https://www.researchgate.net/publication/350965128_Selenium_to_selenoproteins_-_role_in_COVID-19
https://ars.els-cdn.com/content/image/1-s2.0-S2451945620301094-gr2.jpg
söndag 31 juli 2022
Sars-2 koronaviruksen pakkaussignaalin terapeuttinen hyödyntäminen lie vielä tulevaisuuden terapiakeinoja
Viruksen pakkaussignaalin terapeuttinen hyödyntäminen näyttää olevan vielä tulevaisuuden asia. 31.7. 2022 koronavirusten suhteen.
Monilla koronaviruksilla on tunnistetavissa olevat pakkaussignaalit. Sen sijaan Sars-1 ja sars-3 virusten suhteen asia ei oel niin selkeä. Arvellaan, että nsp15 omaisi jotain pakkaussignaaliominaisuutta, ja sitä on koetettu hydyntää mandollisella terapeuttisella strategialla , joka on utkimusvaiheessaan ja riskien pohdintavaiheessa.
https://peerj.com/articles/11686/
Koronavirusten RNA:n pakkauksesta on artikkeli vuodelta 2019 Virologian nettilinkeissä.
LÄHDE: https://www.sciencedirect.com/science/article/pii/S0042682219302569
MPXV Poxvirus leviää vähitellen
https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON393
https://cdn.who.int/media/images/default-source/emergencies/disease-outbreak-news/20220617_table_mpx_multicountry.jpg?sfvrsn=bd8624c7_1
fredag 29 juli 2022
Etelä-Amerikan viimevuotinen Sars-Cov-2viruksen Mu variantti ehti saada kaksi alalinjaa ja yhden sub-alalinjan ( BB.2)
Huomaan vasta tänään Permalink-luettelosta, että MU-variantti (B.1.621) sai
viime vuonna alalinjallensa B.1.621.1 vielä kaksi sub-alalinjaa. Mu
variantin alalinja B.1.621.1 merkattiin "BB" koodilla ja sitten sen alalinjat saivat
virstanpylväät BB.1 ja BB.2 ennen joulua 2021 , jolloin
delta-aalto (B.1.617.2, "AY") alkoi osoittaa saaneensa jo selvää vastustusta. Omikronin (BA.1.1.529, "BA")vaikutus ilmeni vasta hieman myöhemmin- vuodenvaihteessa varsinkin - ja tässä lokakuun marraskuun vaihteessa ei
vielä ollut kovin paljon käsitystä omikronin valtakauden
alkamisesta. Otan sitaatin Mu-variantin sub-alaryhmien
virstanpylvään asettamisesta 17.12. 2021. Huomaa tammikuinen varianttilinjan tarkistus tekstin lopussa. Otan sitaatin päivä päivältä, koska silloin tätä GITHUB aisaa on helpompi käsittää.
(MU variantti
BA.1.621 sai yhden alalinjan ja se merkitään BB, sillä sille
tuli alkuhahmottelussa kaksi sub-alalinjaa: BB.1 ja BB.2. Nämä on merkattu jo varhain ja GITHUB asiasta #232 on tässä muutamia sitaatteja viime vuodelta). Tarkennuksista mainittu loppuyhteenvedossa.
GITHUB pohdinnan alku: lokakuun alussa 1.10.2021.
Two potential sublineages of B.1.621.1, one with Spike Y449N and E583D, the other with Spike S939F #232
Closedc1985.... opened this issue on 1 Oct 2021 · 11 comments
Comments
c1985...commented on 1 Oct 2021
Proposed sublineage 1 Proposed sublineage 2 |
Andreiil mentioned this issue on 31 Oct 2021
Proposal for a new sublineage of MU with S: 449N + S:583D that seems to resist better than others to Delta Expansion #299
A new GISAID upload just came from Colombia. It continues to look like the issue in #299 is real, and S:E583D+S:Y449N continues to expand even as the rest of Mu is close to extinction
FedeGueli commented on 31 Oct 2021
As cited in #299 there is an interesting thread on twitter on sublineage 1 by Ricardo Rivero |
MCB6 commented on 2 Nov 2021
A new GISAID upload just came from Colombia. It continues to look like the issue in #299 is real, and S:E583D+S:Y449N continues to expand even as the rest of Mu is close to extinction |
RicardoRH96 commented on 2 Nov 2021
A new GISAID upload just came from Colombia. It continues to look like the issue in #299 is real, and S:E583D+S:Y449N continues to expand even as the rest of Mu is close to extinction |
It is necessary to keep an eye on this lineage, hope it gets designated soon.
