Henry Niman
@HNimanFC
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Tracking SARS CoV2 in 2019 Pandemic
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Full H5N1 sequences from 9 cats in US (collected in 2024) were just uploaded to GISAID and the NP sequences match the 7 Dairy Cattle and 1 human sequence, with Y52H
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111
345
The H5N1 plot is definitely thickening
There is a change in the NP protein, D52H, that makes humans more susceptible to H5N1 and this mutation is widespread in birds and found in the 7 Dairy Cattle in TX as well as the human in TX, but not in the goats in MN or the Mexico avian
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I am going to use some of the seqs in Spain to demo how quickly BA.2.86 is evolving
Currently one sub-variant, designated BA.2.86.1
def by NSP3 : K1155R (orange)
BA.2.86.1 more common than BA.2.86
Sub-variants of BA.2.86.1 quickly emerged
NSP2 : Y441C largest (mustard yellow)
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Going to be a busy BA.2.86 day. Already have 1 from South Korea, 6 from Spain, 10 from Denmark (flood gates opening wider). Stay tuned
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The H5N1 sequence from the human case in Australia was released at GISAID today
It is clade 2.3.2.1a
Note it has NP Y52H, which is in all Dairy seqs released to date
A/Victoria/149/2024
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BA.2.86 sequences at GISAID have increased to 42, which are named and mapped at link below. In addition, there are 6 sequences from UK not yet public at GISAID. Today, sequences from France, USA (PA), Canada (ON), and Spain were added to map
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@DavidJoffe64
And it's not like they were all in their low 60's. BA.2.86.1 positives were in all decades from 20's to low 60's (the six OH positives were in 20's, 30's, 40's, 50's 60's)
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Looks like a significant BA.2.86.1 outbreak in Alberta (Edmonton) Canada. 15 seqs that are NSP2 Y441C derivatives with NSP L260F and similar collection dates
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Lift off. Time to call Houston. UK BA.2.86 sequences just increased by 31 in ONE day. Look at FREQUENCIES in right column. I think JN.1 has arrived.
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Houston we have a problem
9 of the HMH Slippers have
Spike C1243F
1 more has a mixture
Spike C1243F
also in JN.1.16 SLipper from Ontario Canada (w/ R346T)
Canada/ON-PHL-202405512/2024
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There are now 76 public BA.2.86 sequences. 42 are at GISAID and 34 are at UK site.
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New XDDs late yesterday and today
4 South Korea 🇰🇷
3 Ontario Canada 🇨🇦
2 Finland 🇫🇮
1 Spain 🇪🇸
1 Italy 🇮🇹
1 Slovenia 🇸🇮
1 IL USA 🇺🇸
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18
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First BA.2.86 seqs in China (Shanghai), Luxembourg (earliest col date), and Iceland def two new subvariants. Shanghai ex-Japan matched 2nd Japan seq w/ NS3 T229I (Orange Yellow marker) and Iceland/Luxembourg matched each other NSP6 R252K (Dark Red marker)
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H5N1 quickly getting out of control in dairy herds in Allegan, Clinton, Gratiot, Ingham counties and an additional herd in Isabella in Michigan USA 🇺🇸
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A 7th H5N1 Dairy Cow Seq was uploaded to GISAID,
The H5 of the
7 cows in TX
match
1 human in TX
3 goats in MN
1 wild bird in TX
and at GENbank are closest to
2 wild birds
1 chicken
collected in fall 2023 at three locations in Mexico
only the human PB2 has E627K
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I was on the road all day and this evening I looked at the UK BA.2.86 update and there are something like 20 new sequences, including 7 in Scotland and 1 in Wales. Even got to 100% for 10/4 collection. Check out the daily FREQUENCIES (right column)
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Going through JN.1.11.1 cluster (total seqs = 36)
IDing derivative clusters
Derivatives each require a new letter set
JN.1.11.1 has already reached its 3 branch limit
There already are
2 clusters of 5
1 cluster of 3
1 cluster of 2
Each cluster of 5 involves 3 or 4 countries
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BA.2.86 map has been updated with BA.2.86.1 and UK sequences not at GISAID yet have been added. As is easily seen BA.2.86.1 dominates Europe
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@DavidJoffe64
And how many of the 6 likely hospitalized patients at Cleveland Clinic who had a BA.2.86.1 sequence were >65? Well, I think most reading this thread by now have an idea, so the answer is ZERO.
