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Apr 12 • 6 tweets • 4 min read
Closely monitoring new #omicron sub-lineages - BA.4 & BA.5 (first identified in #SouthAfrica)

No BA.4/BA.5 sequences identified in the #UnitedStates yet. But the key signature mutation Spike L452 is found in >400 BA.2 sequences in the past 3 months.

express.co.uk/news/science/1…
Key Mutations to follow

-Spike L452(R/M/Q)
-Spike L452R* and L452Q is prevalent in #Wastewater samples (will update in a separate thread)

*currently unassigned/unclassified/undesignated sequences and some of them are tagged "ML" by @GISAID

cov-spectrum.org/explore/United…
A quick look at the tree generated from the nextclade tool that @CorneliusRoemer point to earlier -- clades.nextstrain.org
** Tree generated with 662 samples from Waste Water surveillance downloaded from GISAID w/ S:L452R mutation (mostly from California)
#BA4/#BA5 #OmicronUpdates

@GISAID has updated BA.4 and BA.5 designations

- No BA.4/BA.5 sequences from #UnitedStates in GISAID database yet

-Did find some sequences with S:F486V (escape mutant) and M:D3N

-But no reversion at S:493 and no S:L452R
BA4/BA5 Tracker:

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More from @RajlabN

Raj Rajnarayanan Profile picture
Apr 10
#CoronavirusUpdates #HospitalCapacity #UnitedStates

Are we ready to handle another #COVID #WAVE?

In-patients beds are >75% full in 25 States + DC
ICU beds are >75% full in 16 States + DC

public.tableau.com/app/profile/ra… ImageImage
These represent all hospitalizations not just COVID

Data Source: protect-public.hhs.gov/pages/hospital…
Monitoring all hospitalizations because #COVID #hospitalizations reporting and definitions keep changing!
Read 5 tweets
Raj Rajnarayanan Profile picture
Apr 5
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

69.07% BA.2*, <--
26.03% BA.1.1*,
4.18% BA.1* &
0.63% None

*#Omicron

Tracker (by State, by Variant): tinyurl.com/mryj4uu7

Updated 04/04/22 Image
#OmicronVariantUpdates #UnitedStates 04/04/22

BA.2 Sequences with sample collection dates in the last 15 days: 3,503

Hotspots (15-Day trends):

>>#NewYork <<

#Texas, #California, #NewJersey, #Washington, #Florida #Massachusetts, #Illinois Image
#COVID19Updates #DeltaRegion 04/04/2022

Top Circulating Variants (last 15 days) in #Alabama, #Arkansas, #Illinois, #Louisiana, #Mississippi, #Missouri, #Kentucky, #Tennessee

BA.2 is the dominant lineage in the Delta Region

Source: tinyurl.com/mryj4uu76 ImageImageImage
Read 4 tweets
Raj Rajnarayanan Profile picture
Apr 2
#CoronaVirusUpdates #RhodeIsland

Have a look at the recent surge in #Hospitalizations among children (< 18 years old age group; colored yellow)

BA.2 is the most dominant circulating lineage in #RhodeIsland
My hospital tracking tool didn't pick it up (data from HHS). Got to investigate this further.. that surge from @nytimes data chart looks unreal

public.tableau.com/app/profile/ra…
Here's the @CDCgov #Hospitalization tracker (pulls data from HHS) - covid.cdc.gov/covid-data-tra…
Read 7 tweets
Raj Rajnarayanan Profile picture
Mar 26
New #PANGO designations - BA.2.*

BA.2.4Alias of B.1.1.529.2.4, #Singapore lineage

BA.2.5Alias of B.1.1.529.2.5, lineage in #Portugal and other countries

BA.2.6Alias of B.1.1.529.2.6, lineage in #France and other countries

BA.2.7Alias of B.1.1.529.2.7, #USA lineage ImageImage
These are new designations - branching from the BA.2 subvariant

more to follow ..... will update key mutational differences and transmission advantage (if any)
BA.2.4 (aka B.1.1.529.2.4) | prevalent in Singapore

Key mutation: ORF6:M58K

COV-spectrum predicts a growth advantage of 14% over BA.2 and 46% over BA.1.1 in #Singapore

BA.2 and BA.1.1 are currently the dominant lineages in circulation in Singapore Image
Read 29 tweets
Raj Rajnarayanan Profile picture
Mar 20
Tracking sequences with both #omicron and #delta signatures

Flagged by @GISAID as "ML" sequence under investigation (#Recombinant or #Contamination ?)

Sequences are under investigation: 4511

Tracker: tinyurl.com/4cbpnz46 Image
#USA has 2423 sequences under investigation from multiple laboratories.

They contain signatures from both #Delta and #omicron #variants

ML sequence #hotspots: #California, #Texas, #NewYork, #Arkansas and #Minnesota

#deltamicron or #deltacron or #contamination? ImageImageImage
#India has 568 sequences under investigation from multiple laboratories.

They contain signatures from both #Delta and #omicron #variants

ML sequence #hotspots: #Karnataka, #TamilNadu, #Maharashtra, #Gujarat, #WestBengal, #NewDelhi

#deltamicron/#deltacron or #contamination? ImageImageImage
Read 7 tweets
Raj Rajnarayanan Profile picture
Sep 12, 2021
Data Shows #COVID19 Cases Among #SanFrancisco #Children is Low and Schools Remain Safe Settings. #Vaccinations are our best defense to protect children. An estimated 90% of children ages 12 to 17 are fully vaccinated. sfdph.org/dph/alerts/fil…
During the same period, @AmerAcadPeds reports a significant increase in #COVID19 cases among children nationwide. Full report: downloads.aap.org/AAP/PDF/AAP%20…
@SF_DPH emphasized that vaccinations "are our best defense to protect children," noting most #pediatric cases of #COVID19 in the city came from #unvaccinated adults in a household getting the virus and spreading it to unvaccinated children. npr.org/2021/09/10/103…
Read 5 tweets

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