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19 Aug, 7 tweets, 5 min read
🧬8/19 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed

Delta - 96% (πŸ“ˆ1%)
B.1.621 - 2.5% (πŸ“‰1%)
Alpha - 0.8% (πŸ“ˆ0.8%)
All others - 0.6%

*0⃣ sequenced other VOC cases this week*

short 🧡 | Report πŸ‘‰
covidtrackerct.com/variant-survei…
Delta was recently split into several sublineages to help investigate clusters and spread. Here are their frequencies in CT:

B.1.617.2 - 46-56%
AY.4 - 14-28%
AY.12 - 11-14%
AY.3 - 5-8%
AY.6 - 4-6%
AY.3.1 - 1%
AY.10 - <1%

These are all Delta (not 'Delta-plus', just Delta) (2/7) Image
There are lots of people seeing these sublineage dataπŸ‘† and speculatively wildly about some being more transmissible/dangerous.

**The lineages were assigned based on epidemiology**

Please read this thread before falling victim to speculation. (3/7)

Last week I wrote nice obituary for Alpha as we had the first week since early Jan w/ 0⃣ sequenced Alpha cases... (4/7)

So of course we sequence 3 Alphas this week.
(3/363 sequenced samples, 0.8%) (5/7)
A look over at Covidestim shows so encouraging news for Connecticut:

**Rt has dipped below 1, meaning that cases will likely start dropping.**

Cases have been leveling off for a couple weeks now- lets keep this trend going! (6/7)

covidestim.org/us/CT Image
This week I'd like to thank @carolilucas & the entire @VirusesImmunity lab for being wonderful friends & collaborators! Among other things, they are making isolates of our local viruses to answer important questions about variants. πŸ‘πŸ™Œ

e.g. πŸ‘‡ (7/7)
medrxiv.org/content/10.110…

β€’ β€’ β€’

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More from @NathanGrubaugh

Nathan Grubaugh Profile picture
16 Sep
🧬 9/16 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed

πŸ‘‘Delta - 99.6% (480 sequenced)
Mu - 0.2% (1 sequenced)
Non-VOI/C - 0.2% (1 sequenced, B.1.517)

Delta >99% in last 4 reports

short 🧡 | Report πŸ‘‰
covidtrackerct.com/variant-survei…
Connecticut Delta sublineage frequencies for the week of 9/6 (weekly % change over previous 3 weeks)

B.1.617.2 - 44% (πŸ“‰7%, πŸ“‰1%, πŸ“‰4%)
AY.25 - 23% (πŸ“ˆ3%, 0%, πŸ“ˆ2%)
AY.3 - 11% (πŸ“ˆ2%, πŸ“ˆ1%, πŸ“‰1%)
AY.12 - 10% (πŸ“‰1%, πŸ“ˆ2%, πŸ“ˆ2%)
All others - 11% combined

(2/6) Image
B.1.617.2 is decreasing primarily because these sequences are being classified as other sublineages. Otherwise, the Delta AY sublineage frequencies are remaining very stable and there is currently *no evidence that any are more transmissible* in Connecticut. (3/6)
Read 6 tweets
Nathan Grubaugh Profile picture
2 Sep
🧬 9/2 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

Delta - 99.6% (530 sequenced)
Gamma - 0.4% (2 sequenced)
Mu - 0%
All others - 0%

short 🧡 | Report πŸ‘‰
covidtrackerct.com/variant-survei…
Delta is split up into 25 sub-lineages - mostly for tracking purposes. These are the top in CT, along with their defining mutations.

B.1.617.2 - 57%
AY.25 - 18% - synonymous mutation
AY.12 - 10% - Spike T791I
AY.3 - 8% - Orf1ab I3731V

Please read on...
(2/8)
Delta sub-lineage AY.12, with the Spike T791I mutation, has received some attention because its 60-80% in Israel, but its not currently increasing globally. Its been mostly hovering between 4-6% since mid-June.

Fig from @DiseaseOutbreak
tinyurl.com/3xvnhvyh
(3/8)
Read 8 tweets
Nathan Grubaugh Profile picture
12 Aug
🧬8/12 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

Delta - 95% (πŸ“ˆ7%)
B.1.621 - 4% (πŸ“‰4%)
Gamma - <1% (πŸ“‰3%)
Alpha - 0% (πŸ“ˆ1%)

State infections = 55/100k pop/day
State Rt = 1.2

short 🧡 | Report πŸ‘‰
covidtrackerct.com/variant-survei…
217 days ago we reported the first B.1.1.7 (now called Alpha) cases in Connecticut. For the first time since then we report 0⃣ Alpha cases.

Lets quickly recap Alpha's reign (2/10)

Alpha is the first variant to hit the news, and concern over its emergence was the primary motivating factor for the construction of our state genomic surveillance system. Because of our rapid increase in sequencing, we've been able to detect other variants much earlier. (3/10)
Read 10 tweets
Nathan Grubaugh Profile picture
10 Aug
UPDATE: GISAID put a fix in place to accept these sequences, and any sequence with a known FRAMESHIFT, w/o confirmation. πŸ»πŸ‘

Here's what you need to do. Its pretty easy. 🧡 (1/6)
If you go to the Upload > Batch Upload tab, you should see the new "Confirmation options" dropdown menu highlighted in yellow. (2/6)
Now you have options!

The Default is as before, any sequencing with FRAMESHIFTS, like B.1.621, will be kicked back for confirmation and resubmission.

I don't recommend using the default. (3/6)
Read 7 tweets
Nathan Grubaugh Profile picture
5 Aug
🧬8/5 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

88% - Delta (B.1.617.2 + AY.3)
8% - B.1.621 (no greek letter yet)
3% - Gamma (P.1)
<1% - Alpha (B.1.1.7)
0% - everything else

short 🧡 | Report πŸ‘‰
covidtrackerct.com/variant-survei…
Delta in Connecticut (~88%) is a bit behind the national average of 93%, but generally following the national trends. (2/9)

covid.cdc.gov/covid-data-tra…
Besides Delta, the other major story here is B.1.621. It's now firmly the second most frequent variant in CT (~8%), and has so far been able to maintain its ground against the expansion of Delta. Something that Alpha, Gamma, and everything else couldn't do. (3/9)
Read 9 tweets
Nathan Grubaugh Profile picture
29 Jul
πŸ“’ PSA for GISAID submitters/users

All of our B.1.621 + B.1.621.1 (important emerging SARS-CoV-2 variant) submissions are being rejected by GISIAD. This has some important implications that data producers + public health agencies should be aware of.

Technical 🧡(1/12)
We usually have a few sequences/week that get rejected for QC reasons (eg indel in a string of As or Ts). It takes a few days for these to be fixed and reposted. Sometimes longer depending on our bandwidth. These are usually a random distribution so not a problem if delayed(2/12)
This past week we had 40+ sequences get rejected, and almost all of them were B.1.621/B.1.621.1. @JosephFauver found that all of these sequences have a 4 nt deletion in ORF3A that results in a premature stop codon about ~50 nt upstream. GISAID sees these and kicks them back(3/12)
Read 12 tweets

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