MERS-Coronavirus Sequence Acknowledgements

Publicly available sequences

Here is an alignment of 86 publicly available MERS-CoV sequences from humans and camels. The sequence labels should contain enough information to identify each in the list below.

Alignment 86 MERS-CoV Sequences, FASTA format, posted 2014-05-23

Alignment 86 MERS-CoV Sequences, Geneious format, posted 2014-05-23

Alignment 86 MERS-CoV Sequences, coding regions only, FASTA format, posted 2014-05-23

Alignment 86 MERS-CoV Sequences, coding regions only, Geneious format, posted 2014-05-23

FASTA format is compatible with most phylogenetic software. Geneious format is for importing into Geneious 7 and contains gene and CDS annotations for the consensus. For the 'coding regions only' I have adjusted the reading frames, added frame shifts, and removed inter-genic regions so that each gene is in frame.

Sequence Acknowledgements.

This list is not quite up to date. In particular a 2nd batch of sequences from KSA sequenced by The Sanger Institute is missing because I haven't had time to collate the details. 

Name Location Accession Submitting authors/laboratories Date of collection
KSA/EMC KSA JX869059 van Boheemen,S., de Graaf,M., Lauber,C., Bestebroer,T.M., Raj,V.S., Zaki,A.M., Osterhaus,A.D., Haagmans,B.L., Gorbalenya,A.E., Snijder,E.J. and Fouchier,R.A., Viroscience Lab, Erasmus MC 2012-06-13
Qatar/UK England1*

Qatar

KC667074

and

KC164505

Cotten,M.L., Lam,T.T., Watson,S.J., Palser,A.L., Petrova,V., Grant,P., Pybus,O.G., Rambaut,A., Guan,Y., Pillay,D., Kellam,P. and Nastouli,E., Wellcome Trust Sanger Institute

and

Galiano,M., Myers,R., Bermingham,A., Gopal,R. and Zambon,M., Microbiological Services, Health Protection Agency, UK

2012-09-19

and

2012-09-11

England2

KSA

KM015348

Galiano,M., Myers,R., Bermingham,A., Gopal,R. and Zambon,M., Microbiological Services, Health Protection Agency, UK

2013-2-10

Jordan-N3

Jordan

KC776174

Elassal,E.M., Demian,P.N., Defang,G.N., Rozanski,C.H., Curry,J.A., Oyofo,B.A., Al-Sanouri,T.M., Haddadin,A. and Mohareb,E.W., Viral and Zoonotic Diseases Research Program, U.S. Naval Medical Research Unit No. 3, Egypt

between 2012-04-09 and 2012-04-19

Munich/Abu_Dhabi

Abu Dhabi

KF192507

Kallies,R., Corman,V.M. and Drosten,C.,Institute of Virology, University of Bonn Medical Center

2013-03-22

Al-Hasa 1

KSA

KF186567

Cotten,M., Watson,S.J., Palser,A.L., Gall,A., Kellam,P., Zumla,A., Memish,Z.A  and the Kingdom of Saudi Arabia, Ministry of Health, Riyadh 11176, Kingdom of Saudi Arabia

2013-05-09
France 1 UAE/France KF745068 Enouf,V., Briand,D. and van der Werf,S. 2013-05-07
Qatar 3 Qatar KF961221

Galiano,M., Myers,R., Ledesma,J., Lythgow,K., Sadler,C., Omeng-Kumi,N., Ellis,J., Farag,E., Diab,A., Al-Thani,M., Al-Marri,S., Al-Romaihi,H., Al-Khal,A., Al-Dhahiry,S., Al-Hajri,M. and Bermingham,A.

2013-10-13
Qatar 4 Qatar KF961222

Galiano,M., Myers,R., Ledesma,J., Lythgow,K., Sadler,C., Omeng-Kumi,N., Ellis,J., Farag,E., Diab,A., Al-Thani,M., Al-Marri,S., Al-Romaihi,H., Al-Khal,A., Al-Dhahiry,S., Al-Hajri,M. and Bermingham,A.

