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https://twitter.com/GYamey/status/1453132196416524292?s=20&t=REKS2qu5Ti7lby2jmu6Imw

Willsher, K. (2021, October 11). French study of over 22m people finds vaccines cut severe Covid risk by 90%. The Guardian. https://www.theguardian.com/world/2021/oct/11/french-study-vaccines-cut-covid-deaths

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Johnson, S. (2021, June 7). Spat at, abused, attacked: Healthcare staff face rising violence during Covid. The Guardian. http://www.theguardian.com/global-development/2021/jun/07/spat-at-abused-attacked-healthcare-staff-face-rising-violence-during-covid

Chrisafis, A. (2021, July 12). France mandates Covid health pass for restaurants and cafés. The Guardian. http://www.theguardian.com/world/2021/jul/12/france-mandates-covid-health-pass-for-restaurants-and-cafes

American Academy of Pediatrics urges FDA to approve COVID vaccines for children under 12. (2021, September 13). PBS NewsHour. https://www.pbs.org/newshour/show/american-academy-of-pediatrics-urges-fda-to-approve-covid-vaccines-for-children-under-12

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Davis, N. (2021, October 18). Valneva Covid vaccine could be as effective as Oxford jab, study suggests. The Guardian. https://www.theguardian.com/society/2021/oct/18/valneva-covid-vaccine-could-be-as-effective-as-oxford-jab-study-suggests

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Sandra Ciesek. (2021, December 8). Unsere ersten Daten zur Neutralisation von Omicron versus Delta sind fertig: 2x Biontech, 2x Moderna, 1xAZ/1x Biontech nach 6 Monaten 0% Neutralisation bei Omicron, auch 3x Biontech 3 Monate nach Booster nur 25% NT versus 95% bei Delta. Bis zu 37fache Reduktion Delta vs. Omicron https://t.co/w0gHww26sg [Tweet]. @CiesekSandra. https://twitter.com/CiesekSandra/status/1468465347519041539

Lipsitch, M., Krammer, F., Regev-Yochay, G., Lustig, Y., & Balicer, R. D. (2021). SARS-CoV-2 breakthrough infections in vaccinated individuals: Measurement, causes and impact. Nature Reviews Immunology, 1–9. https://doi.org/10.1038/s41577-021-00662-4

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Hamblin, J. (2021, December 9). Perspective | Omicron won’t keep us from ending the pandemic. We’re doing that ourselves. Washington Post. https://www.washingtonpost.com/outlook/2021/12/09/omicron-coronavirus-individual-threat/

Page, M. L. (2021, March 17). UK variant looks set to cause a surge in global coronavirus cases. New Scientist. https://www.newscientist.com/article/mg24933263-900-uk-variant-looks-set-to-cause-a-surge-in-global-coronavirus-cases/

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Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., Schwach, F., Harrison, I., Hellewell, J., Ariani, C. V., Gonçalves, S., Jackson, D. K., Johnston, I., Jung, A. W., Saint, C., Sillitoe, J., Suciu, M., Goldman, N., Panovska-Griffiths, J., … Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 1–11. https://doi.org/10.1038/s41586-021-04069-y

Harris, J. E. (2021). COVID-19 Incidence and Hospitalization During the Delta Surge Were Inversely Related to Vaccination Coverage Among the Most Populous U.S. Counties (p. 2021.08.17.21262195). medRxiv. https://doi.org/10.1101/2021.08.17.21262195

Le Page, M. (2021, November 22). What we know so far about AY.4.2 and other new coronavirus variants. New Scientist. https://institutions.newscientist.com/article/2298363-what-we-know-so-far-about-ay-4-2-and-other-new-coronavirus-variants/?utm_campaign=echobox&utm_medium=social&utm_source=Twitter

ReconfigBehSci. (2021, December 14). RT @thehowie: "...The vaccine provided 70 percent protection in fully vaccinated individuals against severe complications that would requir… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470749072160133128

How are new Covid cases impacting sport? (n.d.). BBC Sport. Retrieved December 23, 2021, from https://www.bbc.com/sport/59682938

ReconfigBehSci. (2021, December 14). RT @thehowie: BREAKING South Africa: 82% increase in cases, week over week. 34.9% positive rate. Record 7-day average. Not near platea… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470814593610047490

Dr Nisreen Alwan 🌻. (2021, December 23). We’re in unchartered territory. Https://t.co/O1GGcXpMll [Tweet]. @Dr2NisreenAlwan. https://twitter.com/Dr2NisreenAlwan/status/1474051397570248716

Kai Kupferschmidt. (2021, December 10). “the severity profile of Omicron cases must be interpreted along with an understanding of its capacity to re-infect (and infect the vaccinated)“ This is what I have been trying to explain the last few days. As usual @nataliexdean does it better (and in color)! [Tweet]. @kakape. https://twitter.com/kakape/status/1469270407995867139

