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PostPosted: Fri Aug 08, 2014 9:04 am 
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Department of Biochemistry/Virology Unit-Central Research Lab., College of Medicine-University of Lagos has released a partial sequence from the fatal case in Lagos ex-Monrovia Liberia.

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PostPosted: Fri Aug 08, 2014 9:05 am 
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LOCUS KM251803 239 bp cRNA linear VRL 01-AUG-2014
DEFINITION Zaire ebolavirus strain LIB/NIG 01072014 RNA-dependent RNA
polymerase (L) gene, partial cds.
ACCESSION KM251803
VERSION KM251803.1 GI:669634858
KEYWORDS .
SOURCE Zaire ebolavirus (ZEBOV)
ORGANISM Zaire ebolavirus
Viruses; ssRNA negative-strand viruses; Mononegavirales;
Filoviridae; Ebolavirus.
REFERENCE 1 (bases 1 to 239)
AUTHORS Omilabu,S. and James,A.
TITLE Detection of Imported Ebola Viral Disease From Liberia to Lagos,
Nigeria in July 2014
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 239)
AUTHORS Omilabu,S.A., James,A.B., Anyanwu,R., Orenolu,O., Salu,M.A.,
Oke,B., Nasidi,A. and Chukwu,O.
TITLE Direct Submission
JOURNAL Submitted (31-JUL-2014) Department of Biochemistry/Virology Unit-
Central Research Lab., College of Medicine-University of Lagos,
Block F, Idi-araba, Surulere, Lagos State 234-100254, Nigeria
COMMENT ##Assembly-Data-START##
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..239
/organism="Zaire ebolavirus"
/mol_type="viral cRNA"
/strain="LIB/NIG 01072014"
/isolation_source="serum"
/host="Homo sapiens"
/db_xref="taxon:186538"
/country="Nigeria: Lagos"
/collection_date="22-Jul-2014"
/note="imported from Liberia"
gene <1..>239
/gene="L"
CDS <1..>239
/gene="L"
/note="Monone_RNA_pol; involved in synthesis of viral RNAs
and transcriptional RNA editing"
/codon_start=1
/product="RNA-dependent RNA polymerase"
/protein_id="AII25372.1"
/db_xref="GI:669634859"
/translation="SLLHQASWHHTSDDFGEHATVRGSSFVTDLEKYNLAFRYEFTAP
FIEYCNRCYGVKNVFNWMHYTIPQCYMHVSDYYNPP"
ORIGIN
1 agcttattgc atcaagcatc atggcaccac acaagtgatg atttcggtga gcatgccaca
61 gttagaggga gtagctttgt aactgattta gagaaataca atcttgcatt taggtatgag
121 tttacagcac cttttataga atattgcaac cgttgctatg gtgttaagaa tgtttttaat
181 tggatgcatt atacaatccc acagtgttat atgcatgtca gtgattatta taatccacc