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@mrmickme
@SocioAnalytic
@xabitron1
Yes, the best previews of coming COVID variants are sequence uploads from Ginkgo Bioworks, which include JN.1 derivative SLipper March Madness
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@UseBy2022
@mvankerkhove
total of 48 BA.2.86 seqs = 42 at GISAID + 6 in UK but not yet GISAID. Numbers will explode. Yesterday 5 wastewater seqs in and around Bangkok. One had a marker that was in 1st seq in Israel, and 1st seq in USA. All collected in late Jul early Aug.
BA.2.86 flying everywhere.
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Time to add another color to the marker key
new derivative of BA.2.86.1 is NSP3 K1689R
limited to the US so far
1st TX
1st PA
3 NY incl one of the first
1st OH not detect by Cleveland Clinic
Levels in US high enough to explode National lab detections (contracted by CDC)
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Ohio just took the lead in the US with FOUR BA.2.86 sequences, raising their total to SIX. Flood gates are opening!
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@MMoltmannPhD
Problem is the appearance of a novel variant at Houston Methodist Hospital HMH.
I have been tracking "FLippers" - JN.1 variants with two key changes
Recently variant tacked on a third key mutation
HMH released 11 seqs and 9 had all three mutations
A 4th mutation was in all 9
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ALERT
All 48 JN.1.4 Ontario Canada FLippers uploaded today
by PHL
matched each other & 1 Ontario JN.1.4
uploaded today by KHS
Canada/ON-KHS-01646-v1/2024 3/26
Two unique markers
(not in any othe JN.1 derivative SLipper)
NSP4 L447F
C14913T (NSP12)
1/2
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JN.1.16 SLipper with M L46F was uploaded from Baiyin Gansu tonight
Wuhan cluster has spread to Baiyin
Gansu/BYCDC016/2024
col 3/6/24 (yesterday)
signaling signifcant concern about this GROWING problem over a large geographic space in China (Baiyin is 700 miles NW of Wuhan)
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The Seq from France had NSP6 R252K, the fourth country (also Iceland, Netherlands, and Luxembourg).
3/4 also have S:L455S (the 4th hasn't completed that region of S). These seqs have a dark red marker
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Yesterday BA.2.86 blew past CH.1.1 and BA.2.75 in category of number of sequences in the past 28 days for UK or England (now only trail XBB.1.5, XBB1.16 and EG.5.1 in Variant table in those categories)
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Note that recent BA.2.86.1 cases have hospitals as originating lab and the sequences are derivatives of BA.2.86.1 (see map legend for definitions and color codes) and many are patients WELL under 65
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Looks like 18 UK BA.2.86 seqs tonight, so it is VERY close to the 1,000 mark for the map
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The recent appearance of Spike R346T on multiple JN.1 derivative
SLipper (L455S + F456L)
SVipper (L455S + F456V)
FLipper (L455F + F456L)
Backgrounds
over a wide geographical area
is cause for concern
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Analysis of the H5N1 sequences linked to the Texas Dairy Cattle outbreak supports a common source based on the 100% identity in the 982 BP sequence of the M gene in 21 samples
4 Texas wild birds col 3/18
7 Dairy Cattle col 3/20
9 feline col shortly thereafter
1 human col 3/28
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7 new UK BA.2.86 sequences tonight, but don't look at the numbers, look at daily FREQUENCIES
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UK announced 28 new BA.2.28 cases. Most (25) have a collection date of 8/26/23. The other three have collection dates of 8/25, 8/27, 8/28. None are public at GISAID
Details to follow
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Accidentally found a JN.1 FLIPPER (flew into SeaTac from Germany)
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Github indicates the Slipper cluster in India 🇮🇳 England 🇬🇧 Israel 🇮🇱 and Singapore 🇸🇬 will be designated JN.1.11 (not yet designated at GISAID- still called JN.1 there)
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@DavidJoffe64
If you want to see how BA.2.86.1 is MOVING, answer the quiz (who would you sequence for baseline surveillance using Cleveland Clinic as the originating lab)? All 6 positives are in counties surrounding and including Cleveland Metro.
