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      Emerging Coxsackievirus A6 Causing Hand, Foot and Mouth Disease, Vietnam

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          Abstract

          Hand, foot and mouth disease (HFMD) is a major public health issue in Asia and has global pandemic potential. Coxsackievirus A6 (CV-A6) was detected in 514/2,230 (23%) of HFMD patients admitted to 3 major hospitals in southern Vietnam during 2011–2015. Of these patients, 93 (18%) had severe HFMD. Phylogenetic analysis of 98 genome sequences revealed they belonged to cluster A and had been circulating in Vietnam for 2 years before emergence. CV-A6 movement among localities within Vietnam occurred frequently, whereas viral movement across international borders appeared rare. Skyline plots identified fluctuations in the relative genetic diversity of CV-A6 corresponding to large CV-A6–associated HFMD outbreaks worldwide. These data show that CV-A6 is an emerging pathogen and emphasize the necessity of active surveillance and understanding the mechanisms that shape the pathogen evolution and emergence, which is essential for development and implementation of intervention strategies.

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          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            R. C. Edgar (2004)
            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

              K Tamura, M Nei (1993)
              Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition/transversion ratio for the entire control region was approximately 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Emerg Infect Dis
                Journal ID (iso-abbrev): Emerging Infect. Dis
                Journal ID (publisher-id): EID
                Title: Emerging Infectious Diseases
                Publisher: Centers for Disease Control and Prevention
                ISSN (Print): 1080-6040
                ISSN (Electronic): 1080-6059
                Publication date (Print): April 2018
                Volume: 24
                Issue: 4
                Pages: 654-662
                Affiliations
                [1]Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam (N.T. Anh, L.N.T. Nhu, H.M.T. Van, N.T.T. Hong, T.T. Thanh, V.T.T. Hang, N.T.H. Ny, L.A. Nguyet, B. Wills, S. Sabanathan, L. Thwaites, H.R. van Doorn, G. Thwaites, M.A. Rabaa, L.V. Tan);
                [2]Hospital for Tropical Diseases, Ho Chi Minh City (T.T.L. Phuong, P.T. Qui, N.V.V. Chau);
                [3]Children’s Hospital 1, Ho Chi Minh City (L.N.T. Nhan, N.T. Hung, T.H. Khanh);
                [4]Children’s Hospital 2, Ho Chi Minh City (H.M. Tuan, H.L. Viet, N.T. Nam, D.C. Viet);
                [5]University of Oxford, Oxford, United Kingdom (L. Thwaites, H.R. van Doorn, G. Thwaites, M.A. Rabaa)
                Author notes
                Address for correspondence: Le Van Tan, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; email: tanlv@ 123456oucru.org
                Article
                Publisher ID: 17-1298
                DOI: 10.3201/eid2404.171298
                PMC ID: 5875260
                PubMed ID: 29553326
                SO-VID: 445a8bcf-9023-47f2-a996-1406e29eb213
                History
                Categories
                Subject: Research
                Subject: Research
                Subject: Emerging Coxsackievirus A6 Causing Hand, Foot and Mouth Disease, Vietnam

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: hand foot and mouth disease,vietnam,deep sequencing,phylogeny,coxsackievirus a6,asia,enteroviruses,viruses
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: hand foot and mouth disease, vietnam, deep sequencing, phylogeny, coxsackievirus a6, asia, enteroviruses, viruses

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