Skip to content

Instantly share code, notes, and snippets.

@jmcastagnetto

jmcastagnetto/README.md

Last active August 21, 2021 23:49
Show Gist options
  • Save jmcastagnetto/15ebcc853d9038f13b04025c1afd4977 to your computer and use it in GitHub Desktop.
Save jmcastagnetto/15ebcc853d9038f13b04025c1afd4977 to your computer and use it in GitHub Desktop.
Download ZIP
Información extra de los linajes de SARS-COV-2 detectados en Perú
Raw
README.md

Usando los datos del "Dataset de Pruebas Moleculares del Instituto Nacional de Salud - INS" al 2021-08-20, y combinando la información con datos de https://cov-lineages.org/lineage_list.html, a continuación se tiene la información extendida de los linajes de SARS-COV-2 en Perú, hasta la fecha.

El campo de frequency tiene el número de registros que mencionan un linaje en particular, y el de result tiene el valor consignado originalmente en el dataset del INS mencionado arriba.

Estructura de datos

name width type
lineage 12 str
frequency 11 int
result 19 str
most_common_countries 20 str
earliest_date 15 str
designated 12 str
assigned 10 str
description 20 str
link 58 str

-- Jesus M. Castagnetto

Raw
sars-cov-2-linajes.csv
lineage frequency result most_common_countries earliest_date designated assigned description link
A.1 1 Linaje A.1 United States of America 82.0%, Australia 8.0%, Canada 6.0%, United Kingdom 1.0%, Iceland 1.0% 2020-02-22 2700 2922 USA lineage https://cov-lineages.org/lineage.html?lineage=A.1
AY.12 15 Linaje AY.12 Denmark 11.0%, United States of America 11.0%, United Kingdom 10.0%, Germany 10.0%, Israel 7.0% 2020-09-07 560 27145 Alias of B.1.617.2.12, Israel lineage, from pango-designation issue #170 https://cov-lineages.org/lineage.html?lineage=AY.12
AY.3.1 2 Linaje AY.3.1 United States of America 100.0%, India 0.0% 2021-05-18 197 1002 Alias of B.1.617.2.3.1, USA lineage, from pango-designation issue #147 https://cov-lineages.org/lineage.html?lineage=AY.3.1
AY.4 4 Linaje AY.4 United Kingdom 67.0%, United States of America 13.0%, Denmark 3.0%, Spain 2.0%, France 2.0% 2021-01-05 34181 154610 Alias of B.1.617.2.4, UK lineage, from pango-designation issue #180 https://cov-lineages.org/lineage.html?lineage=AY.4
AZ.5 1 Linaje AZ.5 Mauritius 96.0%, Canada 2.0%, Philippines 1.0%, South_Africa 1.0% 2021-02-09 166 164 Alias of B.1.1.318.5, Mauritius lineage, from pango-designation issue #171 https://cov-lineages.org/lineage.html?lineage=AZ.5
B.1.1.120 1 Linaje B.1.1.120 United Kingdom 100.0% 2020-06-01 20 30 UK lineage https://cov-lineages.org/lineage.html?lineage=B.1.1.120
B.1.1.208 1 Linaje B.1.1.208 United Kingdom 99.0%, United_Arab_Emirates 1.0% 2020-03-22 45 73 UK https://cov-lineages.org/lineage.html?lineage=B.1.1.208
B.1.1.208 1 Linaje B.1.1.208 United Kingdom 99.0%, United_Arab_Emirates 1.0% 2020-03-22 45 73 UK https://cov-lineages.org/lineage.html?lineage=B.1.1.208
B.1 59 Linaje B.1 United States of America 47.0%, United Kingdom 10.0%, Canada 4.0%, Turkey 3.0%, Germany 3.0% 2020-01-24 46231 73065 A large European lineage the origin of which roughly corresponds to the Northern Italian outbreak early in 2020. https://cov-lineages.org/lineage.html?lineage=B.1
