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#Post#: 217--------------------------------------------------
genbank 2020-04-11
By: gsgs Date: April 11, 2020, 8:50 am
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COVID-sequences links :
Nov20,40432+107300+631
HTML https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide
HTML https://www.cogconsortium.uk/data/
HTML https://civnb.inf
o/sequences/
HTML http://www.insdc.org/
HTML https://www.ebi.ac.uk/
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---------------
other links :
(
HTML https://www.viprbrc.org/brc/home.spg?decorator=vipr).
flu :
HTML https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database
releases :
HTML https://ftp.ncbi.nih.gov/genbank/gbrel.txt
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582 COVID-19 sequences (507 of these full genome) downloaded on
Apr11 from :
[615 on Apr12)
(876 on Apr14 , 795 full)+102 full German ones from
Drosten-tweet s.u.
(1207 on Apr21)
HTML https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide
386 from USA , (earliest from Jan19, IL-Jan21,CA-Jan22,WA-Jan25
94 from China , (66 full , earliest from Dec.23
25 from Spain (earliest Feb26 ,
17 from Iran , (2 full, earliest Mar09
6 from Italy , (1 full, Jan30
...
dates = symptom-onset ?
mutation-picture :
HTML http://magictour.free.fr/sars2-4.GIF
rows are viruses , columns are RNA-nucleotide-positions , black
pixels are mutations
horizontally and vertically sorted so to give maximum black
connected components
community-spread in Washington State since at least Jan19,
one day before Zhong Nanshang raised the alarm on Chinese TV
and 4 days before Wuhan lockdown !
Jan19 was sample-collection, sequence-release date was Mar26
another sequence from WA , Jan25, release date Feb05
also already with that C27969T (my current enumeration) -
mutation typical for WA
MN985325 ,
HTML https://wwwnc.cdc.gov/eid/article/26/6/20-0516_article
China-traveler , symptom-onset = Jan16 , sampled Jan19 , USA-WA
, genbank Mar27
HTML https://www.ncbi.nlm.nih.gov/nuccore/MN985325
had already the C27969T mutation
---------------------------------------------
#Post#: 218--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: April 11, 2020, 11:30 pm
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earliest outside China :
MN970003 MN970003 2020-01-23 290 Thailand lung, oronasopharynx
2020-01-08
MT072688 MT072688 2020-02-18 29811 Nepal oronasopharynx
2020-01-13
MN970004 MN970004 2020-01-23 290 Thailand lung, oronasopharynx
2020-01-13
MN985325 MN985325 2020-01-24 29882 USA oronasopharynx 2020-01-19
MT233526 MT233526 2020-03-26 29847 USA: WA oronasopharynx
2020-01-19
MT246667 MT246667 2020-03-26 29867 USA: WA oronasopharynx
2020-01-19
MN988713 MN988713 2020-01-25 29882 USA: Illinois lung,
oronasopharynx 2020-01-21
MN997409 MN997409 2020-01-28 29882 USA: AZ feces 2020-01-22
MN994468 MN994468 2020-01-28 29883 USA: CA oronasopharynx
2020-01-22
MN994467 MN994467 2020-01-28 29882 USA: CA oronasopharynx
2020-01-23
MT007544 MT007544 2020-01-31 29893 Australia: Victoria
2020-01-25
MT192772 MT192772 2020-03-16 29891 Viet Nam: Ho Chi Minh city
2020-01-22
MT192773 MT192773 2020-03-16 29890 Viet Nam: Ho Chi Minh city
2020-01-22
LC523809 LC523809 2020-02-13 357 Philippines 2020-01-23
MT066159 MT066159 2020-02-14 290 Malaysia oronasopharynx
2020-01-24
MT066157 MT066157 2020-02-14 290 Malaysia oronasopharynx
2020-01-24
MT066158 MT066158 2020-02-14 290 Malaysia oronasopharynx
2020-01-24
MT192759 MT192759 2020-03-16 29862 Taiwan lung, oronasopharynx
2020-01-25
MT020881 MT020881 2020-02-05 29882 USA: WA oronasopharynx
2020-01-25
MT020880 MT020880 2020-02-05 29882 USA: WA oronasopharynx
2020-01-25
LC523808 LC523808 2020-02-13 357 Philippines 2020-01-26
LC522350 LC522350 2020-02-08 182 Philippines 2020-01-26
MT044258 MT044258 2020-02-12 29858 USA: CA oronasopharynx
2020-01-27
MT012098 MT012098 2020-03-06 29854 India: Kerala State
oronasopharynx 2020-01-27
MT044257 MT044257 2020-02-12 29882 USA: IL lung, oronasopharynx
2020-01-28
MT039888 MT039888 2020-02-11 29882 USA: MA oronasopharynx
