Computational protocol: Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes

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Protocol publication

[…] Sequences were assembled in contigs corresponding to the entire nsp12, S or N genes with CodonCode Aligner Software, version 5.0.1 (CodonCode corporation, Centerville, MA, USA). Multiple sequence alignment and phylogenetic analysis were performed using MEGA software, version 6.06 (http://www.megasoftware.net). Twenty-one sequences available in GenBank were added to the alignment, including HCoV-OC43s HKU4_01 and HKU4_02 from Hong-Kong []; HCoV-OC43s BE03 and BE04 from Belgium []; HCoV-OC43s OC43/human/USA/851-15/1985, OC43/human/USA/007-11/2000, OC43/human/USA/925-1/1992, OC43/human/USA/8912-37/1989, OC43/human/USA/953-23/1995, OC43/human/USA/951-18/1995, OC43/human/USA/872-5/1987, OC43/human/USA/901-54/1990, OC43/human/USA/931-85/1993, OC43/human/USA/911-58/1991, OC43/human/USA/008-5/2000, OC43/human/USA/832-27/1983, OC43/human/USA/965-6/1996 and OC43/human/USA/971-5/1997 from the USA, recently submitted by Town et al.; and BCoV Kakewaga, Mebus, and Quebec to root the trees [,,]. The accession numbers corresponding to these sequences are given in . Phylogenetic trees were constructed using the method of neighbor joining, with the substitution model of Kimura-2, implemented in MEGA6 [,]. These trees were used to perform the comparative analysis of our results with those of Lau et al in 2011 []. In order to support neighbour joining trees with a probabilistic method and to estimate divergence time between groups and subgroups, trees of S and N genes were also inferred using the same sequences and a Bayesian Markov Chain Monte Carlo method, implemented in the BEAST package, version 1.8.1 [,]. Inferences were calculated with the one parametric coalescent model with a constant size, under the TN93+G substitution model according to Bayesian Information Criterion (BIC) and Akaike Information Criterion (AIC) values of a model test carried out on MEGA6 software. The tMRCA was estimated using a relaxed molecular clock with an uncorrelated lognormal distribution. The length of MCMC was fixed at 3 × 10−8 states for the both genes. The Tracer software, version 1.5, implemented in the BEAST package, was used to assess the fitness of the model used, focusing the Effective Sampling Size (ESS) data, after a burning of 10%. The target trees were obtained with the maximum credibility clades, with a posterior probability limit of 0.05. The tMRCA age for each genotype was compared for S and N genes. […]

Pipeline specifications

Software tools CodonCode Aligner, MEGA, BEAST
Application Phylogenetics
Organisms Human coronavirus OC43, Homo sapiens
Diseases Respiratory Tract Infections