NCoV, Saudi Arabia: Gene sequences of virus isolates from patients deposited on GenBank

[Giuseppe]

[Source: Saudi Arabia Ministry of Health, full page in Arabic: (LINK). Automatic translation. Edited.]

MERS-CoV, Saudi Arabia: Gene sequences of virus isolates from patients deposited on GenBank

June 11 2013
​

Ministry of Health announced that study on cluster of infections in health care facilities with MERS-COV and gene sequencing of the virus have been done in an integrated manner, within a record period of outbreaks that occurred in the province of Al-Ahsa, where The group of researchers in the Kingdom of Saudi Arabia and the United Kingdom to study for urgent characteristics of genetic arising from the outbreak syndrome respiratory coronary Middle East Corona (MERS-COV), in collaboration with scientists from the University College London and the Institute of the Wellcome Trust Sanger.

This is a positive step towards follow the evolution and mutation virus with the passage of time and help in the diagnostic steps and find a quick mechanism for diagnosis. explained the official spokesman for the Ministry of Health.

Khaled Marghalani it was actually recording the full genetic sequence of (4) of patients outbreaks Ahsa in the Eastern Province on the GenBank database as of today Tuesday, 08/02/1434 corresponding to 11/06/2013 and is available to all in accordance with the established norms and through the site Bank Web site (National Center for Biotechnology Information)

In this context, called upon the ministry to all researchers from home and abroad and specialists reference to GenBank numbers added (from kf186564 to kf186567) to view this information and take advantage of this step scientific ministry hopes to contribute to the the development of science and speed in finding a vaccine for the disease and to learn more about this virus as the current information related to this virus are still few and there is no vaccine or cure.

In this context, WHO issued on its website www.who.org press release through its mission , who visited the Kingdom recently published the experiences Kingdom and experiences in dealing with the virus and know its characteristics through shed more light on the forms epidemic of the virus described limited information about this virus, as demonstrated modes of transmission of the virus from one person to another and how to diagnosis and treatment and offered the organization measures have been taken in the Kingdom of Inquiry and control over in Al-Ahsa and urged all States, in particular the Eastern Mediterranean region to intensify epidemiological investigation procedures, and the Ministry of Health has published this statement on its website www.moh.gov.sa

​

-
-------

 

[Giuseppe]

Re: NCoV, Saudi Arabia: Gene sequences of virus isolates from patients deposited on GenBank

Source: epidemic - Molecular Epidemiology and Evolution of Viral Pathogens, Submitted by Andrew Rambaut on Mon, 2013-06-10 20:10: http://epidemic.bio.ed.ac.uk/coronavirus_analysis (Excerpt)


MERS-Coronavirus Molecular Epidemiology and Genetic Analysis

(...)


Interpretation

Based on the above results and the restricted geographical range of the known cases, it seems unlikely that this virus has been circulating entirely in humans since these sequences shared a common ancestor. Although it is certain that the virus can spread from human to human (familial cases are noted and the large hospital-associated cluster at Al-Hasa, KSA), a single introduction into humans and subsequent epidemic would be unlikely to have remained restricted to the Ariabian Peninsula (the UK case from January was a transitory visitor to Saudi Arabia).

A more likely interpretation of the data would be multiple zoonotic transmissions from an animal reservoir. If the reservoir has a high contact rate with humans (e.g., a domesticated or farmed animal) then multiple small chains of human transmission could be hypothesized allowing for contact with the cases that have been described so far. It is also clear that a group is developing of the more recently isolated viruses (consisting of Qatar/England1, Munich/AbuDhabi, England2 and the Al-Hasa sequences).

(...)


-
-------

.
......

 

[IanM]

Impact of genome variation on diagnsotic assays....NIL

Impact of genome variation on diagnsotic assays....NIL

After a adding in the latest 4 genomes to the existing 5 genomes in an alignment (using Geneious Pro software) I can also note that the new genomes do not introduce any unexpected nucleotide changes in the ORF1a, ORF1b or E gene regions that would interfere with the Corman and crew's real-time RT-PCRs or conventional PCR sequencing assays (published in Eurosurveiilance (2012 Sep 27;17(39). pii: 20285. and 2012 Dec 17(49). pii: 20334.).

There is a mismatch (C:T) in the NSeq-Rev primer and the RdRpSeq-Rev primer, with some/all MERS-CoV strains, but nothing significant given its position within the primer.

These assays are, I believe, in wide use and are part of the WHO PCR testing algorithm for the MERS-CoV; good targets well chosen!