The England 2 Coronavirus (CoV) genome has been assembled using overlapping PCR fragments of between 0.5 and 1.5 kb. The final sequenced genome coverage was between 2 and 11 fold, and the material sequenced was directly from clinical material NOT from a virus isolate.
The genome of England 2 CoV has been annotated using the coding regions defined in the GenBank entry JX869059 (EMC 2012).
Download the sequence and coding regions
Phylogenetic Analysis indicated that England 2 CoV clustered with England1 CoV and the virus identified in the Netherlands (EMC 2012, JX869059). The level of similarity within this cluster of novel coronaviruses was greater than 99.6%.
Figure 1 Phylogenetic Analysis of Complete Coronavirus Genomes
For further information, or to comment on this information please contact Monica.Galiano@hpa.org.uk or Richard.Myers@hpa.org.uk. We welcome feedback.
This sequence is provided for public health purposes. It is made freely available without restrictions in the fastest way possible. Unless acknowledged in publications which use this data, the individual scientists who worked to develop it will not be recognised. Please consider this when you include this sequence in a publication/analysis. Reference to this sequence in publications should be described as England 2 Coronavirus sequence provided by the Health Protection Agency, UK.
The England 1 Coronavirus genome (England1_CoV) was assembled using 80 overlapping PCR fragments of between 0.5-1.5 kb. Degenerate primers were designed against an alignment of EMC virus and bat coronavirus HKU4 & HKU5. The final sequenced genome coverage was between 2 and 11 fold, and the material sequenced was directly from clinical material NOT from a virus isolate.
The genome of England1_CoV has been annotated using the coding regions defined in the GenBank entry JX869059 (EMC 2012). England1_CoV has been submitted to GenBank and the accession number will be added to this document, when it is available.
Download the sequence and coding regions:
England1_CoV was highly similar to the coronavirus sequenced in the Netherlands (EMC 2012, JX869059). The level of sequence diversity between EMC and England1_CoV, coupled with the available epidemiological information may suggest two zoonotic infections rather than human to human transmission.
Phylogenetic analysis (figure 1) showed that the England1_CoV belonged to genotype 2c and indicated that the closest relatives were bat coronaviruses detected in Hong Kong.
Figure 1: phylogenetic analysis of England1_CoV
A phylogenetic analysis of complete coronavirus genomes (figure 2) showed that England1_CoV (red) and EMC 2012 (blue) are closely related and that these viruses form a distinct clade that is related to HKU4 and HKU5 bat coronaviruses. Generation of the whole genome also enabled analysis of different fragments of the polymerase gene. This analysis indicated that there was a bat coronavirus identified in the Netherlands in 2008 that was most closely related to the novel human viruses. However, HKU 4 and HKU5 are the most closely related viruses for which there is a complete genome available.
Figure 2: phylogenetic analysis of complete coronovirus genomes
Reference to this sequence in publications should be described as England 1 Coronavirus sequence provided by the Health Protection Agency.
Phylogenetic tree constructed with partial sequences from the polymerase gene (nsp12) of representative coronaviruses from different groups is displayed in the attached figure.
The sequence obtained at HPA has been tentatively named as London1_novel CoV 2012 (boxed in red). The HPA sequence data is based on direct detection from clinical material from the London case. HPA do not yet have a virus isolate. There will shortly be a GENBANK accession number for the sequence. The attached phylogenetic tree is considered preliminary, as is virus nomenclature, and liable to change as more information or a virus isolate becomes available.
Last reviewed: 21 February 2013