Corneliusroemer commented on 2 Nov 2021
It looks interesting, yes, because it seems to be able to almost compete with Delta - but only in Colombia, not Chile. Colombia doesn't sequence much so the uncertainty is huge. But it does seem to have staying powers which is very interesting. |
MCB6 commented on 2 Nov 2021
Colombia doesn't sequence much so the uncertainty is huge. That's why I got excited today when they nearly doubled the number of last two month's sequences. I don't think it's visible at covSpectrum yet. But still with the grand total of 5 sequences in October, it's too uncertain, and regional variation may obscure any real trends. In Chile it see to be highly regional too, like Atacama in the North? |
MCB6 , you could search on CovSpectrum just the mutations.
https://cov-spectrum.ethz.ch/explore/South%20America/AllSamples/Past3M/variants?aaMutations=S%3A449N%2CS%3A583D
And one can click on Chile's regions to realize that at one point,
this Mu variety accounted for almost all of Atacama's sequences. But
apparently not anymore. The strain dynamics in this region has
several weirdly quick sweeps. Before mid-August it was Chile's usual
Gamma / Lambda mix. Then Mu arrived and in just one months achieved
total dominance (mostly, but not only, this substrain). Then Delta
arrived and in another month the sweep was complete, with the classic
Mu going away first, and the Mu+S:449N+S583D holding for only a
little bit longer.
The number of cases in Atacama has been quite
low during all this era of sweeps, mostly in single digits daily, so
we may be dealing with founder outbreaks rather than with true strain
competition? Which might explain the unrealistically fast changes?
MCB6 commented on 14 Nov 2021
Mu+S:449N+S583D was also in Lima, Peru in early August, seems to have disappeared by mid-September. 10 samples from Peru (they only started extensive sequencing in recent weeks, added over 3,000 genomes so far). Colombia added more October samples today. Mu+S:449N+S583D still accounts for ~10% of the recently collected samples (8 / 85 samples) |
InfrPopGen self-assigned this on 21 Nov 2021
MCB6 commented on 21 Nov 2021
Another batch from Colombia uploaded, including some late-October samples. The slight expansion trend of Mu+Spike_E583D,Spike_Y449N is holding well. In contrast, other varieties of Mu are nearly extinct. |
InfrPopGen pushed a commit to InfrPopGen/pango-designation that referenced this issue on 17 Dec 2021
Added
new lineages BB.1 and BB.2 from cov-lineages#232
with
91 and 23…
InfrPopGen added the designated label on 17 Dec 2021
InfrPopGen commented on 17 Dec 2021
Thanks for submitting. We've added proposal 1 as lineage BB.1 with 91 designated sequences in v1.2.113 and proposal 2 as lineage BB.2 with 238 designated sequences in v1.2.113 |
chrisruis added a commit that referenced this issue on 17 Dec 2021
Merge
pull request #372
from
InfrPopGen/master
chrisruis added this to the BB.1 BB.2 milestone on 17 Dec 2021
----------------------
Kommentti: Mitä CovLineages mainitsevat sen jälkeen näistä varianteista? Tarkistan:
| B.1.621 | United States of America 39.0%, Colombia 26.0%, Chile 9.0%, Ecuador 5.0%, Spain 4.0% | 2020-12-15 | 13; | 11266 | Lineage predominantly in Colombia with several spike mutations, pango-designation issue #57 | Mu |
| B.1.621.1 | United States of America 64.0%, Spain 9.0%, Dominican_Republic 6.0%, Colombia 3.0%, Austria 2.0% | 2021-04-09 | 97; | 1938 | Lineage in multiple countries, pango-designation issue #115 | |
| B.1.621.2 | Colombia 64.0%, Chile 18.0%, United States of America 10.0%, Peru 4.0%, Canada 2.0% | 2021-04-11 | 91; | 691 | Lineage in multiple countries, from pango-designation issue #232 |
| BB.2 | United States of America 97.0%, Dominican_Republic 1.0%, Canada 1.0%, France 1.0%, Spain 0.0% | 2021-05-19 | 238, | 358 | Alias of B.1.621.1.2, from pango-designation issue #232 |
(Kommenttini: Huomaan tammikuulta 2022 merkinnän):
chrisruis commented on 7 Jan
Tärkeä permalink niistä sars-2 varianttidefinitioista, joilla on erityinen koodilyhennys olemassa. Myös rekombinaattien nimet ovat listassa
Aktuelli permalinkki: Nämä koodit ovat olennaisia niille, jotka haluavat seurata viruksen evoluutiotilannetta ja "pysyä kärryillä" koodinimien merkityksestä. Jokaisella VOC variantilla ei ole ollut tarvetta lyhennyskoodille, kuten beeta (VOC) variantilla ( B.1.351, jonka alalinjakirjo jäi kohtalaisen helpoksi käsitellä.mutta esim. delta (AY) ja omikron(BA) ovat hyvin runsaasti versonneet. Tällä hetkellä omikron poimii rekombinaateissaan esiin jopa joitain aiempiakin sekvenssejä, joita selvitellään. Sentakia on hyvä muistutella PANGO-listan muitakin koodeja ja systematiikkaa eddellisvuosilta. Omikronin päärekombinaantit kuitenkin ovat sen omien uudehkojen alalinjojen kesken ja ne ovat listassa mainittuna. Luettelo on suorastaan ihana! Alkuvirus on "A". Jos jokin virus tuli yleisvaaralliseksi, se sai erityisen VOC nimen WHO:ssa ja se on kreikkalainen kirjain, mutta tämä ei permalink ole VOC-luettelo, vaan perustava PANGO-NIMITYS systeemi, jolla on tarpeen mukaan mahdollisuutta laajeta systemaattisesti vaikka kuinka paljon.Tämä ei sinänsä kerro variantin vaaroista. Vaarallisuustaulukko on taas se VOC, VOI, VUM, ja siinä taulukossa jokin variantti saa jonkin helpon maailmankansalaisille tarkoitetun käyttökelpoisen kutsumanimen kielenkäyttöön kreikkalaisesta aakkostosta. Miten helppo se siten on kiinalaisille, thamaalaisille ja niille joilla ei ole eurooppalainen kielikulttuuri perustana? en vain tiedä miten kiinaksi näitä VOC-varianteja kirjoitettaisiin ja erotettaisiin. Onneksi meille on tuo kreikka tuttua jo koulumattesta.