2020-01-29
MT027062 MT027062 2020-02-07 29882 USA: CA oronasopharynx
2020-01-29
MT027063 MT027063 2020-02-07 29882 USA: CA oronasopharynx
2020-01-29
MT027064 MT027064 2020-02-07 29882 USA: CA oronasopharynx
2020-01-29
MT020781 MT020781 2020-02-05 29806 Finland 2020-01-29
MT066156 MT066156 2020-03-09 29867 Italy lung, oronasopharynx
2020-01-30
MT050493 MT050493 2020-03-06 29851 India: Kerala State
oronasopharynx 2020-01-31
MT066175 MT066175 2020-02-14 29870 Taiwan 2020-01-31
MT039887 MT039887 2020-02-11 29879 USA: WI oronasopharynx
2020-01-31
MT008023 MT008023 2020-01-31 322 Italy: Rome oronasopharynx
2020-01
MT008022 MT008022 2020-01-31 322 Italy: Rome oronasopharynx
2020-01
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#Post#: 219--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: April 13, 2020, 1:14 am
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above enumeration is wrong, doesn't consider the first digit
{expecting only flu-sequences}
it is corrected now in the mutations below
[img]
HTML http://magictour.free.fr/sars2-4.GIF[/img]
most genomes are from 2 Washington-strains
WA2,101 genomes , 4+2+1 mutations
C00150T{Spain},C02946T{Spain},C14317T{Spain},A23312G{Spain} ,
{RI-Feb28}
G25472T{CA-Feb29} , C00968T{CA-Feb29} ,
(G29462A{WA-Mar13})
WA1,169 genomes , 2+1+2 mutations
C08691T{China},T28053C{China}, {Wuhan,Dec26}
C17969T{WA-Jan19},
C17656T{Mar-WA},A17767G{Mar-WA} {Iran-Feb26}
we had 2 clearly distinguished strains already in Wuhan, Dec.26
.
Once is the predecessor of WA1 and one is the predecessor of WA2
plusminus some contant , the first and last part of the
sequences (~100 nucleotides)
are skipped because they often contain mutations supposed to be
sequencing errors
18 genomes that didn't easily align because of insertions or
deletions were excluded
there was 1 genome from France, it had a 3bp deletion , none
from Germany
----------------------------------------------------
102 German sequences :
HTML https://civnb.inf
o/public/charite-SARS-CoV-2.fasta.gz
@c_drosten 2020/04/13/08:06UTC
HTML https://civnb.inf
o/sequences/
An overview of #SARS-CoV-2 genome sequences from Germany,
including early releases by
@charitevirology. Some interesting insights into local
clustering and wider dispersal, for
people familiar with German geography.
HTML https://civnb.inf
o/sequences/
102>7+4+87 , >3 different strains
most have C241T,C3037T,A23403G and most of these also have
C14408T
this is WA2 above (add 91)
the one from Jan28 has C241T,C3037T, and A23403G
I assume that was the Webasto-introduction. The whole WA2 and
Spain and maybe Italy, France
seems to have descended from it ! (after C14317 was developed in
Germany)
WA2,101 genomes , 4+2+1 mutations
C00150T{Spain},C02946T{Spain},C14317T{Spain},A23312G{Spain} ,
{RI-Feb28}
G25472T{CA-Feb29} , C00968T{CA-Feb29} ,
(G29462A{WA-Mar13})
#Post#: 222--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: April 13, 2020, 11:57 pm
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Wittkowski paper :
HTML https://www.medrxiv.org/content/10.1101/2020.03.28.20036715v2.full.pdf
> The epidemiological data does not support the hypothesis that
SARS-CoV-2 spread from Munich
> in Germany to Italy.(Kupferschmidt 2020)
> Instead, the virus may have spread from Italy to its
neighboring
> countries, Switzerland, France, Spain, Austria, and Slovenia,
within just a few days
> of arriving from Iran.
there is one partial sequence from Qum, Feb09, at genbank and it
has not the T28688C mutation
which have the sequences from Tehran
Iran sequences seem to have a 6bp insertion at position 14606
Iran1,C08782T,C17753T,A17864G,C18066T,T28150C
Iran2,G01397A,G11083T, TCCTTA-insertion at 14606 ,
C8383T,G9380A,G9748T {Mar09}
WA1,169 genomes , 2+1+2 mutations [add 91 to all positions]
C08691T{China},T28053C{China}, {Wuhan,Dec26}
C17969T{WA-Jan19},
C17656T{Mar-WA},A17767G{Mar-WA} {Iran-Feb26}
#Post#: 223--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: April 14, 2020, 9:26 pm
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[add 91 ?!]