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PostPosted: Fri Aug 08, 2014 9:09 am 
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Select seq gb|KM251803.1| Zaire ebolavirus strain LIB/NIG 01072014 RNA-dependent RNA polymerase (L) gene, partial cds 432 432 100% 9e-118 100% KM251803.1
Select seq gb|KM233118.1| Zaire ebolavirus strain EBOV_84, partial genome 432 432 100% 9e-118 100% KM233118.1
Select seq gb|KM233117.1| Zaire ebolavirus strain EBOV_83, partial genome 432 432 100% 9e-118 100% KM233117.1
Select seq gb|KM233116.1| Zaire ebolavirus strain EBOV_82, partial genome 432 432 100% 9e-118 100% KM233116.1
Select seq gb|KM233115.1| Zaire ebolavirus strain EBOV_81, partial genome 432 432 100% 9e-118 100% KM233115.1
Select seq gb|KM233114.1| Zaire ebolavirus strain EBOV_80, partial genome 432 432 100% 9e-118 100% KM233114.1
Select seq gb|KM233113.1| Zaire ebolavirus strain EBOV_79, partial genome 432 432 100% 9e-118 100% KM233113.1
Select seq gb|KM233112.1| Zaire ebolavirus strain EBOV_78, partial genome 432 432 100% 9e-118 100% KM233112.1
Select seq gb|KM233111.1| Zaire ebolavirus strain EBOV_77, partial genome 432 432 100% 9e-118 100% KM233111.1
Select seq gb|KM233110.1| Zaire ebolavirus strain EBOV_76, partial genome 432 432 100% 9e-118 100% KM233110.1
Select seq gb|KM233109.1| Zaire ebolavirus strain EBOV_75, partial genome 432 432 100% 9e-118 100% KM233109.1
Select seq gb|KM233107.1| Zaire ebolavirus strain EBOV_73, partial genome 432 432 100% 9e-118 100% KM233107.1
Select seq gb|KM233106.1| Zaire ebolavirus strain EBOV_72, partial genome 432 432 100% 9e-118 100% KM233106.1
Select seq gb|KM233105.1| Zaire ebolavirus strain EBOV_71, partial genome 432 432 100% 9e-118 100% KM233105.1
Select seq gb|KM233104.1| Zaire ebolavirus strain EBOV_70, partial genome 432 432 100% 9e-118 100% KM233104.1
Select seq gb|KM233103.1| Zaire ebolavirus strain EBOV_69, partial genome 432 432 100% 9e-118 100% KM233103.1
Select seq gb|KM233102.1| Zaire ebolavirus strain EBOV_68, partial genome 432 432 100% 9e-118 100% KM233102.1
Select seq gb|KM233101.1| Zaire ebolavirus strain EBOV_67, partial genome 432 432 100% 9e-118 100% KM233101.1
Select seq gb|KM233100.1| Zaire ebolavirus strain EBOV_66, partial genome 432 432 100% 9e-118 100% KM233100.1
Select seq gb|KM233099.1| Zaire ebolavirus strain EBOV_65, partial genome 432 432 100% 9e-118 100% KM233099.1
Select seq gb|KM233098.1| Zaire ebolavirus strain EBOV_64, partial genome 432 432 100% 9e-118 100% KM233098.1
Select seq gb|KM233097.1| Zaire ebolavirus strain EBOV_63, partial genome 432 432 100% 9e-118 100% KM233097.1
Select seq gb|KM233096.1| Zaire ebolavirus strain EBOV_62, partial genome 432 432 100% 9e-118 100% KM233096.1
Select seq gb|KM233095.1| Zaire ebolavirus strain EBOV_61, partial genome 432 432 100% 9e-118 100% KM233095.1
Select seq gb|KM233093.1| Zaire ebolavirus strain EBOV_59, partial genome 432 432 100% 9e-118 100% KM233093.1
Select seq gb|KM233092.1| Zaire ebolavirus strain EBOV_58, partial genome 432 432 100% 9e-118 100% KM233092.1
Select seq gb|KM233091.1| Zaire ebolavirus strain EBOV_57, partial genome 432 432 100% 9e-118 100% KM233091.1
Select seq gb|KM233090.1| Zaire ebolavirus strain EBOV_56, partial genome 432 432 100% 9e-118 100% KM233090.1
Select seq gb|KM233089.1| Zaire ebolavirus strain EBOV_55, partial genome 432 432 100% 9e-118 100% KM233089.1
Select seq gb|KM233088.1| Zaire ebolavirus strain EBOV_54, partial genome 432 432 100% 9e-118 100% KM233088.1
Select seq gb|KM233087.1| Zaire ebolavirus strain EBOV_53, partial genome 432 432 100% 9e-118 100% KM233087.1
Select seq gb|KM233086.1| Zaire ebolavirus strain EBOV_52, partial genome 432 432 100% 9e-118 100% KM233086.1
Select seq gb|KM233085.1| Zaire ebolavirus strain EBOV_51, partial genome 432 432 100% 9e-118 100% KM233085.1