B.1.1 53 Linaje B.1.1 United Kingdom 33.0%, United States of America 13.0%, Japan 9.0%, Germany 4.0%, Turkey 3.0% 2020-02-16 23999 43474 European lineage with 3 clear SNPs `28881GA`,`28882GA`,`28883GC` https://cov-lineages.org/lineage.html?lineage=B.1.1
B.1.1.1 47 Linaje B.1.1.1 United Kingdom 55.0%, Peru 9.0%, Belgium 4.0%, United States of America 3.0%, Germany 2.0% 2020-03-02 1745 2827 England https://cov-lineages.org/lineage.html?lineage=B.1.1.1
B.1.1.166 1 Linaje B.1.1.166 United Kingdom 74.0%, Peru 6.0%, Russia 6.0%, South_Korea 6.0%, Philippines 3.0% 2020-03-15 24 35 UK lineage https://cov-lineages.org/lineage.html?lineage=B.1.1.166
B.1.1.220 1 Linaje B.1.1.220 United Kingdom 47.0%, Japan 19.0%, United States of America 16.0%, Germany 4.0%, Philippines 3.0% 2020-03-23 184 462 UK lineage https://cov-lineages.org/lineage.html?lineage=B.1.1.220
B.1.1.221 1 Linaje B.1.1.221 Belgium 77.0%, Peru 10.0%, Netherlands 2.0%, Japan 2.0%, Brazil 2.0% 2020-03-29 79 91 Belgian lineage https://cov-lineages.org/lineage.html?lineage=B.1.1.221
B.1.1.28 1 Linaje B.1.1.28 Brazil 69.0%, Philippines 15.0%, United States of America 6.0%, Japan 2.0%, Paraguay 1.0% 2020-03-05 854 2553 Brazil mostly, absorbed B.1.1.94 and B.1.1.143 https://cov-lineages.org/lineage.html?lineage=B.1.1.28
B.1.1.317 1 Linaje B.1.1.317 Germany 46.0%, Russia 25.0%, Estonia 5.0%, Finland 4.0%, United States of America 3.0% 2020-02-28 311 2291 Russian lineage https://cov-lineages.org/lineage.html?lineage=B.1.1.317
B.1.1.337 1 Linaje B.1.1.337 United States of America 100.0%, Japan 0.0% 2020-06-27 91 261 US https://cov-lineages.org/lineage.html?lineage=B.1.1.337
B.1.1.348 70 Linaje B.1.1.348 United States of America 40.0%, Chile 24.0%, Peru 15.0%, Colombia 8.0%, Spain 3.0% 2020-04-30 56 1072 South America & USA https://cov-lineages.org/lineage.html?lineage=B.1.1.348
B.1.1.372 1 Linaje B.1.1.372 United Kingdom 89.0%, Russia 3.0%, Switzerland 1.0%, Iceland 1.0%, Germany 1.0% 2020-03-08 876 1273 England https://cov-lineages.org/lineage.html?lineage=B.1.1.372
B.1.1.411 1 Linaje B.1.1.411 United States of America 68.0%, Ecuador 20.0%, Canada 3.0%, United Kingdom 2.0%, Indonesia 2.0% 2020-03-22 20 60 Ecuador and US https://cov-lineages.org/lineage.html?lineage=B.1.1.411
B.1.1.485 3 Linaje B.1.1.485 Ghana 52.0%, Peru 24.0%, Togo 2.0%, Denmark 2.0%, France 2.0% 2020-04-09 22 42 Ghanan Lineage https://cov-lineages.org/lineage.html?lineage=B.1.1.485
B.1.1.506 3 Linaje B.1.1.506 Russia 92.0%, New_Zealand 4.0%, Germany 4.0% 2020-05-14 22 24 Mainly Russian https://cov-lineages.org/lineage.html?lineage=B.1.1.506
B.1.1.7 16 Linaje B.1.1.7 United Kingdom 26.0%, United States of America 20.0%, Germany 10.0%, Denmark 6.0%, Sweden 6.0% 2020-02-07 69835 975650 UK lineage of concern, associated with the N501Y mutation. More information can be found at cov-lineages.org/global_report.html https://cov-lineages.org/lineage.html?lineage=B.1.1.7
B.1.1.89 1 Linaje B.1.1.89 United Kingdom 82.0%, Slovenia 3.0%, Australia 3.0%, Spain 1.0%, United States of America 1.0% 2020-03-12 87 154 England https://cov-lineages.org/lineage.html?lineage=B.1.1.89
