Rhiza Labs FluTracker Forum

44 sequences from Greece were released at Genbank, including 9 sequences from 2010. Three of the nine had D225G. Three more from 2009 also had D225G.


A/Thessaloniki/206/2010
A/Thessaloniki/225/2010
A/Kavala/219/2010
A/Thessaloniki/2502/2009
A/Kastoria/2636/2009
A/Thessaloniki/2812/2009

_________________
www.twitter.com/hniman

LOCUS CY056299 981 bp cRNA linear VRL 09-MAR-2010
DEFINITION Influenza A virus(A/Thessaloniki/206/2010(H1N1)) segment 4
sequence.
ACCESSION CY056299
VERSION CY056299.1 GI:290775113
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Thessaloniki/206/2010(H1N1))
ORGANISM Influenza A virus (A/Thessaloniki/206/2010(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 981)
AUTHORS Melidou,A., Gioula,G., Exindari,M., Chatzidimitriou,D. and
Malisiovas,N.
TITLE Molecular and phylogenetic analysis of the haemagglutinin gene of
pandemic influenza H1N1 2009 viruses associated with severe and
fatal infections
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 981)
AUTHORS Melidou,A.
TITLE Direct Submission
JOURNAL Submitted (08-MAR-2010) National Influenza Centre for northern
Greece, 2nd Laboratory of Microbiology, Aristotle University of
Thessaloniki, Medical School, Thessaloniki 54124, Greece
FEATURES Location/Qualifiers
source 1..981
/organism="Influenza A virus
(A/Thessaloniki/206/2010(H1N1))"
/mol_type="viral cRNA"
/strain="A/Thessaloniki/206/2010"
/serotype="H1N1"
/isolation_source="pharyngeal swab"
/host="human; gender M; age 1"
/db_xref="taxon:742799"
/segment="4"
/country="Greece: Thessaloniki"
/collection_date="12-Jan-2010"
gene <1..>981
/gene="HA"
CDS <1..>981
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADD62043.1"
/db_xref="GI:290775114"
/translation="DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKL
RGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELR
EQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPK
LSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGTSRYSKKFKPEIAIRP
KVRGQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCN
TTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSR"
mat_peptide 1..981
/gene="HA"
/product="HA1"
ORIGIN
1 gacacattat gtataggtta tcatgcgaac aattcaacag acactgtaga cacagtacta
61 gaaaagaatg taacagtaac acactctgtt aaccttctag aagacaagca taacgggaaa
121 ctatgcaaac taagaggggt agccccattg catttgggta aatgtaacat tgctggctgg
181 atcctgggaa atccagagtg tgaatcactc tccacagcaa gctcatggtc ctacattgtg
241 gaaacatcta gttcagacaa tggaacgtgt tacccaggag atttcatcga ttatgaggag
301 ctaagagagc aattgagctc agtgtcatca tttgaaaggt ttgagatatt ccccaagaca
361 agttcatggc ccaatcatga ctcgaacaaa ggtgtaacgg cagcatgtcc tcatgctgga
421 gcaaaaagct tctacaaaaa tttaatatgg ctagttaaaa aaggaaattc atacccaaag
481 ctcagcaaat cctacattaa tgataaaggg aaagaagtcc tcgtgctatg gggcattcac
541 catccatcta ctagtgctga ccaacaaagt ctctatcaga atgcagatgc atatgttttt
601 gtggggacat caagatacag caagaagttc aagccggaaa tagcaataag acccaaagtg
661 aggggtcaag aagggagaat gaactattac tggacactag tagagccggg agacaaaata
721 acattcgaag caactggaaa tctagtggta ccgagatatg cattcgcaat ggaaagaaat
781 gctggatctg gtattatcat ttcagataca ccagtccacg attgcaatac aacttgtcag
841 acacccaagg gtgctataaa caccagcctc ccatttcaga atatacatcc gatcacaatt
901 ggaaaatgtc caaaatatgt aaaaagcaca aaattgagac tggccacagg attgaggaat
961 gtcccgtcta ttcaatctag a

_________________
www.twitter.com/hniman

Note that title of submissions focuses on severe and fatal cases:

