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PostPosted: Mon May 12, 2014 6:51 am 
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Release of sequences from six recent cases in Jeddah and Mecca identified 10 polymorphisms that had not been reported previously in any human MERS cases, or had been in a very limited number of sequences. One of the latter polymorphisms is G28941C which lead to changes in two overlapping genes, K60N in ORF8b and D126H the N gene. Previously, this change was found in anal Hasa which appeared late in that outbreak. Although the polymorphisms was in 4 case (AH19, AH26, AH27, AH28), which appeared to be epidemiologically linked based on sample collect dates and sequence data, details on these four cases is largely lacking.

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PostPosted: Mon May 12, 2014 7:03 am 
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The four cases were identified late in the outbreak and were not included in the NEJM paper

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http://www.nejm.org/doi/full/10.1056/NEJMoa1306742

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PostPosted: Mon May 12, 2014 7:09 am 
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AH19 cited as transfer to hospital D but no detail provided and paper silent on AH26, AH27, AH28 even though transmission was discussed.

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Figure 4 Full-size image (105K) Download to PowerPoint


Transmission analysis

Proposed transmission network for all available Al-Hasa MERS-CoV genomes. The light blue nodes show genomes with at least one statistically possible transmission linkage to a known MERS-CoV genome (transmission cases). The coloured nodes in the bottom panel (sporadic cases) are MERS-CoV genomes that cannot be linked by direct transmission to any known MERS-CoV case. Genomes are organised by date of sample collection, and stays in hospital A or D are shown by grey horizontal bars. Red squares show potential transmission, either by shared dialysis session or by direct exposure to a known MERS case. Black arrows show proposed transmission pairs supported by the sequence data, dashed red arrows show proposed transmission pairs not supported by the sequence data. The expected number of differences between each pair of sequences was calculated as the product of the interval between sampling, the evolutionary rate of the virus, and the maximum common length between the two virus genomes. Assuming that the number of differences between two sequences over a length of time is Poisson distributed, with λ equal to the expected number of mutations, the probability of getting the observed number of mutations between the two sequences by chance can be calculated from the cumulative density function of the Poisson distribution. A transmission pair was rejected if the cumulative probability value was less than 0·05. A Bonferroni correction was applied to account for multiple comparisons, resulting in an adjusted significance level of 3·85 × 10−3. ASR=ancestral sequence reconstruction as defined in table 2. MERS-CoV=Middle East respiratory syndrome coronavirus.

http://www.thelancet.com/journals/lance ... 5/fulltext

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PostPosted: Mon May 12, 2014 7:18 am 
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From mBio paper stable 1 listed by collection date

Al-Hasa_19_2013 23 May 2013 1 KF600632
Al-Hasa_18_2013 23 May 2013 1 KF600651
Al-Hasa_21_2013 30 May 2013 1 KF600634
Hafr-Al-Batin_1_2013 4 June 2013 1 KF600628
Taif_1_2013 12 June 2013 1 KJ156949
Wadi-Ad-Dawasir_1_2013 12 June 2013 1 KJ156881
Taif_2_2013 12 June 2013 0.94 KJ156896, KJ156876
Taif_3_2013 13 Jun 2013 0.62 KJ156938, KJ156897, KJ156922, KJ156868, KJ156921, KJ156915,
KJ156906
Taif_4_2013 13 June 2013 0.27 KJ156886, KJ156871
Al-Hasa_26_2013 18 June 2013 0.99 KJ156882, KJ156941, KJ156872
Al-Hasa_27_2013 19 June 2013 0.94 KJ156943, KJ156939
Al-Hasa_28_2013 22 June 2013 0.71 KJ156887, KJ156940, KJ156889, KJ156893, KJ156884, KJ156930,
KJ156928, KJ156909

http://mbio.asm.org/content/5/1/e01062- ... nsion.html

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PostPosted: Mon May 12, 2014 8:04 am 
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AH19 may have been included in this WHO report because hospital D was Aramco and not in Al Hassa and the collection date was May 23. (KSA press release last month indicated 14 MERS cases had been treated at Aramco)
http://www.moh.gov.sa/CoronaNew/PressRe ... 0-002.aspx

29 May 2013 - The Ministry of Health in Saudi Arabia has notified WHO of an additional five laboratory-confirmed cases with Middle East respiratory syndrome coronavirus (MERS-CoV).

All five patients are from the Eastern region of the country, but not from Al-Ahsa, where an outbreak began in a health care facility in April 2013. The patients had underlying medical conditions which required multiple hospital visits. The government is conducting investigations into the likely source of infection in both the health care and the community settings.

The first patient is a 56-year-old man with underlying medical conditions, who became ill on 12 May 2013 and died on 20 May 2013. The second patient is an 85-year-old woman with underling medical conditions who became ill on 17 May and is currently in critical condition. The third patient is a 76-year-old woman with underlying medical conditions who became ill on 24 May 2013 and was discharged from the hospital on 27 May 2013. The fourth patient is a 77-year-old man with underlying medical conditions who became ill on 19 May and died on 26 May 2013. The fifth patient is a 73-year-old man with underlying medical conditions who became ill on 18 May and died on 26 May 2013.

http://www.who.int/csr/don/2013_05_29_ncov/en/

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PostPosted: Mon May 12, 2014 8:07 am 
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AH 26-28 were collected between June 18-22 and may have been among the mild HCW and adolescent case describe by WHO on June 26

26 June 2013 - The Ministry of Health (MoH) in Saudi Arabia has announced seven additional laboratory-confirmed cases and a death in a previously confirmed case of Middle East respiratory syndrome coronavirus (MERS-CoV).

Four cases have been detected among contacts of confirmed cases in Riyadh and the Eastern Region. They range in age from seven to 15 years, and all were asymptomatic. Two further asymptomatic cases have been record among female healthcare workers in the Eastern Region and Al-Ahsa. A seventh case has been detected in a 50 year-old female in the Eastern Region. She is currently hospitalized with pulmonary disease and her condition is considered stable.

In addition, the MoH has announced the death of a previously reported confirmed case from the Eastern Region (the 32 year-old male first reported on 23 June).

http://www.who.int/csr/don/2013_06_26/en/

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PostPosted: Mon May 12, 2014 8:20 am 
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Jeddah_2014_C7149 MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
Jeddah_2014_C7770 MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
Jeddah_2014_C7569 MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
Jeddah_2014_C8826 MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
Jeddah_2014_C9055 MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
Makkah_2014_C9355 MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
KSA-CAMEL-505 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
KSA-CAMEL-378 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
Jeddah_1_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
Al-Hasa_25_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
Taif_3g_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
Bisha_1_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
Taif_1_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
Taif_4b_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
KSA-CAMEL-363 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
KSA-CAMEL-376 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
KSA-CAMEL-503 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMK
Al-Hasa_27b_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMN
Al-Hasa_28h_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMN
Al-Hasa_26c_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMN
Al-Hasa_19_2013 MPIPPLRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLELDPKQHSHSGLLRMASFGSMN
***** ********************************* *******************:

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