B.1.111 1 Linaje B.1.111 United States of America 55.0%, Colombia 22.0%, Spain 3.0%, Canada 3.0%, Trinidad_and_Tobago 3.0% 2020-03-07 169 659 South/ Central American lineage (mostly Trinidad and Colombia, an a small cluster from Norwich) https://cov-lineages.org/lineage.html?lineage=B.1.111
B.1.177 2 Linaje B.1.177 United Kingdom 63.0%, Spain 12.0%, Germany 4.0%, Switzerland 4.0%, Italy 3.0% 2020-02-14 37257 69241 Major mostly European lineage, result of opening borders summer 2020 https://cov-lineages.org/lineage.html?lineage=B.1.177
B.1.177.45 1 Linaje B.1.177.45 Iceland 100.0%, Peru 0.0%, Denmark 0.0%, Spain 0.0%, Lithuania 0.0% 2020-09-12 2460 2483 Iceland https://cov-lineages.org/lineage.html?lineage=B.1.177.45
B.1.2 4 Linaje B.1.2 United States of America 95.0%, Canada 4.0%, Mexico 0.0%, Germany 0.0%, Denmark 0.0% 2020-01-21 21352 92725 USA https://cov-lineages.org/lineage.html?lineage=B.1.2
B.1.205 3 Linaje B.1.205 Peru 98.0%, Israel 2.0% 2020-03-05 28 41 Peruvian https://cov-lineages.org/lineage.html?lineage=B.1.205
B.1.208 3 Linaje B.1.208 France 90.0%, United Kingdom 10.0% 2020-03-15 21 21 French lineage https://cov-lineages.org/lineage.html?lineage=B.1.208
B.1.23 1 Linaje B.1.23 Australia 81.0%, New_Zealand 16.0%, Venezuela 1.0%, United Kingdom 1.0%, Portugal 1.0% 2020-03-18 137 141 New Zealand / Australia https://cov-lineages.org/lineage.html?lineage=B.1.23
B.1.234 1 Linaje B.1.234 United States of America 99.0%, Canada 0.0%, Japan 0.0%, United Kingdom 0.0%, Costa_Rica 0.0% 2020-03-23 1683 6312 USA lineage https://cov-lineages.org/lineage.html?lineage=B.1.234
B.1.243 1 Linaje B.1.243 United States of America 94.0%, Mexico 4.0%, Canada 1.0%, Northern_Mariana_Islands 0.0%, Sweden 0.0% 2020-03-23 4111 12039 USA lineage https://cov-lineages.org/lineage.html?lineage=B.1.243
B.1.429 1 Linaje B.1.429 United States of America 98.0%, Canada 1.0%, Mexico 1.0%, South_Korea 0.0%, Chile 0.0% 2020-04-01 2135 37136 A lineage predominantly circulating in California but with exports to other countries. Characterised by the spike L452R mutation but also has spike:W152C orf1ab:D5584Y and N:T205I. https://cov-lineages.org/lineage.html?lineage=B.1.429
B.1.450 1 Linaje B.1.450 United States of America 97.0%, India 1.0%, Turkey 1.0% 2020-03-14 65 74 USA (TX) https://cov-lineages.org/lineage.html?lineage=B.1.450
B.1.526 8 Linaje B.1.526 United States of America 97.0%, Ecuador 1.0%, Spain 0.0%, Canada 0.0%, Aruba 0.0% 2020-04-21 300 25325 A lineage predominantly circulating in New York but with a few exports to other countries. Characterised by spike mutations T95I and D253G, plus others. The most frequent spike mutation pattern is L5F T95I D253G E484K D614G A701V, with a smaller fraction having S477N instead of E484K. Spike mutation E484K is present in about half of this lineage (as of 2021-02-10) - Very possible not all new additions carry T95I and D253G (someone should check this, e.g. for USA/NY-Wadsworth-21008455-01/2021 and Aruba/AW-RIVM-11403/2021) https://cov-lineages.org/lineage.html?lineage=B.1.526