Systemaattinen taulukko tarvitaan monitoroinnin yhtenäistämiseksi ja tehostamiseski ja se helpottaa yleisvaaran varhaista havaitsemista.
{
"A": "",
"B": "",
"C": "B.1.1.1",
"D": "B.1.1.25",
"G": "B.1.258.2",
"K": "B.1.1.277",
"L": "B.1.1.10",
"M": "B.1.1.294",
"N": "B.1.1.33",
"P": "B.1.1.28",
"Q": "B.1.1.7",
"R": "B.1.1.316",
"S": "B.1.1.217",
"U": "B.1.177.60",
"V": "B.1.177.54",
"W": "B.1.177.53",
"Y": "B.1.177.52",
"Z": "B.1.177.50",
"AA": "B.1.177.15",
"AB": "B.1.160.16",
"AC": "B.1.1.405",
"AD": "B.1.1.315",
"AE": "B.1.1.306",
"AF": "B.1.1.305",
"AG": "B.1.1.297",
"AH": "B.1.1.241",
"AJ": "B.1.1.240",
"AK": "B.1.1.232",
"AL": "B.1.1.231",
"AM": "B.1.1.216",
"AN": "B.1.1.200",
"AP": "B.1.1.70",
"AQ": "B.1.1.39",
"AS": "B.1.1.317",
"AT": "B.1.1.370",
"AU": "B.1.466.2",
"AV": "B.1.1.482",
"AW": "B.1.1.464",
"AY": "B.1.617.2",
"AZ": "B.1.1.318",
"BA": "B.1.1.529",
"BB": "B.1.621.1",
"BC": "B.1.1.529.1.1.1",
"BD": "B.1.1.529.1.17.2",
"BE": "B.1.1.529.5.3.1",
"BF": "B.1.1.529.5.2.1",
"BG": "B.1.1.529.2.12.1",
"XA": ["B.1.1.7","B.1.177"],
"XB": ["B.1.634","B.1.631"],
"XC": ["AY.29","B.1.1.7"],
"XD": ["B.1.617.2*","BA.1*"],
"XE": ["BA.1*","BA.2*"],
"XF": ["B.1.617.2*","BA.1*"],
"XG": ["BA.1*","BA.2*"],
"XH": ["BA.1*","BA.2*"],
"XJ": ["BA.1*","BA.2*"],
"XK": ["BA.1*","BA.2*"],
"XL": ["BA.1*","BA.2*"],
"XM": ["BA.1.1*","BA.2*"],
"XN": ["BA.1*","BA.2*"],
"XP": ["BA.1.1*","BA.2*"],
"XQ": ["BA.1.1*","BA.2*"],
"XR": ["BA.1.1*","BA.2*"],
"XS": ["B.1.617.2*","BA.1.1*"],
"XT": ["BA.2*","BA.1*"],
"XU": ["BA.1*","BA.2*"],
"XV": ["BA.1*","BA.2*"],
"XW": ["BA.1*","BA.2*"],
"XY": ["BA.1*","BA.2*"],
"XZ": ["BA.2*","BA.1*"],
"XAA": ["BA.1*","BA.2*"],
"XAB": ["BA.1*","BA.2*"],
"XAC": ["BA.2*","BA.1*","BA.2*"],
"XAD": ["BA.2*","BA.1*"],
"XAE": ["BA.2*","BA.1*"],
"XAF": ["BA.1*","BA.2*"],
"XAG": ["BA.1*","BA.2*"],
"XAH": ["BA.2*","BA.1*"],
"XAJ": ["BA.2.12.1*","BA.4*"],
"XAK": ["BA.2*","BA.1*","BA.2*"]
}
tisdag 26 juli 2022
26.7. 2022 uusin omikronrekombinantti XAK , saksalainen BA.2/BA.1/BA.2 rekombinaatio
German BA.2/BA.1/BA.2 recombinant with S:K147E, S:R346K, S:460K, S:493 reversion, S:H1101Y [55 seq as of 2022-07-22] #823
Lähete asiasta #823: Fedeueli spotted this one and mentioned it in #773
Description:
Recombinant between: BA.2/BA.1/BA.2
Earliest sequence: 1st of June 2022
Most recent sequence: 23th of June 2022
Country: Germany
Likely breakpoint: between 13195 and 15240 and between 21618 and 21762 [S:27 to S:67]
Private Mutations: C4927T, T5386G (like BA.1), C7834T, C12049T,
A220001G/S:K147E, G22599A/S:R346K, G22992/S:S477N, C24863T/S:H1101Y,
A27507G .
