genetics > genetics
genbank 2020-04-11
gsgs:
COVID-sequences links :
Nov20,40432+107300+631
https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide
https://www.cogconsortium.uk/data/
https://civnb.info/sequences/
http://www.insdc.org/
https://www.ebi.ac.uk/
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other links :
(https://www.viprbrc.org/brc/home.spg?decorator=vipr).
flu : https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database
releases : 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)
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 : 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 , https://wwwnc.cdc.gov/eid/article/26/6/20-0516_article
China-traveler , symptom-onset = Jan16 , sampled Jan19 , USA-WA , genbank Mar27
https://www.ncbi.nlm.nih.gov/nuccore/MN985325
had already the C27969T mutation
---------------------------------------------
gsgs:
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
----------------------------------
gsgs:
above enumeration is wrong, doesn't consider the first digit {expecting only flu-sequences}
it is corrected now in the mutations below
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 : https://civnb.info/public/charite-SARS-CoV-2.fasta.gz
@c_drosten 2020/04/13/08:06UTC
https://civnb.info/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. https://civnb.info/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})
gsgs:
Wittkowski paper :
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}
gsgs:
[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 }
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