Raj Rajnarayanan
@RajlabN
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Assistant Dean of Research and Associate Professor, NYITCOM at Arkansas State University | My Tweets are my own
Joined December 2018
#COVID19 #VariantDashboard - #USA| 05/26/25. #SARSCoV2 #Lineages #30DAYTRENDS. LP.8.1.1 (25.8%).XFG.2 (8%)👀.NB.1.8.1 (7.5%)👀.XFG (5.6%).XEC.4.1 (4.5%).XFJ (4.5%).LP.8.1 (3.5%).LF.7.9 (3%).LF.7.7.2 (2.6%).PQ.2 (2.2%)👁️. Tracker: 1/n
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#SARSCoV2 Updates . Meet #Arcturus's kids and grand-kids . XBB.1.16 (Signature: S:E180V, S:478R).XBB.1.16.1 (S:T547I).FU.1 | Alias of XBB.1.16.1.1 (T3802C).FU.2 | Alias of XBB.1.16.1.2 (C8692T).XBB.1.16.2 (ORF3a:V13L, ORF1a:P926H).XBB.1.16.3 (A2893C)
Two new #SARSCoV2 lineages are going viral in social media even without any nicknames— “FU.1 and FU.2” (XBB.1.16* sub-lineages).
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I would wear a high quality #mask in a crowed airport. WHY? . 1. @CDCgov #COVID19 positivity rate in airports seem to be hovering around 20% (much higher than baseline community positivity rates reported) . H/T @TaylorLorenz
I feel so bad for the boomers at home being subjected to this. Never seen a group of people more triggered over something so innocuous
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H5N1 Update | Avian Flu Clade 2.3.4.4b. Looked at the newly uploaded Human Sequence (ID: 19027114) from Texas . - PB2 contains 👀E627K 👀 . in addition to the mutations found in the dairy cattle and wild bird sequences uploaded earlier (used #Fluserver for mutational analysis)
Avian Flu Clade 2.3.4.4b update. Looked at newly uploaded sequences (GISAID) from Dairy Cattle and birds from Texas . Dairy Cows, Blackbirds and Common Grackle have similar mutation pattern. Likely source?. 1/n
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The BA.1 effect. It's astonishing how easily people dismiss a peak with a million weekly infections by comparing it to the highest point during the BA.1 variant, despite having robust testing and reporting in place.
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Greater than Titan!. Seems like BA.2.75 has the potential to outcompete BA.5*/BA.4* and other circulating BA.2 lineages . Early days but growth advantage will be clear in a couple of weeks.
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#SARSCoV2 #EarlyAnalysis #BA2. Spike mutational profile of newly designated BA.2.86 (BA.X) spotted by @shay_fleishon and @LongDesertTrain . BA.2.86 vs XBB.1.5 (This season's vaccine antigen selected by @US_FDA/@CDCgov). Closely monitored by #VariantHunters and more recently @WHO
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It’s would be prudent to update COVID-19 vaccine antigen . The fear of “not many will take it” should not take this tool away from “many who will take it” or “needs it”. It’s Public Health not popular Health!.
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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
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One by one. Wisconsin #H5N1 human case likely belongs to D.1* type -- currently circulating in Washington State, Louisiana and British Columbia, Canada.
JUST IN: Wisconsin reports its first human case of H5N1 bird flu, linked to poultry
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Yes, we are watching XBB.1.16 closely. Seems to be picking additional mutations already.
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"The Great Decoupling" of reported #COVID19 cases from severe outcomes, such as #hospitalizations and #deaths enabled swift end to pandemic regulations. However, it leaves behind several suffering from long COVID, affecting individuals regardless of infection severity.
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If public health experts learned anything from the COVID-19 pandemic, it’s that if you keep saying “everything is mild” then “the common people tend not to pay attention at all.”.
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👀Increase in newly reported #COVID19 Hospitalizations, as JN.1* overtakes all the circulating lineages in #NewYork . Source: | @HealthNYGov @nycHealthy | * #SARSCoV2 lineage BA.2.86.1.1; #Pirola group
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BA.2.86 Updates. 7th BA.2.86 (#Pirola) sequence from #Virginia (via @CDCgov Traveler Based Genomic Surveillance Program). Traveler from #Japan; Asymptomatic . Collection date 8/10/23. H/T @OliasDave.
We now have a 7th BA.2.86, sampled in the USA on August 10th, so these weekly counts are now:-.2023-07-24 1 of 7659.2023-07-31 3 of 4995.2023-08-07 3 of 1120.2023-08-14 0 of 36.