(20 days ago) "Thanks for analysing these sequences! great job.
edited:
i would add that this sublineage has the S:H69- S:V70- 69/70del
and the S:493Q reverted to wildtype,
both important features.
I am still not completely convinced that it is a simple recombinant
event or something popping up from or next to the "Omicrons" source.
silcn: " apart from the fact this has only been found in Germany, another argument against a link to the Omicron source is the presence of 9866T in the BA.2 section. A combined BA.1/BA.2 chronic infection could certainly produce something like this".
" Good point thx, silcn".
JS, from BA.1 there is also the 5386G that was highlighted by C198.. in the other issue".
(19 days ago) Shay: "In Israel we got a sample (will soon be uploaded to GISAID) of a sample clustering with this branch of a passenger coming from Greece (no contact to Germany)".
"If this is a real recombinant, it means that it's a recombinant +
saltation. Because then we consider the 69/70 del not as part of BA.1
section (As the C21762T mutation of BA.1 is missing). And also it has
many nonBA.2/BA.1 mutations which are highly converged in Omicrons 2nd
gen/stepwise :
S:K147E
S:R346K
S:N460K
and the highly converged reversion in 493".
FedeGueli:
"Thanks shay ,
to me it is still contested if it is a plain recombinant , a
recombinant in a chronic case or something coming from the entourage of
original Omicron source.
The silcn
argument on Germany is weakened by the fact that BA.5+S:346I was barely
sequenced in South Africa and then popped up and emerged fastly in
Germany, representing a brand new branch of BA.5 distinct from the main
designated or even proposed ones
"More:
And i was just reading casually this paper yesterday" :
"Potential evidence of a single recombination event
involving BA.1, BA.2 and BA3 was identified by 3SEQ (P = 0.03), GARD
(delta c-AIC = 20) and RDP5 (GENECONV P = 0.027; RDP P = 0.006) within
the NTD encoding region of spike. The most likely breakpoint locations
for this recombination event were 21690 for the 5′ breakpoint (high
likelihood interval between 15716 and 21761) and 22198 for the 3′
breakpoint (high likelihood interval between 22197 and 22774)." (Tulio
de Oliveira et Al:
https://www.nature.com/articles/s41586-022-04411-y)
the original BA.1/BA.2/BA.3 breakpoint seems to overlap with the
breakpoints of this one described here. Sincerely i dunno know if
significant or not, very far from me i would say to say anything
relevant, but maybe someone else could take a 2nd look at this".
Silcn: "BA.5+S:346I doesn't come directly from the Omicron source though. There have been at least 5 (maybe more, see #455, #561) separate emergences from the Omicron source and in every case most of the early sequences came from South Africa".
FedeGueli: "Yes true i mean if a very transmissible lineage is barely detected in the country where it likely emerged i think a much lower transmissible one can fly under the radar easily. Not saying it is wrong what have you said but that is not the strongest argument vs BA.6 hypothesis, i think. Also as you i think a new recomb in a chronic host different from Omicron source is the most likely explanation".
Josette: "Thanks for all the comments! It gave me some extra insight.
I think it is more complicated than a normal recombinant with 2 breaking
points. I missed the 69/70 del, since it is not in Sc2rf, but that
would make it 2 BA.1 mutation clusters instead of one.
Together with the T5386G BA.1 mutation, which is shown by Sc2rf, and I
did notice, but didn't highlight as BA.1 (just edited it in the first
part of the issue) and the 493 reversion (A23040A) that really makes it
very complicated.
To summarize the nucleotides:
1-4321 BA.2
T5386G BA.1
8393-13195 BA.2
15240-21618 BA.1
C21762C BA.2
21765-21770 BA.1 (69/70del)
21846-22882 BA.2
A23040A S:493Q reversion, no BA.1/2
23048-29510 BA.2
Plus of course several private mutations."