Molecular and phylogenetic analysis of the haemagglutinin gene of
pandemic influenza H1N1 2009 viruses associated with severe and
fatal infections

_________________
www.twitter.com/hniman

LOCUS CY056306 981 bp cRNA linear VRL 09-MAR-2010
DEFINITION Influenza A virus(A/Thessaloniki/225/2010(H1N1)) segment 4
sequence.
ACCESSION CY056306
VERSION CY056306.1 GI:290775127
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Thessaloniki/225/2010(H1N1))
ORGANISM Influenza A virus (A/Thessaloniki/225/2010(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 981)
AUTHORS Melidou,A., Gioula,G., Exindari,M., Chatzidimitriou,D. and
Malisiovas,N.
TITLE Molecular and phylogenetic analysis of the haemagglutinin gene of
pandemic influenza H1N1 2009 viruses associated with severe and
fatal infections
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 981)
AUTHORS Melidou,A.
TITLE Direct Submission
JOURNAL Submitted (08-MAR-2010) National Influenza Centre for northern
Greece, 2nd Laboratory of Microbiology, Aristotle University of
Thessaloniki, Medical School, Thessaloniki 54124, Greece
FEATURES Location/Qualifiers
source 1..981
/organism="Influenza A virus
(A/Thessaloniki/225/2010(H1N1))"
/mol_type="viral cRNA"
/strain="A/Thessaloniki/225/2010"
/serotype="H1N1"
/isolation_source="pharyngeal swab"
/host="human; gender F; age 8"
/db_xref="taxon:742792"
/segment="4"
/country="Greece: Thessaloniki"
/collection_date="13-Jan-2010"
/note="Tamiflu resistant"
gene <1..>981
/gene="HA"
CDS <1..>981
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADD62050.1"
/db_xref="GI:290775128"
/translation="DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKL
RGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELR
EQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPK
LSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGTSRYSKKFKPEIAIRP
KVRGQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCN
TTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSR"
mat_peptide 1..981
/gene="HA"
/product="HA1"
ORIGIN
1 gacacattat gtataggtta tcatgcgaac aattcaacag acactgtaga cacagtacta
61 gaaaagaatg taacagtaac acactctgtt aaccttctag aagacaagca taacgggaaa
121 ctatgcaaac taagaggggt agccccattg catttgggta aatgtaacat tgctggctgg
181 atcctgggaa atccagagtg tgaatcactc tccacagcaa gctcatggtc ctacattgtg
241 gaaacatcta gttcagacaa tggaacgtgt tacccaggag atttcatcga ttatgaggag
301 ctaagagagc aattgagctc agtgtcatca tttgaaaggt ttgagatatt ccccaagaca
361 agttcatggc ccaatcatga ctcgaacaaa ggtgtaacgg cagcatgtcc tcatgctgga
421 gcaaaaagct tctacaaaaa tttaatatgg ctagttaaaa aaggaaattc atacccaaag
481 ctcagcaaat cctacattaa tgataaaggg aaagaagtcc tcgtgctatg gggcattcac
541 catccatcta ctagtgctga ccaacaaagt ctctatcaga atgcagatgc atatgttttt
601 gtggggacat caagatacag caagaagttc aagccggaaa tagcaataag acccaaagtg
661 aggggtcaag aagggagaat gaactattac tggacactag tagagccggg agacaaaata
721 acattcgaag caactggaaa tctagtggta ccgagatatg cattcgcaat ggaaagaaat
781 gctggatctg gtattatcat ttcagataca ccagtccacg attgcaatac aacttgtcag
841 acacccaagg gtgctataaa caccagcctc ccatttcaga atatacatcc gatcacaatt
901 ggaaaatgtc caaaatatgt aaaaagcaca aaattgagac tggccacagg attgaggaat
961 gtcccgtcta ttcaatctag a

_________________
www.twitter.com/hniman

Note that sample above has H274Y (Tamiflu resistant).

_________________
www.twitter.com/hniman

Dr Niman, could you highlight where the mutation, D225G is on the sequence. I am new to this. I usually look at the nucleotide portion, positions 715, 716 and 717 but can't seem to find it. Also when the amino acid part starts with an 'M'.

_________________
Praemonitus, Praemunitus..Forewarned is Forearmed.

These are partial sequences, so the numbering will not match.