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XBB, the “first major highly immune-evasive” group of COVID variants, “will sweep through China,” but the wave will be “largely invisible” owing to low rates of testing and reporting. H/T @ErinMPrater @WellatFortune .
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#WasteWater #SARSCoV2 content is trending up again in #USA . Closely watching for EG.5.1*, XBB.1.16* signals . Source: @BiobotAnalytics . 1/n
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@GISAID Thanks to all the countries that are still supporting #SARSCoV2 testing and rapidly submitting sequences to public databases like @GISAID . #SouthKorea, #USA, #Canada, #China, #Australia, #Singapore, #Austria, #UK, #Spain & #Japan have submitted a lion's share of sequences 🙏
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Closely following this 👀. #Pigs have both #avian-type and #human-type receptors in their respiratory tracts. Allowing them to be infected by both avian and human influenza viruses == facilitating potential #reassortment of viral segments.
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XBB.1.16* should definitely be designated as a #VOI by @WHO . Growth advantage over current lineages ✅.Spread in multiple-countries ✅.Epidemiological ✅.Clinical: Unknown. Add to this #SARSCoV2 Testing ⬇️and Global genomic surveillance ⬇️.
Tracking XBB.1.16* (#Arcturus) over time - Globally. Total Sequences: 474. Spotted in #India #USA #Brunei #Singapore #UK #Australia #Japan #NewZealand #Canada #Germany #Denmark #SouthKorea #Malaysia #Ireland #Italy #Austria #China . Tracker: 03/22/2023
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Thank you Dr. @PeterHotez! . Your constant engagement and attempts to educate people with science and fact-based information is amazing!.
Joe, you have my cell, my email, I’m always willing to speak with you.
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Agree w/ @EricTopol 100% . New COVID Booster (XBB.1.5) is only a few spike mutations away from the top circulating SARSCoV2 lineages and should be effective in preventing severe COVID and hospitalizations especially in senior and vulnerable populations (comorbid conditions).
The EG.5.1 #SARSCoV2 variant is gaining in the US and in many places globally. Here's the spike protein cf XBB.1.5 with only 2 new mutations (F456L and Q52H). The new Covid boosters, directed vs XBB.1.5, are closely aligned, should be v effective vs severe Covid, and are overdue
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#H5N1 #AvianInfluenza Updates . Quick analysis of the newly uploaded H5N1 sequences from human cases in #Washington . These sequences contain NA S247N -- implicated in #antiviral drug resistance/reduced drug sensitivity. 1/n
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Clear uptick of #COVID19 #Hospitalizations in #NewYork 👀 . EG.5.1* (#Eris)is the top circulating #SARSCoV2 lineage in NY . #WasteWater signals (#Biobot / @CDCgov) are increasing in #NorthEast #USA region. 1/n
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BA.2.75* is poised to outcompete other circulating omicron lineages. It would be prudent to check VE of the bivalent vaccines against BA.2.75* . Even if its takes additional time to generate few good bridging/supplemental studies or short trial. its worth the wait.
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#H5N1 #LessonLearned - Domestic and Farm cats!. Common theme among H5N1 clade 2.3.4.4b infected Cats:.- Present multiple symptoms almost immediately.- Neurologic, Respiratory, rapid decline leading to death . (or compassionate euthanasia).- Pick PB2 mammalian adaptations . 1/n
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“A lot of people think ‘endemic’ means end,” but it actually means that it’s transitioned to become a permanent threat" - @asosin . H/T @DohenyKathleen @WebMD.
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Two new #SARSCoV2 lineages are going viral in social media even without any nicknames— “FU.1 and FU.2” (XBB.1.16* sub-lineages).
Great work by @CorneliusRoemer in designating a lot of new lineages tonite. also new sublineages of XBB.1.16 (.2 and FU.s), more 478Rers and 456Lers
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Lineages to watch . 1. BQ.1*.2. BQ1.1* .3. BA.2.75.2* .4. XBB - Recombinant of BJ.1 and BM.1.1.1.5. BA.2.3.20 . All lineages have appreciable ACE2 affinity;.1-4 are highly immune evasive;.1 & 2 evade many therapeutics - #Evusheld and #Bebtelovimab.
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BA.2.86* #Pirola Updates. #UnitedKingdom has uploaded 27 sequences to GISAID today- majority of these sequences were from a single care-home outbreak. While this is not surprising for a lineage like BA.2.86*, the attack rate of ~87% is still high. 1/n.
Details of the BA.2.86 Care Home outbreak - attack rate of 86.6%.