Josette: " changed the title
German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:S477N, S:H1101Y and 5 other private mutations
German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:H1101Y and 5 other private mutations
19 days ago
Silcn: " also possible that 69/70del occurred independently rather than being BA.1-derived. Wouldn't be too surprising given the other additional spike mutations".
(18 days ago)
FedeGueli: "Thanks, Josette! I suggest to edit your main comment so it would be clearer for everyone !"
FedeGueli: " Silcn, that is possible, but in a landscape of multiple breakpoints and a key reversion for other Omicron lineages i dont know how much we can be sure of that or not".
Silcn: "Josette, also interesting that you mention BA.3, because something very similar happened there: it contains S:G446S from BA.1 in an otherwise ancestral BA.2-derived section. Again, impossible to know if it arose independently or though recombination. Still doesn't change my opinion that this lineage probably has nothing to do with the Omicron source (the C9866T is convincing enough for me). The S:R493Q reversion doesn't make things any more complicated than they already are: it is extremely common in saltation-derived BA.2 sequences/lineages with multiple Spike mutations."
Shay: " As I mentioned yesterday, a first Israeli sample (traveler from Greece) :
(15 days ago)
Ulrich: "We have two cases in Austria as well, currently uploading to Github".
FedeGueli: " Ulrich, thx a lot! To the highest Authorities: C.R. C.R A.H. IPG : in my view this has to be granted an early designation, whatever as recombinant or something else, still very different from everything else circulating (or better saying that it has a unique mix of mutations actually on the rise) .
Ulrich: "What I find remarkable about this variant is that it appears to be convergent evolution with BA.2.75 (147, 460, 493) and with regards to the 493 reversion even BA.5. It seems obvious the virus has identified the next surfaces to optimise."
Shay : "Ulrich This is why it might be a combination of recombination+saltation in a chronic patient. The mutations converged in this one are indeed more related to variants that arose outside SA and the parallel BA.1-5. And the recombination is much cleaner than could be seen in cases where presumably a wide range of variants been co-evolved like might be in the original chronic patient ( like BA.3 probably coming from the same body where BA.1 and BA.2 evolved and XB probably coming from the same body were B.1.631 and B.1.634 evolved)."
"If anyone needs -here is a comparison of the mutational profile of this variant , BA.1 and BA.2
PDI 823 .xlsx "
FedeGueli: " Thx, Shay!"
Shay: "For CovSpectrum query i would replace to :
[4-of:C4927T,C7834T,C12049T,A22001G,G22599A,T22942G,C24863T,A27507G]
searching 4 out of the 8 unique mutations in this lineage (not present in BA.1 or BA.2)."
Josette: Here's a link for Shays 's query. ( Kts. linkistä)
(11 days ago)
Josette: "We found another one. Also I tried to illustrate a bit what the mutations are like":
(9 days ago)
Fede Gueli: " 23 sequences as today
Early signs of growth advantage vs BA.5 limited to Germany".
(6 days ago)
Shay: "27 samples as of yesterday".
Ulrich: "With the search term Spike_K147E, Spike_N460K, Spike_G339D, Spike_H69del currently a total of 60 cases are found. We mostly sequence only spike and selected regions in Austria, so these samples are only found with a term that does not demand too many mutations beyond spike. Could we maybe adapt the search term to account for that? 2 samples were also full-genome sequenced already. Really looking like growth advantage. Plus the spread across Germany and beyond says it all...https://user-images.githubusercontent.com/109073004/180005968-d957dfe5-c284-47fc-aa58-67036b0ec2a8.png
FedeGueli: "Ulrich, i would add Spike_H1101Y to your query".
C.Roemer. "FedeGueli, I would recommend using advanced query with NextcladePangoLineage:BA.5* instead of just two mutations which do not immediately show which lineage you compare to. I've edited your growth advantage query
Josedtte, I think your sc2rf plot is confusing as it has Delta BA.2 as parents rather than BA.1 and BA.2. Can you explain why you did that and maybe change it to BA.1/BA.2 if this is a mistake? It's confusing because the title of the issue suggests this is a BA.2/BA.1/BA.2 recombinant.