Wuhan1, Dec.26
-
Wuhan2
C08691T{China},T28053C{China}, {Wuhan,Dec26}
WA1,169 genomes , 2+1+2 mutations
C08691T{China},T28053C{China}, {Wuhan,Dec26}
C17969T{WA-Jan19},
C17656T{Mar-WA},A17767G{Mar-WA} {Iran-Feb26}
WA2,101 genomes , 4+2+1 mutations
C00150T{Spain},C02946T{Spain},C14317T{Spain},A23312G{Spain} ,
{RI-Feb28}
G25472T{CA-Feb29} , C00968T{CA-Feb29} ,
(G29462A{WA-Mar13})
Webasto,
C241T,C3037T,A23403G { C14408T }
#Post#: 227--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: April 23, 2020, 9:15 pm
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2020/04/23 , 1432 sequences in total
many (>100) sequences from NY today
Hong Kong , collected in Jan
#Post#: 232--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: April 27, 2020, 9:26 pm
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2020/04/28 , 10567 genomes from UK :
HTML https://www.cogconsortium.uk/data/
2020/05/22 , the total number of sequences is 16380
2020/09/03 , 48561 sequences
#Post#: 234--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: May 14, 2020, 9:28 pm
---------------------------------------------------------
2020/05/15 , 3812 genomes , 3415 of these are easily aligned
(no insertions or deletions) , full size
2049 (=60%) of these have C241T
2088 have C3037T
2114 have C14408T
2113 have A24403G
------------------------------
1434 have G25563T
1234 have C1059T
2126 from USA
81 from France
69 from China
809 from Australia:Victoria
91 from Greece:Athens
38 from India:Ahmedabad
23 from Thailand
21 from Taiwan
20 from HongKong
18 from India
12 from PuertoRico
(German and UK sequences see above )
why so many C-->T
#Post#: 255--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: September 28, 2020, 8:52 pm
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2020/09/28
24923 COVID-19 sequences at genbank (was 16438 on 2020/08/18),
file sars2-19
24185 complete ones (>29400 nucleotides)
22,208,199,355,6040,5033,2561,2869,4494,639,219 with collection
months 2019/12,...,2020/09
USA:14091,AUS:5562,IND:570,EGY:233,BGD:231,THA:227,CHN:195,IRN:1
01,GRC:98,GER:92,
PER:89,FRA:89,JPN:84,IRQ:76,MEX:66,ITA:60,SAU:58,TUR:57,SPA:48,G
HA:46
USA:WA=3455,CA=1953,FL=1520,WI=1340,VA=903,MA=876,MI=493,NY=318
human:22574,mink:13,mink:12,5:cat,2:dog,tiger:1
onp:6269,saliva:54,swab:310,saliva/onp:54,lung/oronasopharynx:49
,lung:28,blood:3,feces:4,
1:onp/onp,1:placenta,1:urine
#Post#: 258--------------------------------------------------
Re: genbank 04/11
By: gsgs Date: October 28, 2020, 9:19 pm
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2020/10/29 , 36846 sequences
----------------------------------------
Charite has 544 German sequences now,
36 from October , all with the D614G mutation
HTML https://civnb.inf
o/sequences/
the most frequent mutations from October are :
36,C3037T,C241T,C14408T,A23403G
14,G28883C,14,G28882A,14,G28881A
10,G21255C
9,T445C
9,G29645T
9,G25563T
9,C6286T
9,C28932T
9,C22227T
8,G27870T
8,C6040T
8,C27944T
8,C26801T
8,C21614T
7,C28854T
27 (10 from October) are the new Spanish strain "20A.EU1"
from this paper :
HTML https://www.medrxiv.org/content/10.1...063v1.full.pdf
mutation picture :
HTML http://magictour.free.fr/sars2de5.GIF
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