Rhiza Labs FluTracker Forum

The place to discuss the flu
It is currently Thu Oct 19, 2017 2:09 pm

All times are UTC - 5 hours [ DST ]




Post new topic Reply to topic  [ 14 posts ]  Go to page 1, 2  Next
Author Message
PostPosted: Sat May 10, 2014 12:03 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Recently released sequences from cases in Jeddah and Mecca define a novel sub-clade, which has three changes in the ORF8b gene (L6Q, L40P, K60N). ORF8 was disrupted by the 29 nt deletion in the SARS novel sub-clade that spread worldwide after the incident at the Metropole Hotel on February 20/21, 2003.

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 12:10 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
The 29-nucleotide deletion results in the splitting of a single ORF8ab into two overlapping ORFs, ORF8a
and ORF8b. The ORF8ab region encodes for a single protein 8ab of 122 amino acids while ORF8a and ORF8b encode for proteins 8a and 8b of 39 and 84 amino acids, respectively



http://www.hkupasteur.hku.hk/publicatio ... t_2010.pdf

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 12:18 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
8 Polymorphisms Define Novel Jeddah Sub-clade
Nucleotide Protein Camel
ORF1a
C2490T 378
C5658T P1794S 378 505 503 363
T12257C 378 505

ORF1ab
T16174C 505 503

Spike
C23804T 378 505 503
A23953G Q833R

ORF8b
T28778A L6Q
T28880C L40P 378 505
The above 8 polymorphisms are not in any other published human sequence and camel sequences from Taif which share 6 of the 8 in various combinations are indicated above. Two additional polymorphisms, found in either Taif2 or an Al Hafa sub-clade are below.

Taif 2
ORF1ab
C17836T 503 363

AH19 AH26 AH27 AH28
ORF8b/N
G28941C K60N/D126H 378 505

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 12:59 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Latest tree from Andrew Rambaut

Image

http://epidemic.bio.ed.ac.uk/mers-cov_jeddah_outbreak

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 1:21 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
niman wrote:
8 Polymorphisms Define Novel Jeddah Sub-clade
Nucleotide Protein Camel
ORF1a
C2490T 378
C5658T P1794S 378 505 503 363
T12257C 378 505

ORF1ab
T16174C 505 503

Spike
C23804T 378 505 503
A23953G Q833R

ORF8b
T28778A L6Q
T28880C L40P 378 505
The above 8 polymorphisms are not in any other published human sequence and camel sequences from Taif which share 6 of the 8 in various combinations are indicated above. Two additional polymorphisms, found in either Taif2 or an Al Hafa sub-clade are below.

Taif 2
ORF1ab
C17836T 503 363

AH19 AH26 AH27 AH28
ORF8b/N
G28941C K60N/D126H 378 505

Note that novel sub-clade has ORF 8b changes L6Q, L40P, K60N

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 1:27 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
8 Polymorphisms Define Novel Jeddah Sub-clade
Nucleotide Protein Camel
ORF1a
C2490T 378
C5658T P1794S 378 505 503 363
T12257C 378 505

ORF1ab
T16174C 505 503

Spike
C23804T 378 505 503
A23953G Q833R

ORF8b
T28778A L6Q
T28880C L40P 378 505
The above 8 polymorphisms are not in any other published human sequence and camel sequences from Taif which share 6 of the 8 in various combinations are indicated above. Two additional polymorphisms, found in either Taif2 or an Al Hafa sub-clade are below.