Select seq gb|KM233084.1| Zaire ebolavirus strain EBOV_50, partial genome 432 432 100% 9e-118 100% KM233084.1
Select seq gb|KM233083.1| Zaire ebolavirus strain EBOV_49, partial genome 432 432 100% 9e-118 100% KM233083.1
Select seq gb|KM233082.1| Zaire ebolavirus strain EBOV_48, partial genome 432 432 100% 9e-118 100% KM233082.1
Select seq gb|KM233081.1| Zaire ebolavirus strain EBOV_47, partial genome 432 432 100% 9e-118 100% KM233081.1
Select seq gb|KM233080.1| Zaire ebolavirus strain EBOV_46, partial genome 432 432 100% 9e-118 100% KM233080.1
Select seq gb|KM233079.1| Zaire ebolavirus strain EBOV_45, partial genome 432 432 100% 9e-118 100% KM233079.1
Select seq gb|KM233077.1| Zaire ebolavirus strain EBOV_43, partial genome 432 432 100% 9e-118 100% KM233077.1
Select seq gb|KM233076.1| Zaire ebolavirus strain EBOV_42, partial genome 432 432 100% 9e-118 100% KM233076.1
Select seq gb|KM233075.1| Zaire ebolavirus strain EBOV_41, partial genome 432 432 100% 9e-118 100% KM233075.1
Select seq gb|KM233074.1| Zaire ebolavirus strain EBOV_40, partial genome 432 432 100% 9e-118 100% KM233074.1
Select seq gb|KM233073.1| Zaire ebolavirus strain EBOV_39, partial genome 432 432 100% 9e-118 100% KM233073.1
Select seq gb|KM233072.1| Zaire ebolavirus strain EBOV_38, partial genome 432 432 100% 9e-118 100% KM233072.1
Select seq gb|KM233071.1| Zaire ebolavirus strain EBOV_37, partial genome 432 432 100% 9e-118 100% KM233071.1
Select seq gb|KM233070.1| Zaire ebolavirus strain EBOV_36, partial genome 432 432 100% 9e-118 100% KM233070.1
Select seq gb|KM233069.1| Zaire ebolavirus strain EBOV_35, partial genome 432 432 100% 9e-118 100% KM233069.1
Select seq gb|KM233067.1| Zaire ebolavirus strain EBOV_33, partial genome 432 432 100% 9e-118 100% KM233067.1
Select seq gb|KM233066.1| Zaire ebolavirus strain EBOV_32, partial genome 432 432 100% 9e-118 100% KM233066.1
Select seq gb|KM233065.1| Zaire ebolavirus strain EBOV_31, partial genome 432 432 100% 9e-118 100% KM233065.1
Select seq gb|KM233064.1| Zaire ebolavirus strain EBOV_30, partial genome 432 432 100% 9e-118 100% KM233064.1
Select seq gb|KM233063.1| Zaire ebolavirus strain EBOV_29, partial genome 432 432 100% 9e-118 100% KM233063.1
Select seq gb|KM233062.1| Zaire ebolavirus strain EBOV_28, partial genome 432 432 100% 9e-118 100% KM233062.1
Select seq gb|KM233061.1| Zaire ebolavirus strain EBOV_27, partial genome 432 432 100% 9e-118 100% KM233061.1
Select seq gb|KM233060.1| Zaire ebolavirus strain EBOV_26, partial genome 432 432 100% 9e-118 100% KM233060.1
Select seq gb|KM233059.1| Zaire ebolavirus strain EBOV_25, partial genome 432 432 100% 9e-118 100% KM233059.1
Select seq gb|KM233058.1| Zaire ebolavirus strain EBOV_24, partial genome 432 432 100% 9e-118 100% KM233058.1
Select seq gb|KM233057.1| Zaire ebolavirus strain EBOV_23, partial genome 432 432 100% 9e-118 100% KM233057.1
Select seq gb|KM233056.1| Zaire ebolavirus strain EBOV_22, partial genome 432 432 100% 9e-118 100% KM233056.1
Select seq gb|KM233055.1| Zaire ebolavirus strain EBOV_21, partial genome 432 432 100% 9e-118 100% KM233055.1
Select seq gb|KM233054.1| Zaire ebolavirus strain EBOV_20, partial genome 432 432 100% 9e-118 100% KM233054.1
Select seq gb|KM233053.1| Zaire ebolavirus strain EBOV_19, partial genome 432 432 100% 9e-118 100% KM233053.1
Select seq gb|KM233052.1| Zaire ebolavirus strain EBOV_18, partial genome 432 432 100% 9e-118 100% KM233052.1
Select seq gb|KM233051.1| Zaire ebolavirus strain EBOV_17, partial genome 432 432 100% 9e-118 100% KM233051.1
Select seq gb|KM233050.1| Zaire ebolavirus strain EBOV_16, partial genome 432 432 100% 9e-118 100% KM233050.1
Select seq gb|KM233049.1| Zaire ebolavirus strain EBOV_15, partial genome 432 432 100% 9e-118 100% KM233049.1