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Two SLIPPERS in Wales match 3 last week bringing total in Wales to FIVE.
All 5 have Spike L455S and F456L and share T26691C
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There appear to be a surprisingly high number of JN.1 seqs from the US (primarily NY submitted by PRI and CDC) which were submitted to Genbank last week which are NOT at GISAID
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Detail on JN.1 Slipper cluster with
Spike L455S, F456L, V1104L
NSP3 T1465I
G17334T
India/KA-RFNB-20224/2023
Col 12/2023 Bengaluru Karnataka India
India/KA-RFNB-20370/2023
Col 12/2023 Bengaluru Karnataka India
India/MH_BJCOG_INSACOG_6141/2023
Col 12/25/2023 Pune Maharashtra India
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One of the BA.2.86.1 seqs released at GISAID yesterday
England/CLIMB-CM7YJUMY/2023 9/18
had C13971T (nsp12), which was shared with the first four sequences from Scotland, as well as three additional seqs from England supporting the spread of this variant from Scotland to England
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New map marker C1960T (BA.2.86.2 candidate) coming (call Houston)
Australia/NSW (3)
England (1)
Luxembourg (1)
France (2)
South Africa (3)
USA/VA-GBW (1)
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Note that the 56 Denmark JN.1 seqs uploaded today (MANY labeled as "designation in process") DOUBLES the total of JN.1 seqs for Denmark
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After cracking 10,000 JN.1 / JN.1.1 uploads less than an hour ago, uploads are already more than halfway to 11,000 uploads
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BA.2.86 just expanded to BA.2.86.1 which appears to be sequences with NSP:K1155R (Orf1a:K1973R), which includes the UK cluster and new GISAID sequences from France (2 and counting)
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@BishopBlougram
Note that there are 8 BA.2.86 seqs with originating lab as one of two Karolynska University Hospitals in the Stockholm area suggesting 6 seqs are from 6 patients at 2 hospitals with the same unique sequence suggesting this version of BA.2.86.1 is putting people in hospitals
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The JN.1.11.1 derivatives are finally starting to get new names
Largest branch + Spike K1086R
tacked onto 46 JN.1.11* seqs and 3 JN.1.16
branch with JN.1.11* + K1086R is now KP.1
(h/t
@HarrySpoelstra
)
However, KP.1 is already branching and KP.1.1 will likely add Spike R346T
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12
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@mrmickme
Dairy Cows something to look at
proximity to Swine is a concern because swine have H1N1/09.
PB2 E627K is a first step toward mammalian adaptation (virus grows faster at lower temp, which is 37C for mammals vs 41C for birds), but that adaptation has been seen previously.
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12
37
many countries uploaded multiple JN.1 seqs this AM including
170 Singapore
79 France
18 England
5 Italy
4 Spain
3 Scotland
3 Norway
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36
Looks like a serious problem. 2 UK and 14 Portugal seqs also appear to also be JN.1 this morning
1
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36
38/50 JN.1 derivatives uploaded from Nigeria 🇳🇬 last night have Spike R346T
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First BA.2.86 Sequence from Japan - Sequences (COVID) - Recombinomics Inc.
Tokyo
collected 8/24/23
Spike ins16MPLF, V483del
NSP3 K1155R
BA.2.86.1
1
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37
@mrmickme
@SocioAnalytic
@xabitron1
There is no doubt that JN.1 derivatives collected in March will have strikingly high frequencies of new and improved SARS CoV2 sequences.
Visibility will be improved with ORD and MIA testing.
0
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H5N1 confirmed in Wyoming Dairy Farm. Location withheld.
First reported case (will not be the last and probably not the first).
Spead in state fairs expected as disaster looms due to lack of testing and reporting.
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36
First Two BA.2.86 Sequences from Seville Spain - Sequences (COVID) - Recombinomics Inc.
map update
Spain/AN-PMC-37141/2023
Spain/AN-PMC-37142/2023
Sevilla collected 8/29/23
Spike V483del
NSP3 K1155R
BA.2.86.1
1
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35
Looks like explosion of JN.1 in Canada being driven in part by NSP16 T91M.