B.1.575 2 Linaje B.1.575 United States of America 90.0%, Spain 4.0%, Dominican_Republic 2.0%, Bonaire 1.0%, Aruba 1.0% 2020-10-23 1535 2835 USA and Aruba lineage with spike mutations "S:P681H","S:S494P" and "S:T716I". https://cov-lineages.org/lineage.html?lineage=B.1.575
B.1.605 1 Linaje B.1.605 United States of America 79.0%, Turkey 9.0%, Denmark 2.0%, United Kingdom 2.0%, India 2.0% 2020-03-08 33 386 USA lineage https://cov-lineages.org/lineage.html?lineage=B.1.605
B.1.617.2 79 Linaje B.1.617.2 United Kingdom 46.0%, United States of America 21.0%, India 5.0%, Denmark 4.0%, Netherlands 3.0% 2020-09-22 15078 248123 Predominantly India lineage with several spike mutations, pango-designation issue #49 https://cov-lineages.org/lineage.html?lineage=B.1.617.2
B.1.621 50 Linaje B.1.621 United States of America 37.0%, Colombia 13.0%, Mexico 13.0%, Spain 11.0%, Ecuador 6.0% 2021-01-11 13 2220 Lineage predominantly in Colombia with several spike mutations, pango-designation issue #57 https://cov-lineages.org/lineage.html?lineage=B.1.621
B.1.625 1 Linaje B.1.625 United States of America 49.0%, Colombia 33.0%, Germany 7.0%, Mexico 4.0%, Spain 2.0% 2020-11-16 91 243 Predominantly Colombia and USA lineage, from pango-designation issue #93 https://cov-lineages.org/lineage.html?lineage=B.1.625
C.11 15 Linaje C.11 Chile 98.0%, Canada 1.0%, Argentina 1.0% 2020-04-01 64 93 Alias of B.1.1.1.11 https://cov-lineages.org/lineage.html?lineage=C.11
C.11 1 Sublinaje C.11 Chile 98.0%, Canada 1.0%, Argentina 1.0% 2020-04-01 64 93 Alias of B.1.1.1.11 https://cov-lineages.org/lineage.html?lineage=C.11
C.13 2 Linaje C.13 Peru 80.0%, United States of America 17.0%, Japan 3.0% 2020-03-29 19 35 Alias of B.1.1.1.13, Peruvian https://cov-lineages.org/lineage.html?lineage=C.13
C.14 15 Linaje C.14 Peru 92.0%, Japan 2.0%, United States of America 2.0%, Brazil 1.0%, Democratic Republic of the Congo 1.0% 2020-03-20 73 185 Alias of B.1.1.1.14, Peruvian https://cov-lineages.org/lineage.html?lineage=C.14
C.23 1 Linaje C.23 United States of America 90.0%, Pakistan 4.0%, Mexico 2.0%, Peru 2.0%, Denmark 1.0% 2020-05-11 54 160 Alias of B.1.1.1.23, Mainly USA https://cov-lineages.org/lineage.html?lineage=C.23
C.32 2 Linaje C.32 Peru 97.0%, Denmark 3.0% 2020-05-07 15 38 Alias of B.1.1.1.32, Peru https://cov-lineages.org/lineage.html?lineage=C.32
C.33 5 Linaje C.33 Peru 88.0%, Japan 6.0%, United States of America 6.0% 2020-05-18 7 16 Alias of B.1.1.1.33, Peru https://cov-lineages.org/lineage.html?lineage=C.33
C.36 1 Linaje C.36 Egypt 33.0%, Germany 12.0%, United Kingdom 11.0%, United States of America 8.0%, Denmark 7.0% 2020-03-13 221 963 Alias of B.1.1.1.36, Egypt mainly and other countries https://cov-lineages.org/lineage.html?lineage=C.36
C.36 1 Sublinaje C.36 Egypt 33.0%, Germany 12.0%, United Kingdom 11.0%, United States of America 8.0%, Denmark 7.0% 2020-03-13 221 963 Alias of B.1.1.1.36, Egypt mainly and other countries https://cov-lineages.org/lineage.html?lineage=C.36
