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Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition.

ABSTRACT: Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Predictions on 47 additional coronaviruses precisely conformed to conclusions or speculations by other researchers. Our approach is implemented as a web server that can be accessed at http://bioinfo.ihb.ac.cn/seq2hosts.

SUBMITTER: Tang Q

PROVIDER: S-EPMC4660426 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition.

Tang Qin Q Song Yulong Y Shi Mijuan M Cheng Yingyin Y Zhang Wanting W Xia Xiao-Qin XQ

Scientific reports 20151126

Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector mac ...[more]

PMID: 26607834

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Project description:The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.

Project description:Background/objectiveArtificial bone models (ABMs) are used in orthopaedics for research of biomechanics, development of implants and educational purposes. Most of the commercially available ABMs approximate the morphology of Europeans, but they may not depict the Asian anatomy. Therefore, our aim was to develop the first Asian ABM of the pelvis and compare it with the existing pelvic ABM (Synbone®; Caucasian male).MethodsOne hundred clinical computed tomography (CTs) of adult pelvises (male n = 50, female n = 50) of Malay, Chinese and Indian descent were acquired. CTs were segmented and defined landmarks were placed. Three 3D statistical pelvic model and mean models (overall, male, female) were generated. Anatomical variations were analysed using principal component analysis. To measure gender-related differences and differences to the existing ABM, distances between the anterior superior iliac spines (ASIS), the anterior inferior iliac spines (AIIS), the promontory and the symphysis (conjugate vera, CV) as well as the ischial spines (diameter transversa, DT) were quantified.ResultsPrincipal component analysis displayed large variability regarding the pelvic shape and size. Female and male statistical models were similar in ASIS (225 ± 20; 227 ± 13 mm; P = 0.4153) and AIIS (185 ± 11; 187 ± 10 mm; P = 0.3982) and differed in CV (116 ± 10; 105 ± 10 mm; P < 0.0001) and DT (105 ± 7; 88 ± 8 mm; P < 0.0001). Comparing the unisex mean model with the pre-existing ABM, the ASIS (226; 275 mm; P < 0.0001), the AIIS (186; 209 mm; P < 0.0001) and the CV (111; 105 mm; P < 0.0001) differed significantly. Both models were similar regarding DT (97; 95 mm; P = 0.6927). The analysis revealed notable gender- and size-dependent anatomical variations within the Asian population. Chinese, Malay and Indian descents did not differ notably. The overall Asian model was smaller than the existing ABM.The translation potential of this articleOwing to the large differences between the Asian ABM and the pre-existing ABM, as well as differences between genders, the use of an Asian- and gender-specific ABM is important to consider in research, biomechanics and implant development for this population.

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Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition.

Publications

Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition.

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