Wednesday, September 18, 2013

Recent MERS-CoV Sequences from the Kingdom of Saudi Arabia

At Epidemic - Molecular Epidemiology and Evolution of Viral Pathogens, Andrew Rambaut has compiled a list of 21 recently reported sequences of the Middle East Respiratory Coronavirus (MERS-CoV) from the Kingdom of Saudi Arabia (KSA).[1]

Lacking age and sex, and only having the collection date makes it difficult to correlate the sequence samples with previous, individually identified cases in the KSA. For provinces and cities in KSA that have only a few reported MERS-CoV cases, correlation of the sequences with individual cases is straight forward as the sample name is a clue to the geographic location. 

For several of the recently released sequences, case information is provided below. 

Bisha_1_2012 is likely from the 60-year-old-male from the town of Bisha in Asir Province. He experienced onset on June 6, 2012, was hospitalized on June 13, 2012 and died on June 24, 2012. He is not reported as part of any cluster of cases. 

Riyadh_1_2012 is likely from a retired 70-year-old male from Riyadh who is reported to have experienced onset on October 5, 2012, was hospitalized on October, 13, 2012 and died on October 23, 2012. He is one of two individuals reported as a family cluster (see Riyadh_2_2012 below).

Riyadh_2_2012 is likely from a 39-year-old male factory worker from Riyadh who is reported to have experienced onset on October 24, 2012, was hospitalized on October 28, 2013 and died on November 2, 2012. He is possibly the son of the individual who represents sample Riyadh_1_2012.

Riyadh_3_2013 seems to be a sample collected in February of 2013 from one of three brothers from Riyadh who were infected with MERS-CoV. All three brothers lived in one large house with 10 other adults. The 51-year-old male was being treated in a Riyadh hospital when he apparently experienced onset from MERS-CoV on February 13, 2013.  He died on February 24, 2013. This cluster of 3 cases is reported in the September issue of the International Journal of Infectious Diseases.[2] Apparently only two household members, two  brothers of the index case, were infected, a 39- year-old and a 40-year-old.  The 39-year-old died on March 2, and the other individual recovered. 

WHO confirmed the 39-year-old in an update published on March 12, 2013.  The 40-year-old was reported by WHO on March 23, 2013 as a recovered individual who had contact with a previous case (his brother[s]).  The 51-year-old male was not reported by WHO until August 28, 2013.  WHO did not identify these three cases as a family cluster. 

Buraidah_1_2013 may possibly be from a 63-year-old male from the city of Buraydah in Al-Qassim Province.  The collection date for this sample is May 13, 2013, however, the man is reported to have been hospitalized on May 15, 2013 and died on May 20, 2013. He is not reported as part of a cluster of cases and no other MERS-CoV cases have been officially reported from Al-Qassim Province in May 2013.   If there are no reporting errors in the collection date or the dates of hospitalization and death, then there is one additional unconfirmed, unaccounted case from Al-Qassim Province. 

Hafr Al-Batin_1_2013 is likely from a 21-year-old male from the town of Hafar Al-Batin, in the Eastern Province. This case was reported in June 2013. He is not reported as part of a cluster of cases.

Al-Hasa Sequences

A large outbreak of MERS-CoV cases occurred in April and May 2013 in the Eastern Province of KSA. [3] At least 24 individuals were confirmed cases and about half of them died. Most of infections occurred in nosocomial settings in the city of Al-Hofuf (also referred as Al-Hasa), although some cases were reported from a regional hospital more than 160 km away. 

Without more details about the sequences it is not possible to associate any Al-Hasa sequence with any specific individual from this outbreak. However, the reported collection dates for the Al-Hasa samples all fall after May 2, 2013. So it is unlikely that any of these sequences are from the 5-6 individuals in the cluster who died before May 2, 2013. 

It is not clear how representative these sequences are for the range of MERS-CoV infections in the KSA. 

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