Taif 2
ORF1ab
C17836T 503 363

AH19 AH26 AH27 AH28
ORF8b/N
G28941C K60N/D126H 378 505

Note that novel sub-clade has ORF 8b changes L6Q, L40P, K60N

AH29 has K60N

LOCUS AGV08488 112 aa linear VRL 17-SEP-2013
DEFINITION ORF8b [Middle East respiratory syndrome coronavirus].
ACCESSION AGV08488
VERSION AGV08488.1 GI:540362707
DBSOURCE accession KF600632.1
KEYWORDS .
SOURCE Middle East respiratory syndrome coronavirus (MERS-CoV)
ORGANISM Middle East respiratory syndrome coronavirus
Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales;
Coronaviridae; Coronavirinae; Betacoronavirus; unclassified
Betacoronavirus.
REFERENCE 1 (residues 1 to 112)
AUTHORS Cotten,M., Watson,S.J., Palser,A.L., Gall,A., Kellam,P., Zumla,A.
and Memish,Z.A.
TITLE Direct Submission
JOURNAL Submitted (29-AUG-2013) Kingdom of Saudi Arabia, Ministry of
Health, Riyadh 11176, Kingdom of Saudi Arabia
COMMENT Method: conceptual translation.
FEATURES Location/Qualifiers
source 1..112
/organism="Middle East respiratory syndrome coronavirus"
/isolate="Al-Hasa_19_2013"
/host="Homo sapiens"
/db_xref="taxon:1335626"
/country="Saudi Arabia"
/collection_date="23-May-2013"
Protein 1..112
/product="ORF8b"
CDS 1..112
/coded_by="KF600632.1:28753..29091"
ORIGIN
1 mpipplrkml giggdrtekl ipgmelsnwl pggtsttlel dpkqhshsgl lrmasfgsmn
61 maplmllqll grgtltmiql llhnsrpvls flktstlrgl eaivnhlqep la

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 1:35 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
LOCUS AHY22532 112 aa linear VRL 04-MAY-2014
DEFINITION ORF8b [Middle East respiratory syndrome coronavirus].
ACCESSION AHY22532
VERSION AHY22532.1 GI:620988531
DBSOURCE accession KJ713295.1
KEYWORDS .
SOURCE Middle East respiratory syndrome coronavirus (MERS-CoV)
ORGANISM Middle East respiratory syndrome coronavirus
Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales;
Coronaviridae; Coronavirinae; Betacoronavirus; unclassified
Betacoronavirus.
REFERENCE 1 (residues 1 to 112)
AUTHORS Briese,T., Mishra,N., Jain,K., Zalmout,I.S., Jabado,O.J.,
Karesh,W.B., Daszak,P., Mohammed,O.B., Alagaili,A.N. and
Lipkin,W.I.
TITLE Middle East Respiratory Syndrome Coronavirus Quasispecies That
Include Homologues of Human Isolates Revealed through Whole-Genome
Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia
JOURNAL MBio 5 (3) (2014)
PUBMED 24781747
REMARK Publication Status: Online-Only
REFERENCE 2 (residues 1 to 112)
AUTHORS Mishra,N., Briese,T. and Lipkin,W.I.
TITLE Direct Submission
JOURNAL Submitted (15-APR-2014) Mailman School of Public Health, Columbia
University, The Center for Infection and Immunity, 722 West 168
Street 17th Floor, Room 1701, New York, NY 10032, USA
COMMENT Method: conceptual translation.
FEATURES Location/Qualifiers
source 1..112
/organism="Middle East respiratory syndrome coronavirus"
/isolate="KSA-CAMEL-505"
/isolation_source="nasal swab"
/host="Camelus dromedarius"
/db_xref="taxon:1335626"
/country="Saudi Arabia"
/collection_date="Nov-2013"
Protein 1..112
/product="ORF8b"
CDS 1..112
/coded_by="KJ713295.1:28762..29100"
ORIGIN
1 mpipplrkml giggdrtekl ipgmelsnwl pggtsttlep dpkqhshsgl lrmasfgsmn
61 maplmllqll grgtltmiql llhnsrpvls flktstlrgl eaivnhlqep la

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 1:45 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Jeddah_2014_C7149
MPIPPQRKMLGIGGDRTEKLIPGMELSNWLPGGTSTTLEPDPKQHSHSGLLRMASFGSMN
MAPLMLLQLLGRGTLTMIQLLLHNSRPVLSFLKTSTLRGLEAIVNHLQEPLA

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 2:27 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
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
***** ********************************* *******************:

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Sat May 10, 2014 4:11 pm 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
It's NOT only a movie

We have sequenced partial spike protein genes from another 25 viruses, showing 100 percent sequence identity with above-mentioned genomes

http://www.promedmail.org/direct.php?id=2432140

_________________
www.twitter.com/hniman


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 14 posts ]  Go to page 1, 2  Next

All times are UTC - 5 hours [ DST ]


Who is online

Users browsing this forum: Google [Bot], Yahoo [Bot] and 64 guests


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
cron
Powered by phpBB® Forum Software © phpBB Group