C.36.3 1 Linaje C.36.3 Germany 21.0%, United States of America 17.0%, Switzerland 10.0%, United Kingdom 8.0%, Italy 7.0% 2021-01-06 494 1476 Alias of B.1.1.1.36.3, Europe and USA lineage, from pango-designation issue #80 https://cov-lineages.org/lineage.html?lineage=C.36.3
C.37 2994 Linaje C.37 Chile 34.0%, Peru 28.0%, United States of America 18.0%, Mexico 4.0%, Ecuador 4.0% 2020-11-08 370 4150 Alias of B.1.1.1.37, lineage in Peru, Chile, USA and Germany, from pango-designation issue #52 https://cov-lineages.org/lineage.html?lineage=C.37
C.37 22 Sublinaje C.37 Chile 34.0%, Peru 28.0%, United States of America 18.0%, Mexico 4.0%, Ecuador 4.0% 2020-11-08 370 4150 Alias of B.1.1.1.37, lineage in Peru, Chile, USA and Germany, from pango-designation issue #52 https://cov-lineages.org/lineage.html?lineage=C.37
C.37.1 6 Linaje C.37.1 United States of America 26.0%, Peru 20.0%, Spain 12.0%, Germany 8.0%, Switzerland 7.0% 2021-02-19 106 217 Alias of B.1.1.1.37.1, lineage outside of South America, from pango-designation issue #158 https://cov-lineages.org/lineage.html?lineage=C.37.1
C.4 12 Linaje C.4 Peru 93.0%, Turkey 2.0%, United States of America 2.0%, Republic of Serbia 1.0%, Switzerland 1.0% 2020-05-19 24 84 Alias of B.1.1.1.4, Peruvian https://cov-lineages.org/lineage.html?lineage=C.4
N.4 1 Linaje N.4 Chile 94.0%, Brazil 3.0%, Peru 1.0%, United States of America 1.0%, New_Zealand 0.0% 2020-03-25 123 232 Alias of B.1.1.33.4, Chilean https://cov-lineages.org/lineage.html?lineage=N.4
P.1 832 Linaje P.1 United States of America 37.0%, Brazil 30.0%, Canada 9.0%, Chile 5.0%, Mexico 4.0% 2020-04-07 271 54867 Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutaions with likely functional significance E484K, K417T, and N501Y. Described in https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586. https://cov-lineages.org/lineage.html?lineage=P.1
P.1 3 Sublinaje P.1 United States of America 37.0%, Brazil 30.0%, Canada 9.0%, Chile 5.0%, Mexico 4.0% 2020-04-07 271 54867 Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutaions with likely functional significance E484K, K417T, and N501Y. Described in https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586. https://cov-lineages.org/lineage.html?lineage=P.1
P.1.1 5 Linaje P.1.1 Italy 36.0%, United States of America 28.0%, Germany 8.0%, Mexico 4.0%, Brazil 4.0% 2021-01-07 108 4240 Alias of B.1.1.28.1.1, European lineage in Italy and Germany https://cov-lineages.org/lineage.html?lineage=P.1.1
P.1.4 22 Linaje P.1.4 Brazil 89.0%, Switzerland 5.0%, Chile 2.0%, United States of America 1.0%, Peru 1.0% 2021-03-19 93 328 Alias of B.1.1.28.1.4, Brazil lineage, from pango-designation issue #141 https://cov-lineages.org/lineage.html?lineage=P.1.4
P.1.7 32 Linaje P.1.7 Brazil 50.0%, Italy 28.0%, United States of America 6.0%, Spain 5.0%, Chile 4.0% 2020-11-07 272 1041 Alias of B.1.1.28.1.7, Brazil lineage, from pango-designation issue #141 https://cov-lineages.org/lineage.html?lineage=P.1.7
P.2 1 Linaje P.2 Brazil 55.0%, United States of America 27.0%, Canada 4.0%, Suriname 2.0%, Argentina 2.0% 2020-04-13 424 4460 Alias of B.1.1.28.2, Brazilian lineage https://cov-lineages.org/lineage.html?lineage=P.2
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment