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Published Date: 2012-11-14 14:56:37
Subject: PRO/AH/EDR> Novel coronavirus - Saudi Arabia (16): whole genome sequence
Archive Number: 20121114.1409556

NOVEL CORONAVIRUS - SAUDI ARABIA (16): WHOLE GENOME SEQUENCE
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In this posting:
[1] Health Protection Agency (HPA) press release
[2] Health Protection Agency (HPA): whole genome sequence

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[1] HPA press release
Date: Tue 13 Nov 2012
Source: Health Protection Agency (HPA), News Centre, Press release [edited]
http://www.hpa.org.uk/webw/HPAweb&HPAwebStandard/HPAweb_C/1317136932841

Whole genome sequence from the UK case of novel coronavirus
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The Health Protection Agency (HPA) has today published the completed whole genome sequence from the UK case of confirmed novel coronavirus, which was diagnosed on 22 Sep 2012. The patient continues to receive treatment in a London hospital.

Today's publication of the full genome sequence will enable scientists to see how closely the UK case is linked to the 1st case of confirmed novel coronavirus, which was diagnosed in a patient from Saudi Arabia in June [2012], and who subsequently died. Analysis of the variation in the genomic sequences, coupled with the 3 month gap between patients infected with this coronavirus, indicate that there are probably independent sources of infection. Genomic analysis also indicates that the closest relative to this coronavirus was a bat virus identified in 2008 in the Netherlands.

Professor Maria Zambon, director of HPA's reference microbiology services, said: "We are very pleased to be able to share the completed whole genome sequence data with the scientific community. It has been very technically challenging to try to recover and piece together an entire virus from miniscule amounts of material. However, understanding more about the diversity of virus will help with efforts to determine its origin as well as to develop strategies for treatment and prevention, such as vaccine development, should further cases emerge There have been huge technological leaps since viruses such as H5N1 and SARS [severe acute respiratory syndrome] were discovered 10-15 years ago. The speed of response is a testament to the lessons learnt by the scientific and health community after SARS. Rapid disclosure of data enables diverse groups of scientists to study the virus in real time to help with the global health response, and HPA are pleased to contribute to that."

There has been one further case of novel coronavirus infection identified in Saudi Arabia since the UK case was diagnosed in September [2012], which brings the total reported globally to 3 cases. No travel restrictions are in place but people returning from the Middle East with severe respiratory symptoms, such as shortness of breath, should seek medical advice and mention which countries they have visited.

Professor Zambon continued: "With the close of the annual Hajj pilgrimage [24-29 Oct 2012], we anticipate that there may be a small number of returning travellers to the UK who require investigation as possible cases of novel coronavirus, and we are fully prepared for this. The HPA has also contributed senior medical staff to World Health Organization missions to Qatar and Saudi Arabia to assist in the ongoing investigations in these countries, and is providing scientific assistance to several countries in the region."

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[2] Health Protection Agency (HPA): whole genome sequence
Date: Tue 13 Nov 2012
Source: Health Protection Agency (HPA) [summ., edited]
http://www.hpa.org.uk/webw/HPAweb&HPAwebStandard/HPAweb_C/1317136246479

Whole genome sequence
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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 the EMC [the Netherlands slate] 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. [The sequence and coding regions can be downloaded at: England1_CoV genome sequence (Text Document, 61 KB); http://www.hpa.org.uk/webc/HPAwebFile/HPAweb_C/1317136950605.]

England1_CoV was highly similar to the [other novel] 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 2 zoonotic infections rather than human to human transmission.

The phylogenetic analysis showed that the England1_CoV belonged to [coronavirus] genotype 2c and indicated that the closest relatives were bat coronaviruses detected in Hong Kong.

A phylogenetic analysis of complete coronavirus genomes showed that England1_CoV and EMC 2012 are closely related and that these viruses form a distinct clade that is related to HKU4 and HKU5 bat coronaviruses [coronaviruses isolated from bats in Hong Kong]. Generation of the whole genome also enabled analysis of different fragments of the polymerase gene. This analysis indicated that there was a bat coronavirus [isolated in Hong Kong] identified in the Netherlands in 2008 that was most closely related to the novel human viruses. However, HKU4 and HKU5 are the most closely related viruses for which there is a complete genome available.

[Interested readers are recommended to access the original document at the source URL above to view these informative phylogenetic trees. - Mod.CP]

The Institut fur Virologie at the Universitaets Klinikum, Bonn, Germany, which has played a major role in developing and validating the assays and reagents, has recommended a testing algorithm that starts with a screening PCR for coronaviruses and is followed by assays specific for the novel strain. This laboratory can also offer positive control material and a link to a source of reagents for the recommended assays. The assays published have been tested by HPA on the limited clinical material available, so at least a preliminary validation of utility in clinical material has been performed. More data on this will be published shortly. There are likely to be a number of commercial developments in the near future with kits becoming available.

The sequence data that HPA has from the London case is based on direct genomic detection in clinical material. The HPA does not yet have a virus isolate, although clinical material is in tissue culture in an attempt to make virus isolates. The patient clinical material that HPA have does not react with the specific molecular detection assays that have been developed for the OC23, 229E, NL63, or SARS [coronaviruses].

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[These phylogenetic analyses show that the England1_CoV was highly similar to the [other novel] coronavirus sequenced in the Netherlands (EMC 2012, JX869059).

The level of sequence diversity between the viruses sequenced in the UK and the Netherlands, coupled with the available epidemiological information, suggest that 2 separate zoonotic infections occurred rather than human to human transmission.

The phylogenetic analyses also showed that the England1_CoV belonged to [coronavirus] genotype 2c and indicated that the closest relatives were 2 bat coronaviruses detected in Hong Kong.

It is likely that sensitive reagents for virus surveillance will soon be available. - Mod.CP

It would be interesting to know if the 2 isolates are similar to the isolate from the 3rd case reported by the Ministry of Health of Saudi Arabia (see ProMED-mail Novel coronavirus - Saudi Arabia (15): new case 20121104.1391285). - Mod.MPP]

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