_________________
www.twitter.com/hniman

LOCUS CY056304 1045 bp cRNA linear VRL 09-MAR-2010
DEFINITION Influenza A virus(A/Kavala/219/2010(H1N1)) segment 4 sequence.
ACCESSION CY056304
VERSION CY056304.1 GI:290775123
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Kavala/219/2010(H1N1))
ORGANISM Influenza A virus (A/Kavala/219/2010(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1045)
AUTHORS Melidou,A., Gioula,G., Exindari,M., Chatzidimitriou,D. and
Malisiovas,N.
TITLE Molecular and phylogenetic analysis of the haemagglutinin gene of
pandemic influenza H1N1 2009 viruses associated with severe and
fatal infections
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1045)
AUTHORS Melidou,A.
TITLE Direct Submission
JOURNAL Submitted (08-MAR-2010) National Influenza Centre for northern
Greece, 2nd Laboratory of Microbiology, Aristotle University of
Thessaloniki, Medical School, Thessaloniki 54124, Greece
FEATURES Location/Qualifiers
source 1..1045
/organism="Influenza A virus (A/Kavala/219/2010(H1N1))"
/mol_type="viral cRNA"
/strain="A/Kavala/219/2010"
/serotype="H1N1"
/isolation_source="pharyngeal aspirate"
/host="human; gender M; age 25"
/db_xref="taxon:742791"
/segment="4"
/country="Greece: Kavala"
/collection_date="12-Jan-2010"
gene 14..>1045
/gene="HA"
CDS 14..>1045
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADD62048.1"
/db_xref="GI:290775124"
/translation="MEAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVPVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTNADQQSLYQNADAYVFV
GSSRYSKKFKPEIAIRPKVRGQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFHNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSR"
sig_peptide 14..64
/gene="HA"
mat_peptide 65..1045
/gene="HA"
/product="HA1"
ORIGIN
1 aaaagcaaca aaaatggagg caatactagt agttctgcta tatacatttg caaccgcaaa
61 tgcagacaca ttatgtatag gttatcatgc gaacaattca acagacactg tagacacagt
121 actagaaaag aatgtaccag taacacactc tgttaacctt ctagaagaca agcataacgg
181 gaaactatgc aaactaagag gggtagcccc attgcatttg ggtaaatgta acattgctgg
241 ctggatcctg ggaaatccag agtgtgaatc actctccaca gcaagctcat ggtcctacat
301 tgtggaaaca tctagttcag acaatggaac gtgttaccca ggagatttca tcgattatga
361 ggagctaaga gagcaattga gctcagtgtc atcatttgaa aggtttgaga tattccccaa
421 gacaagttca tggcccaatc atgactcgaa caaaggtgta acggcagcat gtcctcatgc
481 tggagcaaaa agcttctaca aaaatttaat atggctagtt aaaaaaggaa attcataccc
541 aaagctcagc aaatcctaca ttaatgataa agggaaagaa gtcctcgtgc tatggggcat
601 tcaccatcca tctactaatg ctgaccaaca aagtctctat cagaatgcag atgcatatgt
661 ttttgtgggg tcatcaagat acagcaagaa gttcaagccg gaaatagcaa taagacccaa
721 agtgaggggt caagaaggga gaatgaacta ttactggaca ctagtagagc cgggagacaa
781 aataacattc gaagcaactg gaaatctagt ggtaccgaga tatgcattcg caatggaaag
841 aaatgctgga tctggtatta tcatttcaga tacaccagtc cacgattgca atacaacttg
901 tcagacaccc aagggtgcta taaacaccag cctcccattt cataatatac atccgatcac
961 aattggaaaa tgtccaaaat atgtaaaaag cacaaaattg agactggcca caggattgag
1021 gaatgtcccg tctattcaat ctaga

_________________
www.twitter.com/hniman

Thanks, why do they not publish the 'whole' sequence?

_________________
Praemonitus, Praemunitus..Forewarned is Forearmed.

Just copy and paste the nucleotide sequence into the BLAST search box

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Select "other" database and when you get the result, chose display with "query anchored and dots for match" and new polymorphisms, including A716G will be obvious.

_________________
www.twitter.com/hniman