Updated genetic analysis with new Jordan-N3 genome.
NAMRU-3 have released a genome sequence from one of the early patients in Jordan. This sequence, collected in April 2012, is the most divergent novel coronavirus given its time of sampling. A genetic...
View ArticleAvian Influenza A H7N9 emerging human cases around Shanghai, China
BackgroundBackground information - Geography and temporal informationAnalysis and interpretationThe main findings of the phylogenetic analysis is that although the human cases are a H7N9 virus, this...
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Avian Influenza H7N9, human cases, Shanghai, China - Molecular Evolution and...
Phylogenetic AnalysisMaximum likelihood phylogenetic trees (Phyml, HKY+G) for each gene segment using closest matches in NCBI. Rooted with temporal information using Pathogen. The general pattern is...
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H7N9 - Neuraminidase
The new Human H7N9 neuraminidase sequences have a partial stalk deletion between amino acid positions 67 and 73.In N1 neuraminidases (particularly Highly Pathogenic Avian Influenza H5N1) stalk...
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Initial N9 Neuraminidase Tree
Eurasian N9-NA (segment 6) from avian complete genome sequences, and the new H7N9 NA sequences were analysed in BEAST, using the SRD06, relaxed log normal clock and GMRF skyride. The estimated time to...
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Initial H7-Hemagglutinin Tree
Eurasian H7-HA (segment 4) from avian complete genome sequences, and the new H7N9 NA sequences were analysed in BEAST, using the SRD06, relaxed log normal clock and GMRF skyride. The estimated time to...
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Genome mutations in novel human H7N9 influenza virus
This is the analysis of mutations in the virus genomes occurred before and during the emergence of human H7N9 in China.Based on the inferred phylogeny, we estimated (in HYPHY) the amino acid...
View ArticleH7N9 Background
BackgroundHuman cases as currently reported (2013-04-02).Sequences released in Epiflu database on GISAID:CaseCollection dateEpiflu (segments 1-8)IsolateSubmitterMale 87 (Deceased)2013-02-19 -...
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Reassortment history leading to human H7N9 outbreak
To look at the reassortment history of the outbreak viruses it was necessary to compile a dataset that contained exactly the same strains in the alignments for each segment. To do this I used GISAID's...
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NS segment reassortment prior to the H7N9 outbreak in humans
In addition to the previously described reassortment events (in HA and NA) leading up to the outbreak in humans, the emerging H7N9 influenza A strain also seems to have undergone a somewhat recent...
View ArticleProbable human to human transmission within the UK
HPA has just posted that a family member of the recent UK case has been infected. The family member had not travelled recently so it is likely this is a case of human-to-human...
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Preliminary genetic analyses
Genetic analysisCurrently have 2 complete genome sequences, hCoV-EMC & England1_CoV Polyprotein 1a coding sequence: 61 differences in 21,237 nucleotides, divergence 0.00287 subst/site S protein: 10...
View ArticleWhat is the rate of evolution of a virus?
Question: What is the rate of evolution of a virus?Possible approaches:Requirements:Instructions:
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Novel Human Coronavirus Molecular Epidemiology and Genetic Analysis - Origin...
Novel Human Coronavirus Molecular Epidemiology and Genetic AnalysisThis is an update of an older analysis based on only 2 sequences.We now have 3 complete genome sequences:NameAccessionSourceDate of...
View ArticleNew (third) sequence released.
The HPA released a sequence from the recent UK patient. This third temporally sampled virus allows us to make an initial estimate of the rate of evolution and to have more certainty in the dates of...
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Genome Mutations of Novel Human Betacoronavirus 2c
It is useful to trace the mutations arise in the pathogen genome during the disease emergence.Here it is the analysis of mutations occurred in the four novel human betacoronavirus 2c(HuCoV2c) genome...
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Update to map of likely infection locations
With some information kindly provided by Henry Niman (harvested from a variety of reports), I have updated the map of cases:http://epidemic.bio.ed.ac.uk/coronavirus_backgroundCombined with the updated...
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Novel Human Coronavirus Molecular Epidemiology and Genetic Analysis - Origin...
Novel Human Coronavirus Molecular Epidemiology and Genetic AnalysisThis is an update of an older analysis based on only 3 sequences.We now have 4 complete genome sequences:NameAccessionSourceDate of...
View ArticleAvian Influenza A H7N9 emerging human cases around Shanghai, China
GISAID data acknowledgementsWe gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiFlu™ Database on which this analysis is based. A list of the...
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H7N9 - Neuraminidase
We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiFlu™ Database on which this analysis is based. A list of the sequences, their submitting...
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