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Increased Prevalence of Severe Fever with Thrombocytopenia Syndrome in Eastern China Clustered with Multiple Genotypes and Reasserted Virus during 2010–2015

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      Abstract

      Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne viral disease with high mortality. Since January 2010, we have conducted an epidemiological surveillance and etiological study of SFTS in Jiangsu and Anhui provinces. From January 2010 through December 2015, a total of 286 SFTS cases were confirmed in Jiangsu and Anhui provinces with a case fatality rate of 16.1%. The majority of confirmed SFTS cases were distributed in the border area of Jiangsu and Anhui provinces. Our findings suggest that the SFTS prevalence rate rose since 2010 and reached its highest in 2015. Phylogenetic analysis demonstrated that the majority of the SFTSV strains (83.6%) from Jiangsu and Anhui provinces belonged to genotypes A and D. Notably, we identified three strains of SFTSV clustered into the genotype E. This is the first report of the genotype E SFTSV strains in mainland of China. A reassortment between genotype A and D was found in the central region of the endemic areas, where three SFTSV genotypes (A, C and D) were co-circulating.

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      Evaluation of methods for detecting recombination from DNA sequences: computer simulations.

      Recombination is a key evolutionary process that shapes the architecture of genomes and the genetic structure of populations. Although many statistical methods are available for the detection of recombination from DNA sequences, their absolute and relative performance is still unknown. Here we evaluated the performance of 14 different recombination detection algorithms. We used the coalescent with recombination to simulate DNA sequences with different levels of recombination, genetic diversity, and rate variation among sites. Recombination detection methods were applied to these data sets, and whether they detected or not recombination was recorded. Different recombination methods showed distinct performance depending on the amount of recombination, genetic diversity, and rate variation among sites. The model of nucleotide substitution under which the data were generated did not seem to have a significant effect. Most methods increase power with more sequence divergence. In general, recombination detection methods seem to capture the presence of recombination, but they are not very powerful. Methods that use substitution patterns or incompatibility among sites were more powerful than methods based on phylogenetic incongruence. Most methods do not seem to infer more false positives than expected by chance. Especially depending on the amount of diversity in the data, different methods could be used to attain maximum power while minimizing false positives. Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand.
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        Possible emergence of new geminiviruses by frequent recombination.

        Although exchange of genetic information by recombination plays a role in the evolution of viruses, the extent to which it generates diversity is not clear. We analyzed genomes of geminiviruses for recombination using a new statistical procedure developed to detect gene conversions. Geminiviruses (family, Geminiviridae) are a group of plant viruses characterized by a genome of circular single-stranded DNA (approximately 2700 nucleotides in length) encapsidated in twinned quasi-isometric particles. Complete nucleotide sequences of geminiviruses were aligned, and recombination events were detected by searching pairs of viruses for sequences that are significantly more similar than expected based on random distribution of polymorphic sites. The analyses revealed that recombination is very frequent and occurs between species and within and across genera. Tests identified 420 statistically significant recombinant fragments distributed across the genome. The results suggest that recombination is a significant contributor to geminivirus evolution. The high rate of recombination may be contributing to the recent emergence of new geminivirus diseases. Copyright 1999 Academic Press.
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          Fever with thrombocytopenia associated with a novel bunyavirus in China.

          Heightened surveillance of acute febrile illness in China since 2009 has led to the identification of a severe fever with thrombocytopenia syndrome (SFTS) with an unknown cause. Infection with Anaplasma phagocytophilum has been suggested as a cause, but the pathogen has not been detected in most patients on laboratory testing. We obtained blood samples from patients with the case definition of SFTS in six provinces in China. The blood samples were used to isolate the causal pathogen by inoculation of cell culture and for detection of viral RNA on polymerase-chain-reaction assay. The pathogen was characterized on electron microscopy and nucleic acid sequencing. We used enzyme-linked immunosorbent assay, indirect immunofluorescence assay, and neutralization testing to analyze the level of virus-specific antibody in patients' serum samples. We isolated a novel virus, designated SFTS bunyavirus, from patients who presented with fever, thrombocytopenia, leukocytopenia, and multiorgan dysfunction. RNA sequence analysis revealed that the virus was a newly identified member of the genus phlebovirus in the Bunyaviridae family. Electron-microscopical examination revealed virions with the morphologic characteristics of a bunyavirus. The presence of the virus was confirmed in 171 patients with SFTS from six provinces by detection of viral RNA, specific antibodies to the virus in blood, or both. Serologic assays showed a virus-specific immune response in all 35 pairs of serum samples collected from patients during the acute and convalescent phases of the illness. A novel phlebovirus was identified in patients with a life-threatening illness associated with fever and thrombocytopenia in China. (Funded by the China Mega-Project for Infectious Diseases and others.).
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            Author and article information

            Affiliations
            [1 ]Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
            [2 ]ISNI 0000 0001 2314 964X, GRID grid.41156.37, , Medical School, Nanjing University, ; Nanjing, China
            [3 ]ISNI 0000 0004 1761 1174, GRID grid.27255.37, , School of Public Health, Shandong University, ; Jinan, China
            [4 ]Jiangning Center for Disease Prevention and Control, Jiangning, China
            [5 ]Lishui Center for Disease Prevention and Control, Lishui, China
            [6 ]Xuyi Center for Disease Prevention and Control, Xuyi, China
            [7 ]Yixing Center for Disease Prevention and Control, Yixing, China
            [8 ]ISNI 0000000419368657, GRID grid.17635.36, , College of Veterinary Medicine, University of Minnesota at Twin Cities, ; Saint Paul, MN USA
            [9 ]ISNI 0000 0004 1790 425X, GRID grid.452524.0, , Clinical Laboratory, Jiangsu Province Hospital of TCM, Affiliated Hospital of Nanjing University of TCM, ; Nanjing, China
            Contributors
            bao2000_cn@163.com
            Journal
            Sci Rep
            Sci Rep
            Scientific Reports
            Nature Publishing Group UK (London )
            2045-2322
            26 July 2017
            26 July 2017
            2017
            : 7
            28747674
            5529542
            6853
            10.1038/s41598-017-06853-1
            © The Author(s) 2017

            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/.

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