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#H5N1 #AvianInfluenza updates . Recently uploaded H5N1 sequences contain concerning PB2 mutation E627K (both B3.13 and D1.1 genotypes) and D701N (D1.1). A mutation reported to increase virulence in mammalian models. 1/n
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Time to take JN.1* seriously. Already produced a few kids worth monitoring. 1) XDD - JN.1*/EG.5.1.1* recombinant (spotted by @JosetteSchoenma) .2) #SLip - Picked up Spike F456L adjacent to L455S (@LongDesertTrain) .3) Few Non-Spike mutations described in
Tracking #SARSCoV2 #Lineages - Globally |11/25/23. Top lineages -#30DayTrends (#G30):. HV.1 (16.4%)⬆️.HK.3 (10.5%).JN.1 (4.8%)🚀👀.EG.5.1.1 (4.7%).JG.3 (4.4%).JD.1.1 (3.8%).EG.5.1 (3.5%).EG.5.1.3 (2.7%).FL.1.5.1 (2.6%).BA.2.86.1 (2.5%). Track 1/n
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"Experts are closely monitoring JN.1 (BA.2.86.1.1)" “. has all the features of becoming a dominant lineage”. “With travel and the holidays coming up, we know that it's gonna spread everywhere". H/T @hlavinka_e @Salon .
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@COVIDnewsfast @DrEricDing #Poland (44% share of BA.2 sequences carry H78Y mutation), #Sweden (38%) and #Denmark (28%) are BA.2+Orf3a:H78Y hotspots. Several European countries are catching up!
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#Omicron family swells to 653+ #sublineages!. Currently, we are watching "Omicron" Great-Great-Great grand kids. especially the recombinant family members. Expected to outcompete other circulating Omicrons including Omicron-BQ*. XBB.1.5* poised to take over North America soon!
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Status of Genomic Surveillance in the World . Global genomic surveillance is significantly down & the negative impact of Global & National Emergency End Declarations is evident!. Source: GISAID
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Closely following this. Will update as soon as sequence is publicly available.
BREAKING: Mexico reports its first human case of H5N1 bird flu, source unknown. The patient - a 3-year-old girl from Durango - is in serious condition.
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As of now, there is no official announcement from the @CDCgov or @US_FDA regarding the timing of new #COVID19 vaccines or specific recommendations (in the interim). Agree 100% with @PeterHotez. Need updates on the guidelines from CDC/FDA ASAP!. 3/n.
A common question I’m being asked is whether to hold out for the new Covid vaccines or just go ahead and get another XBB while transmission is high now? It would help if CDC or FDA gave us a heads up on timing and any recommendations.
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BA.2.86* #Pirola updates. Meet new sub-lineages:. BA.2.86.1(ORF1a:K1973R).JN.1BA.2.86.1.1 (S:L455S, ORF1a:R3821K, ORF7b:F19L).JN.2BA.2.86.1.2 (ORF1a:Y621C).JN.3BA.2.86.1.3 (ORF1a:T2087I).BA.2.86.2(ORF7a:E22D).BA.2.86.3(C222T, C1960T, T12775C).JQ.1BA.2.86.3.1 (S:T95I)
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BA.3 . our old friend is back donning new mutations. A timely reminder that viruses "evolve". Continuous genomic surveillance isn’t optional. it's essential!. H/T @LongDesertTrain.
So this BA.3 (now designated BA.3.2) had not reappeared since I posted this thread. until today, when a BA.3.2 showed up in the Netherlands—the first detection outside of South Africa. April 2 collection date. BA.3 ain't dead yet. 1/7
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BA.2.86 (#Pirola) updates. 8th BA.2.86 sequence is uploaded from #Mpumalanga, #SouthAfrica . Specimen collection date: 7/28/2023 via baseline surveillance. 1/n
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Looks like @Novavax updated vax approval is not far behind. .
Doses of Novavax’s updated protein-based #Covid vaccine arrived in the US today and will be ready for release pending EUA and recommendation from the @CDCgov and ACIP. Novavax will present the latest data on its vaccine at ACIP’s Sept.12, 2023 meeting.
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BA.2.86 shows higher infectivity than all other #omicrons tested in Calu-3, a human airway epithelial cell line and a good preclinical respiratory model. H/T @ShanLuLiu1.
We find that BA.2.86 has low infectivity in 293T-ACE2 cells, similar to @yunlong_cao results, but high infectivity in CaLu-3 cells - actually the highest among all Omicron variants tested.
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Tracking XBB.1.16* (#Arcturus) over time - Globally. Total Sequences: 205. Spotted in #India, #USA, #UnitedKingdom, #Singapore, #Australia, #SouthKorea, #Denmark, #Italy, #Ireland, #Germany, #Canada, #Austria. Tracker: Updated: 03/17/2023
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Avian Flu Clade 2.3.4.4b update. Looked at newly uploaded sequences (GISAID) from Dairy Cattle and birds from Texas . Dairy Cows, Blackbirds and Common Grackle have similar mutation pattern. Likely source?. 1/n
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“#COVID19 hospitalizations increased 20.4% the week ending December 30, 2023. In that same period, deaths went up by 12.5%, with COVID-19 deaths accounting for 3.6% of total deaths in the United States.”.
CDC continues to track the rise of the JN.1 variant, which now accounts for 62% of circulating COVID-19 variants in the U.S. Existing vaccines, tests, and treatments work against JN.1.
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XBB.1.5 is poised to outcompete all other circulating lineages in #England, #UnitedKingdom including CH.1.1* and BQ.1*/BQ.1.1*(unless something else pop up). (Growth advantage charts generated w/ @GenSpectrum )
Tracking XBB.1.5* lineage over time in Europe | 01/09/2023. Emerging hotspots #UnitedKingdom , #Denmark, #Austria^^, #France, #Germany, #Netherlands . ^^ data includes targeted surveillance as well
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#SARSCoV2 updates. Meet new #recombinant sub-lineages EG & EK. Yup! maxed X** letter codes and now moving to EG*, EK* etc. EG.1 |Alias of XBB.1.9.2.1 | Signature mutations: S:Q613H, N:L219F . EK.1 | Alias of XBB.1.5.13.1 | Signature mutations: S:K417S . 1/n.
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Closely watching JN.1.6.1 (Signature mutation Spike R346T). Spike R346T is one of the legacy mutations!. It clearly stands out in the ACE2 binding vs Immune escape charts!. 1/n
#COVID19 #VariantDashboard - #USA .#SARSCoV2 #Lineages #30DAYTRENDS . JN.1 (27.7%)👁️.HV.1 (14.9%)⬇️.JN.1.4 (11.5%)⬆️👀.JN.1.1 (5.9%).JD.1.1 (2.8%).HK.3 (2.4%).JG.3 (1.9%).FL.1.5.1 (1.4%).BA.2.86.1 (1.3%).JN.1.2 (1.3%). Tracker: | 01/11/24.1/n
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Tracking #SARSCoV2 #Lineages - Globally |06/08/24. Top lineages -#30DayTrends (#G30). KP.2.3 (8.7%).KP.2 (8.7%).KP.3.1 (7.7%).KP.3 (6.2%).KP.3.2 (5.1%).LB.1 (5%).KP.1.1 (4.9%). Track: 1/n
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#WasteWater #SARSCoV2 content is trending up again in #NE #USA . Closely watching for EG.5.1*, XBB.2.3* & XBB.1.16* signals in NE USA. Source: @BiobotAnalytics . H/T @MAPdonnelly . 1/n
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Status of Genomic Surveillance in the World . Global genomic surveillance is significantly down & the negative impact of Global & National Emergency End Declarations is evident! . Source: GISAID; updated 8/23/2023
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XBB.1.9.1 spotted in #China | . Qinghai / Xining - Specimen collection date 2/23/23.Sichuan / Meishan - Specimen collection date 2/19/23. XBB.1.9.1 is expected to have a significant growth advantage over other circulating variants (BA.7.14*, BA.5.2.48* & BA.5.2.49*) and XBB.1.5*
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Good news!. @moderna_tx XBB.1.5 #COVID19 vaccine generates a strong human immune response against BA.2.86 (#Pirola).
We announced today clinical trial data for our updated COVID-19 vaccine candidate in humans against BA.2.86 (Pirola), a variant under monitoring. Read more ⬇.
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Closely monitoring newly reported #COVID19 #Hospitalizations in #NewYork state (@HealthNYGov). Already crossed previous year's peak, poised to cross Jan 2021 peak if this trend continues. #MaskUP, #Ventilate and get #Boosted!
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#SARSCoV2 #VariantDashboard #Japan. Top lineages (#30DayTrends):. XBB.1.16 (15.2%).EG.5.1 (11.7%)👀⬆️.XBB.1.5 (4.4%)⬇️.XBB.1.16.1 (4.3%).FL.4 (4.2%).XBB.1.9.1 (3.8%).XBB.1.16.2 (3.6%).EG.1 (3.1%).XBB.2.3.2 (2.9%).FU.1 (2.5%). |Updated 07/21/2023
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Tracking #SARSCoV2 #Lineages - Globally |07/20/24. Top lineages -#30DayTrends . KP.3.1.1 (14.2%)👀.KP.2.3 (7.9%).KP.3.1 (7.8%).KP.3.3 (7.7%).KP.3.2 (3.8%).KP.3 (3.4%).KP.3.1.4 (3.4%).KP.2 (3.4%).LB.1 (2.7%).KP.2.2 (2.7%). Track #G30 : 1/n
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Global #SARSCoV2 #VariantDashboard | #15DayTrends - updated 12/10/2023. JN.1 has surpassed all major circulating lineages, yet in certain regions, it hasn't claimed the top spot. Given current knowledge, it's anticipated to outcompete soon. 1/n
Tracking #SARSCoV2 #Lineages - Globally |12/09/23. Top lineages -#30DayTrends (#G30):. HV.1 (16.1%)⬇️.JN.1 (9.6%)🚀👀.HK.3 (6.8%)⬇️.JG.3 (4.5%).JD.1.1 (3.8%).JN.1.1 (3.7%)⬆️👀.BA.2.86.1 (3.1%).EG.5.1.1 (2.9%).JN.2 (2%) ⬆️. . 1/n
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#COVID19 #VariantDashboard - #UnitedStates . XBB.1.5 is the top circulating lineage in USA . TOP lineages (15-DAY TRENDS):. 18.1% XBB.1.5👀🚀.17.1% BQ.1.1.10.2% BQ.1.4.4% BQ.1.22.4.3% XBB.1.2.2% BQ.1.1.3. Tracker: #OmicronUpdates 12/26/22 . 1/n
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SARSCoV2 BA.2 #subvaraints carrying #MainProtease (#MPro) mutations associated with reduced #nirmatrelvir (#Paxlovid) activity . Top #NSP5 (MPro) mutations: H164N, G15S, T135I. Should investigate if these NSP5 mutations are also associated with Paxlovid rebound. 1/n
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Wish you and your family a Happy and Healthy New Year 2024
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Excellent news! @Novavax's updated #COVID booster induced neutralizing responses to emerging subvariants EG.5.1 (#Eris) and XBB.1.16.6 (#Arcturus sub-lineage) with Spike F456L in addition to XBB.1.5 (#Kraken), XBB.1.16 (#Arcturus) and XBB.2.3 (#Acrux). H/T @HarrySpoelstra.
The good news for today!!. Data have shown that Novavax's COVID booster induces broadly neutralizing responses against XBB subvariants, including EG.5.1 and XBB.1.16.6.
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@EricTopol @Mike_Honey_ BA.2.75 is already in the USA. Two sequences were uploaded in GISAID yesterday with sample collection dates 6/14/22 (Washington) and 6/15/22 (California).
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BA.2.86 (#Pirola) updates. According to the @MichiganHHS "7 cases of the highly mutated BA.2.86 strain have been found worldwide including one case in Washtenaw County. The person with the BA.2.86 case is an older adult with mild symptoms". @wcpublichealth.
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XBB.1.5 booster and recent infections may offer some protection against BA.2.86 (#Pirola). Based on previously available data, they are expected to work against current top lineages EG.5.1 (#Eris), FL.1.5.1 (#Fornax) etc . Get boosted as soon as XBB.1.5 booster is available. 1/n.
Real-time data update: we've got our first BA.2.86 (see red arrow) neutralization results. Short 🧵with much credit to @DannySheward and the rest of the team.
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.@Walgreens's #COVID19 #Index . Test positivity is > 40% . (treat this like an election exit poll - includes tests performed at Walgreens sites nationwide). 1) We are still riding the #UglyPeak.2) Potentially many missed and unreported cases.3) Pandemic is far from over!
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#CoronaVirusUpdates #China . 20 new SARSCoV2 sequences were uploaded from #Beijing today!. Mostly BF.7 and BA.5.2
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Before tackling a new health threat, such as 'Disease X,' it is essential to openly acknowledge and analyze the shortcomings and gaps in our response to the current ongoing pandemic. 1/n.
‘Disease X’ is a placeholder for an unknown pathogen that could cause a global emergency. History has taught us that we must anticipate new threats. Failing to prepare leaves the world prepared to fail. At #WEF24 today, I spoke about @WHO initiatives that are supporting
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#CoronovirusUpdates #potential new lineage (sub-branch) - BA.2 + S:I210T mutation. Observed increasing % of this mutation among BA.2.2 (S:I1221T) sequences from #UnitedKingdom . Right now, 88% of BA.2.2 from UK contains S210T. This mutation is not present in BA.2.2 from #HongKong
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