

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          Most cited references113

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

                Contributors
                suzanne.kaptein@kuleuven.be
                louis.lambrechts@pasteur.fr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                10 February 2021
                10 February 2021
                2021
                : 12
                : 916
                Affiliations
                [1 ]Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
                [2 ]GRID grid.415751.3, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, , Laboratory of Virology and Chemotherapy, ; Leuven, Belgium
                [3 ]GRID grid.4861.b, ISNI 0000 0001 0805 7253, GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, , University of Liège, ; Liège, Belgium
                [4 ]GRID grid.415751.3, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, , Laboratory of Clinical and Epidemiological Virology, ; Leuven, Belgium
                [5 ]GRID grid.4830.f, ISNI 0000 0004 0407 1981, Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, , University of Groningen, ; Groningen, The Netherlands
                [6 ]GRID grid.418221.c, Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, , Institut de Recherche Biomédicale des Armées (IRBA), ; Marseille, France
                [7 ]GRID grid.5399.6, ISNI 0000 0001 2176 4817, IRD, SSA, AP-HM, UMR Vecteurs—Infections Tropicales et Méditerranéennes (VITROME), , Aix Marseille University, ; Marseille, France
                [8 ]GRID grid.483853.1, ISNI 0000 0004 0519 5986, IHU Méditerranée Infection, ; Marseille, France
                [9 ]GRID grid.419250.b, National Center for Genetic Engineering and Biotechnology (BIOTEC), ; Pathum Thani, Thailand
                [10 ]GRID grid.428999.7, ISNI 0000 0001 2353 6535, Mouse Genetics Laboratory, , Institut Pasteur, ; Paris, France
                [11 ]GRID grid.428999.7, ISNI 0000 0001 2353 6535, Evolutionary Genomics of RNA Viruses Group, , Institut Pasteur, ; Paris, France
                [12 ]GRID grid.412188.6, ISNI 0000 0004 0486 8632, Laboratorio de Enfermedades Tropicales, Departamento de Medicina, , Fundación Universidad del Norte, ; Barranquilla, Colombia
                [13 ]GRID grid.418576.9, ISNI 0000 0004 0635 3907, Institut Louis Malardé, ; Papeete, Tahiti French Polynesia
                [14 ]GRID grid.507680.c, ISNI 0000 0001 2230 3166, Viral Diseases Branch, , Walter Reed Army Institute of Research, ; Silver Spring, MD USA
                [15 ]GRID grid.418508.0, ISNI 0000 0001 1956 9596, Arbovirus and Viral Hemorrhagic Fevers Unit, , Institut Pasteur Dakar, ; Dakar, Senegal
                Author information
                http://orcid.org/0000-0001-8657-6841
                http://orcid.org/0000-0002-3140-0651
                http://orcid.org/0000-0002-8874-675X
                http://orcid.org/0000-0003-2326-4255
                http://orcid.org/0000-0003-3078-8719
                http://orcid.org/0000-0002-9372-5398
                http://orcid.org/0000-0002-8351-1142
                http://orcid.org/0000-0001-8420-7743
                http://orcid.org/0000-0002-0033-7514
                http://orcid.org/0000-0002-8560-3008
                http://orcid.org/0000-0002-7935-0219
                http://orcid.org/0000-0001-5958-2138
                Article
                21199
                10.1038/s41467-021-21199-z
                7876148
                33568638
                a30a584d-7180-4752-ba85-be960e0ef758
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 15 August 2020
                : 16 January 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/100010687, EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018);
                Award ID: 734584
                Award Recipient :
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                © The Author(s) 2021

                Uncategorized
                viral epidemiology,viral transmission,experimental models of disease
                Uncategorized
                viral epidemiology, viral transmission, experimental models of disease

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