2013-10-13
C7149, C7569, C7770, C8826, C9055 Jeddah, KSA Institute of Virology, U Bonn Christian Drosten & colleagues 2014-04-03, 05, 07, 12, 14
C9355 Makkah, KSA Institute of Virology, U Bonn Christian Drosten & colleagues 2014-04-15
Indiana/USA-1_Saudi_Arabia_2014 Riyadh, KSA KJ813439 Tao et al, CDC, Atlanta 2014-04-30
Florida/USA-2_Saudi_Arabia_2014 Jeddah, KSA KJ829365 Tao et al, CDC, Atlanta 2014-05-10
Greece/Saudi_Arabia_2014 KSA KJ782549 KJ782550 Tsiodras et al (2014) Eurosurveillance, Volume 19, Issue 16, 24 April 2014 2014-04-18

* This virus has been sequenced twice from isolates from the same patient (the second sequence doesn't have a precise date of collection but presumably was similar to the first).


Batch of sequences published by Cotten,M., Watson,S.J., Palser,A.L., Gall,A., Kellam,P., Zumla,A. and Memish,Z.A. as part of a new study of MERS-CoV diversity in the Kingdom of Saudi Arabia.

Name Location Accession Date of collection
Riyadh_1_2012 KSA KF600612 2012-10-23
Riyadh_3_2013 KSA KF600613 2013-02-05
Al-Hasa_10_2013 KSA KF600614,KF600624,KF600641,KF600642,KF600653 2013-05-02
Al-Hasa_14_2013 KSA KF600615,KF600643 2013-05-08
Al-Hasa_13_2013 KSA KF600616,KF600637,KF600640,KF600650,KF600656 2013-05-07
Al-Hasa_22_2013 KSA KF600617,KF600619,KF600621,KF600625,KF600631,KF600633 2013-05-09
Al-Hasa_8_2013 KSA KF600618,KF600626,KF600635,KF600638 2013-05-01
Bisha_1_2012 KSA KF600620 2012-06-19
Al-Hasa_9_2013 KSA KF600622,KF600639,KF600648,KF600649,KF600654 2013-05-01
Al-Hasa_7_2013 KSA KF600623,KF600655 2013-05-01
Al-Hasa_12_2013 KSA KF600627 2013-05-07
Hafr-Al-Batin_1_2013 KSA KF600628 2013-06-04
Al-Hasa_11_2013 KSA KF600629,KF600636,KF600646 2013-05-03
Buraidah_1_2013 KSA KF600630 2013-05-13
Al-Hasa_19_2013 KSA KF600632 2013-05-23
Al-Hasa_21_2013 KSA KF600634 2013-05-30
Al-Hasa_16_2013 KSA KF600644 2013-05-12
Al-Hasa_15_2013 KSA KF600645 2013-05-11
Al-Hasa_17_2013 KSA KF600647 2013-05-15
Al-Hasa_18_2013 KSA KF600651 2013-05-23
Riyadh_2_2012 KSA KF600652 2012-10-30

A table of dromedary camel virus genomes:

Strain Country Accession Host Date Location
Camel_Egypt_NRCE-HKU205 Egypt KJ477102 Camelus dromedarius 2013-11 Chu et al (2014) Emerging Infect. Dis. 20
Camel_Al-Hasa_KFU_1_2013 Al-Hasa, KSA KJ650295 Camelus dromedarius 2013-11-30 Hemida et al (2014) Emerging Infect. Dis. 20
Jeddah-Camel-1 Jeddah, KSA KF917527 Camelus dromedarius 2013-11-08 Azhar et al (2014)
Qatar_2_2014 Qatar KJ650098 Camelus dromedarius 2014-02-16 Stalin Raj et al (2014) Emerging Infect. Dis.
KSA-CAMEL-376 KSA KJ713299 Camelus dromedarius 2013-11 Briese et al (2014) MBio 5, PMID:24781747
KSA-CAMEL-363 KSA KJ713298 Camelus dromedarius 2013-11 Briese et al (2014) MBio 5, PMID:24781747
KSA-CAMEL-503 KSA KJ713297 Camelus dromedarius 2013-11 Briese et al (2014) MBio 5, PMID:24781747
KSA-CAMEL-378 KSA KJ713296 Camelus dromedarius 2013-11 Briese et al (2014) MBio 5, PMID:24781747
KSA-CAMEL-505 KSA KJ713295 Camelus dromedarius 2013-11 Briese et al (2014) MBio 5, PMID:24781747
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