Here's a quick summary of how I think about this recombinant
Spike is mostly BA.2* but with some notable changes:
- Missing: T19I, 24-26del, 27S not there because that part is from BA.1* parent
- Donated: 69-70del convergent with many VOCs
- Additional S:R346K, convergent with BA.1.1
- Additional S:K147E, S:N460K and reverted S:493 convergent with BA.2.75
I've added a BA.1/BA.2 sc2rf pic to the first post in this issue to keep things simple for those reading from top to bottom, Josette
I tried to find which branch the BA.2* donor is from but couldn't find anything interesting in Germany/Europe. For the BA.1 part, there are no private mutations so if anything one can go by exclusion principle.
corneliusroemer
changed the title
German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:H1101Y and 5 other private mutations
German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:460K, S:493 reversion, S:H1101Y and 4 other private mutations
6 days ago
Josette Shoenma: "Thanks, Cornelius Roemer . Somehow I forgot to include it. Couldn't have done my analysis without it. Here is the one I made from the first 16 sequences. It won't be very different..."
corneliusroemer
changed the title
German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:460K, S:493 reversion, S:H1101Y and 4 other private mutations
German BA.2/BA.1/BA.2 recombinant with S:K147E, S:R346K, S:460K, S:493 reversion, S:H1101Y [55 seq as of 2022-07-22]
5 days ago
Corneliusroemer:
@chrisruis @InfrPopGen @thomasppeacock
There are now at least 55 sequences of this recombinant, 37 have been submitted since Tuesday! I would strongly recommend quick designation as the criteria are satisified, the Spike profile is very interesting and there appears to be growth, too.
Here are recent EPI_ISLs of complete sequences (3 are Spike only) so you can designate even if these sequences aren't yet in the Usher tree (maybe excluded due to long branch? @AngieHinrichs
|
Thanks @corneliusroemer
-- yep, they are filtered out due to having too many reversions
relative to BA.2 placement by nextclade, but I've been manually
exempting the EPI_ISL's from Josette's initial list and EPI_ISL_13719505
from the cov-spectrum query as of a few days ago. They're in the tree,
on a branch with the label proposed823 (Pango lineage assigned by
UShER). .... I will exempt the rest from your list, so they should be added in tomorrow's build. CorneliusRoemer: " Thanks AngieHinrichs , My list was created using manual AA substitution queries in GISAID - not super reliable. So not surprised you catch a few more."
InfrPopGen commented 4 days ago
|
måndag 25 juli 2022
Transposaaseista ja transposoneista - löytyykö uusia hyödynnettäviå terapioita?
Parhaimmillaan -positiivisimmin ajatellen- tämä genomin transposoni-transposaasi-järjestelmä joka tunnistaa jakso jaksolta genomia ja pystyy siirtämään tai palauttamaan jotakin geenikohtaa tai estämäänkin kohdan mobilisoitumisen - on genomin stabilaation perustava yksikkö. Sen tapa tunnistaa DNA-koodia minimipätkä pätkältä moninaisilla variaatioilla (monine jäsenineen) muistuttaa jollain tavalla rreologisen kudoksen imusolujen kykyjä tunnistaa prosessoidun antigeenin pätkiä ja tunnistaa itsensä ja ei -itsen. Olen ajatellut, että tämä itsen tunistus täytyy olla genomissa vanhempi asia kuin myöhäisenä aikana ilmentyvien proviruksia muodostavien virusten elämänhistoria, joten on olemassa ikivanha itsen tunnistusominaisuus genomissa. On luonnollista, että virus joka haluaa tuhota ihmistä hyökkää tähän järjestelmään, joten täytyy löytää keino, miten tukea järjestelmää. On otettava selvää sen järjestelmän jäsenistä ja mitä se järjestelmä tarvitsee voidakseen hyvin. Mielestäni sinkki (Zn) on yksi sen tarvitsema tekijä, toinen lienee K1-vitamiinipitoinen ravinto ja muut antioksidanttistatusta ylläpitävät seikat jne jne yleiskuntoon ja terveelliseen elämäntapaan liittyvät asiat ja toksiinien välttö ja vältettävien infektioitten välttämiseen pyrkivä yleinen järkevä käyttäytyminen , johon valtiot kovasti ovat nytkin panostaneet informaatiovirtaansa. Olen juuri katsomassa ihmisen sinkkiproteiinien joukosta niitä, jotka ovat myös transposaaseja tai muuten ilmenevät pitkin DNA:ta Niitä on aika paljon. Nyt kun on lähinnä kyse long-Covid-19 oireista toipumisesta, pitäisi ottaa huomioon, että ihmisen genomillakin on piilevät kykynsä korjautua, mutta hyvää yleiskunnon hoitoa ja aikaa ja kärsivällisyyttä tarvitaan. JA turhien infektioiden mahdollista välttöä ja järkevää hygieniaa kannattaa pitää yllä.
https://pubmed.ncbi.nlm.nih.gov/22367875/
The Sleeping Beauty transposon toolbox-
(Ihmisessä on itsessään se Sleeping Beauty toolbox myöskin ihan Luojan toimesta) .