Select seq gb|KM233048.1| Zaire ebolavirus strain EBOV_14, partial genome 432 432 100% 9e-118 100% KM233048.1
Select seq gb|KM233047.1| Zaire ebolavirus strain EBOV_13, partial genome 432 432 100% 9e-118 100% KM233047.1
Select seq gb|KM233046.1| Zaire ebolavirus strain EBOV_12, partial genome 432 432 100% 9e-118 100% KM233046.1
Select seq gb|KM233045.1| Zaire ebolavirus strain EBOV_11, partial genome 432 432 100% 9e-118 100% KM233045.1
Select seq gb|KM233044.1| Zaire ebolavirus strain EBOV_10, partial genome 432 432 100% 9e-118 100% KM233044.1
Select seq gb|KM233043.1| Zaire ebolavirus strain EBOV_9, partial genome 432 432 100% 9e-118 100% KM233043.1
Select seq gb|KM233042.1| Zaire ebolavirus strain EBOV_8, partial genome 432 432 100% 9e-118 100% KM233042.1
Select seq gb|KM233041.1| Zaire ebolavirus strain EBOV_7, partial genome 432 432 100% 9e-118 100% KM233041.1
Select seq gb|KM233040.1| Zaire ebolavirus strain EBOV_6, partial genome 432 432 100% 9e-118 100% KM233040.1
Select seq gb|KM233039.1| Zaire ebolavirus strain EBOV_5, partial genome 432 432 100% 9e-118 100% KM233039.1
Select seq gb|KM233038.1| Zaire ebolavirus strain EBOV_4, partial genome 432 432 100% 9e-118 100% KM233038.1
Select seq gb|KM233037.1| Zaire ebolavirus strain EBOV_3, partial genome 432 432 100% 9e-118 100% KM233037.1
Select seq gb|KM233036.1| Zaire ebolavirus strain EBOV_2, partial genome 432 432 100% 9e-118 100% KM233036.1
Select seq gb|KM233035.1| Zaire ebolavirus strain EBOV_1, partial genome 432 432 100% 9e-118 100% KM233035.1
Select seq gb|KM034563.1| Zaire ebolavirus strain G3687-1, partial genome 432 432 100% 9e-118 100% KM034563.1
Select seq gb|KM034562.1| Zaire ebolavirus strain G3686-1, partial genome 432 432 100% 9e-118 100% KM034562.1
Select seq gb|KM034561.1| Zaire ebolavirus strain G3683-1, partial genome 432 432 100% 9e-118 100% KM034561.1
Select seq gb|KM034560.1| Zaire ebolavirus strain G3682-1, partial genome 432 432 100% 9e-118 100% KM034560.1
Select seq gb|KM034559.1| Zaire ebolavirus strain G3680-1, partial genome 432 432 100% 9e-118 100% KM034559.1
Select seq gb|KM034558.1| Zaire ebolavirus strain G3679-1, partial genome 432 432 100% 9e-118 100% KM034558.1
Select seq gb|KM034557.1| Zaire ebolavirus strain G3677-2, partial genome 432 432 100% 9e-118 100% KM034557.1
Select seq gb|KM034556.1| Zaire ebolavirus strain G3677-1, partial genome 432 432 100% 9e-118 100% KM034556.1
Select seq gb|KM034555.1| Zaire ebolavirus strain G3676-2, partial genome 432 432 100% 9e-118 100% KM034555.1
Select seq gb|KM034554.1| Zaire ebolavirus strain G3676-1, partial genome 432 432 100% 9e-118 100% KM034554.1
Select seq gb|KM034553.1| Zaire ebolavirus strain G3670-1, partial genome 432 432 100% 9e-118 100% KM034553.1
Select seq gb|KM034552.1| Zaire ebolavirus strain EM-098, partial genome 432 432 100% 9e-118 100% KM034552.1
Select seq gb|KM034551.1| Zaire ebolavirus strain EM-096, partial genome 432 432 100% 9e-118 100% KM034551.1
Select seq gb|KM034550.1| Zaire ebolavirus strain EM-095, partial genome 432 432 100% 9e-118 100% KM034550.1
Select seq gb|KM034549.1| Zaire ebolavirus strain EM-095B, partial genome 432 432 100% 9e-118 100% KM034549.1
Select seq gb|KJ660348.1| Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Gueckedou-C05, complete genome 432 432 100% 9e-118 100% KJ660348.1
Select seq gb|KJ660347.1| Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Gueckedou-C07, complete genome 432 432 100% 9e-118 100% KJ660347.1
Select seq gb|KJ660346.1| Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Kissidougou-C15, complete genome 432 432 100% 9e-118 100% KJ660346.1
Select seq gb|KC242790.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/5 Luebo, complete genome 423 423 100% 5e-115 99% KC242790.1

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PostPosted: Fri Aug 08, 2014 9:49 am 
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niman wrote:
Select seq gb|KM251803.1| Zaire ebolavirus strain LIB/NIG 01072014 RNA-dependent RNA polymerase (L) gene, partial cds 432 432 100% 9e-118 100% KM251803.1
Select seq gb|KM034549.1| Zaire ebolavirus strain EM-095B, partial genome 432 432 100% 9e-118 100% KM034549.1
Select seq gb|KJ660348.1| Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Gueckedou-C05, complete genome 432 432 100% 9e-118 100% KJ660348.1
Select seq gb|KJ660347.1| Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Gueckedou-C07, complete genome 432 432 100% 9e-118 100% KJ660347.1
Select seq gb|KJ660346.1| Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Kissidougou-C15, complete genome 432 432 100% 9e-118 100% KJ660346.1
Select seq gb|KC242790.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/5 Luebo, complete genome 423 423 100% 5e-115 99% KC242790.1

Note that all 98 sequences at Genbank that are identical to the Lagos index (Patrick Sawyer) are from 2014 collections from Guinea (3 collected in March) or Sierra Leone (95 collected in June).

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PostPosted: Fri Aug 08, 2014 9:56 am 
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niman wrote:
LOCUS KM251803 239 bp cRNA linear VRL 01-AUG-2014
DEFINITION Zaire ebolavirus strain LIB/NIG 01072014 RNA-dependent RNA polymerase (L) gene, partial cds.
AUTHORS Omilabu,S. and James,A.
TITLE Detection of Imported Ebola Viral Disease From Liberia to Lagos, Nigeria in July 2014

/organism="Zaire ebolavirus"
/mol_type="viral cRNA"
/strain="LIB/NIG 01072014"
/isolation_source="serum"
/host="Homo sapiens"
/db_xref="taxon:186538"
/country="Nigeria: Lagos"
/collection_date="22-Jul-2014"
/note="imported from Liberia"

Note that sample was collected on July 22, which is two days after Patrick Sawyer arrived in Lagos.

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PostPosted: Fri Aug 08, 2014 10:02 am 
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Note also that in spite of PCR confirmation at two labs in Nigeria, as well as deposit of the partial sequences at Genbank on July 31, this case has not been listed as confirmed by WHO, in part due to refusal of courier to deliver sample to WHO regional lab in Senegal.

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PostPosted: Fri Aug 08, 2014 10:07 am 
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niman wrote:
Note also that in spite of PCR confirmation at two labs in Nigeria, as well as deposit of the partial sequences at Genbank on July 31, this case has not been listed as confirmed by WHO, in part due to refusal of courier to deliver sample to WHO regional lab in Senegal.

From August 6 WHO update (none of the 9 cases in Nigeria have been confirmed)
New Confirmed Probable Suspect Totals

Nigeria
Cases 5 0 2 7 9
Deaths 0 0 1 0 1

http://www.who.int/csr/don/2014_08_06_ebola/en/

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PostPosted: Fri Aug 08, 2014 10:19 am 
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niman wrote:
Note also that in spite of PCR confirmation at two labs in Nigeria, as well as deposit of the partial sequences at Genbank on July 31, this case has not been listed as confirmed by WHO, in part due to refusal of courier to deliver sample to WHO regional lab in Senegal.

The lab in LUTH under Prof Omilabu received samples on July 22nd and the next day provided results of a pan-FILOVIRUS family diagnosis, that is evidence of presence of a virus belonging to the family of Ebola virus (including Marburg, Ebola-Zaire, Ebola-Sudan Bundibugyo virus, Reston virus, and Taï Forest virus).

Samples were also sent to Prof. Happi’s lab at the Redeemer’s University (RUN), late on July 23. The Happi team worked and tested and confirmed that the virus was the specific Ebola-Zaire type virus early on July 25, 2014. All these happened before confirmation came in from Dakar. I understand the RUN lab will commence sequencing studies pretty soon. My congratulations to our colleagues in LUTH and RUN for a great job.

- See more at: http://www.vanguardngr.com/2014/07/ebol ... S8wmV.dpuf

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PostPosted: Fri Aug 08, 2014 10:24 am 
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niman wrote:
niman wrote:
Note also that in spite of PCR confirmation at two labs in Nigeria, as well as deposit of the partial sequences at Genbank on July 31, this case has not been listed as confirmed by WHO, in part due to refusal of courier to deliver sample to WHO regional lab in Senegal.

The lab in LUTH under Prof Omilabu received samples on July 22nd and the next day provided results of a pan-FILOVIRUS family diagnosis, that is evidence of presence of a virus belonging to the family of Ebola virus (including Marburg, Ebola-Zaire, Ebola-Sudan Bundibugyo virus, Reston virus, and Taï Forest virus).

Samples were also sent to Prof. Happi’s lab at the Redeemer’s University (RUN), late on July 23. The Happi team worked and tested and confirmed that the virus was the specific Ebola-Zaire type virus early on July 25, 2014. All these happened before confirmation came in from Dakar. I understand the RUN lab will commence sequencing studies pretty soon. My congratulations to our colleagues in LUTH and RUN for a great job.

- See more at: http://www.vanguardngr.com/2014/07/ebol ... S8wmV.dpuf

Lagos University Teaching Hospital (LUTH)
http://luthnigeria.org/

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PostPosted: Fri Aug 08, 2014 10:36 am 
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niman wrote:
niman wrote:
Note also that in spite of PCR confirmation at two labs in Nigeria, as well as deposit of the partial sequences at Genbank on July 31, this case has not been listed as confirmed by WHO, in part due to refusal of courier to deliver sample to WHO regional lab in Senegal.

From August 6 WHO update (none of the 9 cases in Nigeria have been confirmed)
New Confirmed Probable Suspect Totals

Nigeria
Cases 5 0 2 7 9
Deaths 0 0 1 0 1

http://www.who.int/csr/don/2014_08_06_ebola/en/


Nigeria
Cases 4 0 7 6 13
Deaths 1 0 2 0 2
http://www.who.int/csr/don/2014_08_08_ebola/en

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