A few weeks ago it was in one Alberta seq
Followed by 1 in Saskatchewan
Then 5 in Ontario
2 in Alberta
5 more in the Ontario seqs uploaded tonight
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35
Dairy Heard H5N1 B3.13
spilling over to poultry flocks & Alpacas
extent of spread to farms associated mammals
incl/ cats, red foxes, and Virginia opposums
unclear due to slow release of seqs
Pooled Commercial milk also B3.13
A/dairy_cow/Colorado/UW-9084466/2024
See HA tree
0
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Looks like UK JN.1 frequencies are approaching Denmark's. Tonight's UK daily BA.2.86 update shows an explosion of JN.1 seqs which are 17 higher today than yesterday (note that on 11/11 UK had 11 BA.2.86 seqs and 7 of them were JN.1)
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34
This evening uploads bring the JN.1 derivative seq total to 16,663
Expect dramatic uptick in JN.1 uploads later today (in spite of holiday season) and much higher in early 2024 because of the holiday season
JN.1 will be the dominant variant worldwide in the near term
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@manamath
@MMoltmannPhD
I follow emerging variants and am praticularly interested in SLippers (L455S + F455L) = JN.1.16 with S R346T
HMH seqs added S C1243F
They had uploaded 1 previously as had Ontario Canada and a US Internal Passenger, but then HMH added NINE
9 ta once is VERY unusual for emerging
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34
KP.2 SLipper w/ S R346T + T22795G (S)
ON Canada 🇨🇦 3/3
Tokyo Japan 🇯🇵 3/2
Tokyo Japan 🇯🇵 3/2
Tokyo Japan 🇯🇵 3/2
Tokyo Japan 🇯🇵 3/2
SFO CA USA 🇺🇸 ex Taiwan 🇹🇼 2/29
ON Canada 🇨🇦 2/28
IAD VA USA 🇺🇸 ex India 🇮🇳 2/28
SFO CA USA 🇺🇸 ex Germany 🇩🇪 2/27
SFO CA USA 🇺🇸 ex UNK 2/27
1/2
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34
@DavidJoffe64
Anyone can answer. How many of the 6 BA.2.86.1 positives in Ohio being sequence as baseline surveillance using Cleveland Clinic as the originating lab were over 65?
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Fourteenth BA.2.86 Sequence from New York USA - Sequences (COVID)
map update
USA/NY-CDC-QDX85192853/2023
New York
9/14/23 collection
Spike ins16MPLF, V483del
NSP3 K1155R
BA.2.86.1
NSP2 Y441C
NSP14 S221A
NSP14 N408K
NSP15 V69M
T26229C (ORF 3a)
T27134C (M)
3
7
33
Have already blown through JN.1 17,000 marker for GISAID uploads. Currently at 17,176, largely from UK uploads this AM, with some from Spain (details to come)
0
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34
SLipper March Madness - Singapore
JN.1.3 R346T
Singapore/R18MQ14/2024 3/25
JN.1.11.1
Singapore/R18MQ4/2024 3/21
JN.1.16
Singapore/R18MQ52/2024 3/25
Singapore/R18MQ62/2024 3/20
JN.1.16.1 R346T
Singapore/R18MQ19/2024 3/20
pg 1
2
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34
10 of the JN.1 seqs uploaded from Houston Methodist have Spike T572I, the defining change for JN.1.1.1
Total number of JN.1 derivative sequences with Spike T572I is 324 (although only about 1/2 are designated JN.1.1.1)
Most of the seqs have been uploaded in the past two weeks
0
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34
28/129 South Australia Australia 🇦🇺 JN.1 derivative seqs uploaded tonight were SLippers
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32
Actually, one of the HMH seqs was from an earlier upload
USA/TX-HMH-M-138376/2024 1/23
So it looks like all 9 JN.1.16 w/ R346T had C1243F (1 as a mixture - G25290K)
2
2
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Thirty Fifth BA.2.86 Sequence from England - Sequences (COVID) - Recombinomics Inc.