Affiliations
- PMID: 22367875
- DOI: 10.1007/978-1-61779-603-6_13
Abstract
The mobility of class II transposable elements (DNA transposons) can be experimentally controlled by separating the two functional components of the transposon: the terminal inverted repeat sequences that flank a gene of interest to be mobilized and the transposase protein that can be conditionally supplied to drive the transposition reaction. Thus, a DNA molecule of interest (e.g., a fluorescent marker, an shRNA expression cassette, a mutagenic gene trap or a therapeutic gene construct) cloned between the inverted repeat sequences of a transposon-based vector can be stably integrated into the genome in a regulated and highly efficient manner. Sleeping Beauty (SB) was the first transposon ever shown capable of gene transfer in vertebrate cells, and recent results confirm that SB supports a full spectrum of genetic engineering in vertebrate species, including transgenesis, insertional mutagenesis, and therapeutic somatic gene, transfer both ex vivo and in vivo. This methodological paradigm opened up a number of avenues for genome manipulations for basic and applied research. This review highlights the state-of-the-art in SB transposon technology in diverse genetic applications with special emphasis on the transposon as well as transposase vectors currently available in the SB transposon toolbox.
Retrovirusinfektion impaktista keuhkoon artikkeli vuodelta 2007
https://pubmed.ncbi.nlm.nih.gov/17492233/
ottaen huomioon miten yleinen on krooninen retrovirusinfketiotila maailman eri kansoissa, tulee mieleen , voisiko sars-2 viruspandemian aikaisista virussekvenssianalyyseistä havaita, jos näytteet ovat toista kroonista rNA-virusinfeketiota potivista ja minkä vaikutuksen tekee toinen krooninen RNA-virus yleensäkin nykyiseen pandemiaan. Ja pitäisikö globaalisti seuloa positiiviset pandemiat kahden viruksen osalta saman tien, koska molemmat ovat pahimmissä vaikutuksissaan syvän keuhko-impaktin aiheuttajia. - Ja molemmat virukset voivat yhteisevoluutiossa hankkia toisiltaan ominaisuuksia ihmiskunta-aikanaan.
(muita RNA-iruksia tässä mainitsemattakaan)
Päivitys voittoisimmasta omikronlinjasta BA.5 *
| Lineage | Most common countries | Earliest date | # designated | # assigned | Description | WHO Name |
|---|---|---|---|---|---|---|
| BA.5 | United States of America 24.0%, United Kingdom 15.0%, Germany 11.0%, France 7.0%, Denmark 7.0% | 2021-11-15 | 863 | 10602 | Alias of B.1.1.529.5, from pango-designation issue #517 | Omicron |
| BA.5.1 | United Kingdom 14.0%, France 13.0%, Germany 11.0%, Denmark 10.0%, United States of America 10.0% | 2021-11-15 | 3033 | 60693 | Alias of B.1.1.529.5.1, Portugal lineage | |
| BA.5.1.1 | United States of America 70.0%, Canada 13.0%, Mexico 5.0%, United Kingdom 3.0%, Germany 1.0% | 2021-12-14 | 192 | 2534 | Alias of B.1.1.529.5.1.1, USA lineage | |
| BA.5.1.2 | Denmark 24.0%, France 13.0%, United Kingdom 12.0%, United States of America 11.0%, Germany 10.0% | 2022-04-19 | 89 | 961 | Alias of B.1.1.529.5.1.2, mainly found in Denmark, Portugal and Luxembourg, from pango-designation issue #790 | |
| BA.5.1.3 | Germany 52.0%, Denmark 10.0%, United States of America 9.0%, Spain 7.0%, United Kingdom 5.0% | 2022-04-30 | 243 | 2097 | Alias of B.1.1.529.5.1.3, mainly found in Germany Portugal and Spain, from pango-designation issue #765 | |
| BA.5.1.4 | Denmark 44.0%, United Kingdom 20.0%, Germany 5.0%, Ireland 4.0%, United States of America 4.0% | 2022-05-25 | 116 | 446 | Alias of B.1.1.529.5.1.4, mainly found in Denmark and England, from pango-designation issue #801 | |
| BA.5.1.5 | 180 | 0 | Alias of B.1.1.529.5.1.5, mainly found in UK, Denmark, and Belgium, from pango-designation issue #835 | |||
| BA.5.1.6 | 275 | 0 | Alias of B.1.1.529.5.1.6, Mexico lineage | |||
| BA.5.1.7 | 121 | 0 | Alias of B.1.1.529.5.1.7, Canada lineage | |||