map update
England/CLIMB-CM7YRDUI/2023
England
Collected 8/31/23
NS7a E22D
E S68F
NSP3 D1031N
NSP14 H283Y
0
7
33
First BA.2.86 Sequence from France - Sequences (COVID) - Recombinomics Inc.
map update
France/GES-IPP17379/2023
Grand Est
collected 8/21/23
Spike ins16MPLF and V483del detected
6
10
33
Although the lineage matches the seqs from Mexico, the matches are from 2019 and earlier, raising concerns of silent spread or lack of reporting recent sequences
3
10
30
First BA.2.86 Sequence from Germany - Sequences (COVID) - Recombinomics Inc.
map update
Germany/BY-RKI-I-1137445/2023
Bavaria collected 8/21/23
S:ins16MPLF, MPLF483del
NSP3:K1155R
BA.2.86.21
1
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32
SLipper EXPLOSION
JN.1 derivative Seqs with Spike F456L uploaded to GISAID at 1,013
I will post new SLippers by variant name
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31
@manamath
@MMoltmannPhD
It is concerning when 9 come from a hosp, even for a hosp that upload every two weeks w/ lots of uploads
SLippers w/ S R346T will be MUCH more common in a few weeks when uploads include collections from this month
then you will see why S C1243F is alarming (like S K187R)
1
5
31
It looks like France just added 19 JN.1 seqs (in addition to 3 in Ontario Canada, and one in Houston, TX)
2
9
29
Houston Methodist Hospital uploaded 673 JN.1 derivative seqs to GISAID from Houston Texas USA 🇺🇸
0
6
30
First XDD Sequence from Denmark - Sequences (COVID)
map update
Denmark/DCGC-663246/2023
Denmark
11/6/23
NSP1 K47R
C2334T NSP2
G5720A NSP3
C6541T NSP3
NSP6 R252K
C18894T NSP14
Spike L455S
E T11A
A27507C NS7a
G27915T NS8
T28297C N
C29625T NS10
XDD
2
10
31
There are some major changes in daily UK-COG numbers. I didn't capture yesterday's and I am assuming today's has been updated. I see TEN new JN.1 compared to 10/31 numbers as well as major jumps in BA.2.86
3
7
28
5 new UK BA.2.86 seqs
only 61 sequences added
frequency today was higher than yesterday.
On 10/4 only 6 were sequenced and 3 were BA.2.86
number rose to 14 and frequency for the day increased Looks like the next major update for recent dates will have many BA.2.86 / JN.1 seqs
3
5
30
Puyang is just under 400 miles NNE of Wuhan. The JN.1.16 SLipper is spreading rapidly in China and is clearly a cause for concern as evidenced by the rapid release of the Baiyin seq which was imported to Wuhan from Thailand
1
4
29
New JN.1.11.1 Slipper cluster w/ G28621A
England/CLIMB-CM7YEKZS/2024
USA/NJ-CDC-LC1091174/2024
USA/CA-KP000382/2024 Kaiser Southern CA
Singapore/R4MQ70/2024
USA/NC-USAFSAM-S22099/2024 Air Force
Note all 5 seqs were collected in 2024
This is the 2nd 5 member cluster of JN.1.11.1
0
6
30
Note that
6 out of 24
JN.1 derivative seqs from
Oman
uploaded today
2/25/24
had
Spike R346T
compared to
8 out of67
in the
1/24/24
upload
1
4
30
All 49 JN.1.4 SLippers also had
2 polys shared w/ many other JN.1.4 Flippers
NSP8 T145I
NSP13 S589N
This clonal expansion was STRIKING in size and the unique polys indicated it was sudden
2
9
27
First BA.2.86 Sequences from Pennsylvania - Sequences (COVID) - Recombinomics Inc.
map update
USA/PA-DHSS-B1305664/2023 collected 8/20/23
SE PA
Spike ins16XXXX, V483del detected
1
10
30
Time for an interactive H5N1 map!
emphasis on B3.13 constellation of 2.3.4.4b
(aka US Dairy Herds and associated spillage)
Opacity levels remain EXTREMELY high (size and location of Herds withheld) but H5N1 is a reportable disease and US WHO reports incl Co (but size withheld)
1
10
29