| BA.5.1.8 | 74 | 0 | Alias of B.1.1.529.5.1.8, Peru lineage | |||
| BA.5.2 | United States of America 18.0%, United Kingdom 13.0%, Indonesia 10.0%, Israel 9.0%, Germany 8.0% | 2021-11-15 | 2103 | 22494 | Alias of B.1.1.529.5.2, mainly found in South Africa, England and USA, from pango-designation issue #551 | |
| BA.5.2.1 | United States of America 39.0%, United Kingdom 12.0%, Germany 6.0%, Denmark 6.0%, Israel 5.0% | 2021-10-20 | 1707 | 37763 | Alias of B.1.1.529.5.2.1, mainly found in South Africa, England and USA, from pango-designation issue #657 | |
| BA.5.2.2 | France 41.0%, Martinique 19.0%, United States of America 7.0%, French_Guiana 5.0%, United Kingdom 5.0% | 2022-05-02 | 91 | 819 | Alias of B.1.1.529.5.2.2, France and Martinique lineage | |
| BA.5.2.3 | United Kingdom 51.0%, Denmark 13.0%, United States of America 6.0%, France 5.0%, Germany 4.0% | 2022-05-11 | 95 | 1135 | Alias of B.1.1.529.5.2.3, UK lineage | |
| BA.5.2.4 | Australia 58.0%, United Kingdom 18.0%, New_Zealand 5.0%, United States of America 5.0%, Ireland 4.0% | 2022-05-15 | 20 | 92 | Alias of B.1.1.529.5.2.4, Australia lineage | |
| BA.5.2.5 | 51 | 0 | Alias of B.1.1.529.5.2.5, Indonesia lineage | |||
| BA.5.3 | Germany 47.0%, United States of America 14.0%, Austria 8.0%, Denmark 5.0%, United Kingdom 4.0% | 2022-01-05 | 490 | 2021 | Alias of B.1.1.529.5.3, mainly found in Germany and South Africa, from pango-designation issue #550 | |
| BA.5.3.1 | Israel 19.0%, United States of America 15.0%, United Kingdom 13.0%, Germany 13.0%, South_Africa 8.0% | 2022-02-23 | 308 | 2307 | Alias of B.1.1.529.5.3.1, mainly found in South Africa, Austria, and England, from pango-designation issue #625 | |
| BA.5.3.2 | Germany 68.0%, Denmark 12.0%, United Kingdom 7.0%, Austria 2.0%, France 2.0% | 2022-04-11 | 138 | 1312 | Alias of B.1.1.529.5.3.2, mainly found in Germany, from pango-designation issue #697 | |
| BA.5.3.3 | United Kingdom 80.0%, Denmark 5.0%, Netherlands 2.0%, France 2.0%, United States of America 2.0% | 2022-04-05 | 147 | 758 | Alias of B.1.1.529.5.3.3, UK lineage | |
| BA.5.3.4 | Germany 76.0%, United Kingdom 5.0%, Denmark 5.0%, Israel 3.0%, Netherlands 2.0% | 2021-11-15 | 152 | 518 | Alias of B.1.1.529.5.3.4, Germany lineage | |
| BA.5.5 | United States of America 86.0%, Canada 3.0%, United Kingdom 3.0%, Israel 1.0%, Denmark 1.0% | 2022-01-10 | 2145 | 15397 | Alias of B.1.1.529.5.5, mainly found in USA, from pango-designation issue #656 | |
| BA.5.6 | United States of America 74.0%, Canada 4.0%, Israel 3.0%, United Kingdom 3.0%, Peru 2.0% | 2021-12-14 | 430 | 6101 | Alias of B.1.1.529.5.6, USA lineage | |
| BA.5.6.1 | 44 | 0 | Alias of B.1.1.529.5.6.1, Peru lineage | |||
| BA.5.7 | 70 | 0 | Alias of B.1.1.529.5.7, Australia lineage | |||
| BA.5.8 | 1277 | 0 | Alias of B.1.1.529.5.8, mainly found in England, USA, Denmark and Scotland, from pango-designation issue #743 | |||
| BA.5.9 | 217 | 0 | Alias of B.1.1.529.5.9, mainly found in Germany, Switzerland and Denmark, from pango-designation issue #753 |
Prenumerera på:
Inlägg (Atom)
It looks like BB.1 clusters outside of B.1.621.1 in recent UShER trees. It still clusters within B.1.621 so we've updated BB.1 to B.1.621.2 and withdrawn BB.1 in v1.2.122
YHTEENVETONA:
Tässä tammikuisessa (2022) päivityksessä on joulukuussa (2021) ryhmitelty BB.1 siirretty suoraan Mu variantin toiseksi alalinjaksi BA.1.621.2 , joten ensimmäisen alalinjan BA.1.621.1 sub-alalinjaksi 2 jää vain BB.2. Tarkemmin ilmaistuna B.1.621.1.2
Nimitys BB.1 poistettiin luettelosta kokonaan pois , koska siihen aluksi ryhmitetyt virusnäytteet osoittautuivat olevan suoraa Mu-alalinjaa ( joka ei tarvitse koodia BB eli alalinjan sub-linjamerkintää), kun oli usheroitu varianttien klusteroitumista edelleen. Ne klusteroituivat päälinjalle (mu) , eikä sen ensimmäiselle alalinjalle. Siksi niistä tuli toinen Mu alalinja. Ihmettelinkin ensin, että mistä se tuli, mutta GITHUB-teksti selvensi asian.