Yaniv Erlich. (2021, December 8). Updated table of Omicron neuts studies with @Pfizer results (which did the worst job in terms of reporting raw data). Strong discrepancy between studies with live vs pseudo. Https://t.co/InQuWMAm4l [Tweet]. @erlichya. https://twitter.com/erlichya/status/1468580675007795204

ReconfigBehSci. (2021, December 12). RT @ryan_landay: > A new diverse genome has appeared within the B.1.1.529 lineage that has all of the shared mutations of B.1.1.529, some o… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470066521615605766

ReconfigBehSci. (2021, December 9). RT @RachelLavin: As Omicron reality dawns, consider investing in better masks: "....Tight-fitting FFP2 masks provide 75 times better pro… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1474030898551087113

Campbell, D., Sabbagh, D., & Devlin, H. (2022, January 7). Military deployed at London hospitals due to Omicron staff shortages. The Guardian. https://www.theguardian.com/world/2022/jan/07/military-deployed-at-london-hospitals-due-to-omicron-staff-shortages

ReconfigBehSci. (2021, November 26). RT @mvankerkhove: Following the meeting of the @WHO TAG-VE today, WHO classifies B.1.1.529 as a variant of concern named Omicron. We call… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464302372100976650

ReconfigBehSci. (2021, December 12). RT @EricTopol: If you think Prior Covid protects against Omicron (B.1.1.529), think again https://medrxiv.org/content/10.1101/2021.12.08.21267491v1 and "Neutralizing antibo… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470434736304803845

ReconfigBehSci. (2021, November 26). vaccine equity has been a disaster, but I do wonder whether the exclusive focus on donations does the US/EU comparison justice. The EU allowed the export of huge numbers of EU produced doses at a time when the US did not (and EU itself was struggling to meet demand). [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464255575416520749

ReconfigBehSci on Twitter: “RT @BNODesk: BREAKING: U.S. reports 716,714 new coronavirus cases, setting world record for cases in one day” / Twitter. (n.d.). Retrieved January 7, 2022, from https://twitter.com/SciBeh/status/1478987541332348933

Karan, A. (2022). We cannot afford to repeat these four pandemic mistakes. BMJ, 376, o631. https://doi.org/10.1136/bmj.o631

ReconfigBehSci. (2021, December 23). Risk of hospital stay 40% lower with Omicron than Delta, UK data suggests https://t.co/VupN8hY4qq [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1473916654421643266

ReconfigBehSci. (2021, November 26). maybe this is a good moment to remind people that makers of mRNA vaccines have been extensively prepping for the possibility of new variants. Biontech/Pfizer have given a timeline of 100 days to the delivery of a retooled version of their vaccine [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464225264523747359

Kissane, E. (2021, December 23). We’re About to Lose Track of the Pandemic. The Atlantic. https://www.theatlantic.com/ideas/archive/2021/12/were-about-to-lose-track-of-the-pandemic/621097/

ReconfigBehSci. (2021, December 11). RT @MackayIM: Booster access brought forward to slow spread of Omicron COVID-19 variant https://t.co/PukbPydylw [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1469633384511119364

Eric Topol. (2022, January 2). As the world turns.....vertical the Omicron signature (|) @OurWorldInData https://t.co/LOBiaiBapD [Tweet]. @EricTopol. https://twitter.com/EricTopol/status/1477433315896430592

ReconfigBehSci. (2021, December 13). RT @DrEricDing: 11) Omicron is doubling every 1.6 days in UK 🇬🇧 according to @DrWilliamKu’s figure. That’s way faster growth than in South… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470451594378502154

Prof. Christina Pagel. (2021, December 23). UKHSA surveillance report shows reinfections rising sharply as Omicron takes hold https://t.co/UGArY4sbOA [Tweet]. @chrischirp. https://twitter.com/chrischirp/status/1474041921249189896

Thomas, T., & Duncan, P. (2021, December 23). If Omicron is the dominant variant in UK, why is the number of confirmed cases so low? The Guardian. https://www.theguardian.com/world/2021/dec/23/if-omicron-is-the-dominant-variant-in-uk-why-is-the-number-of-confirmed-cases-so-low

ReconfigBehSci. (2021, December 13). Important update on the now withdrawn @BallouxFrancois tweet identifying hopeful turning of the corner in SA omicron data [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470311016114364420

ReconfigBehSci. (2021, December 11). RT @DrEricDing: DOUBLING % in one day: The spike of probable #Omicron variant in Scotland🏴󠁧󠁢󠁳󠁣󠁴󠁿 has critically surged—Now at 13.3%, up fro… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1469596523222781954

ReconfigBehSci. (2021, December 8). RT @kallmemeg: NEW: @UKHSA Mini Omicron Update Omicron VOC-21NOV-01 (B.1.1.529) update on cases, S gene target failure and risk assessment… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1468673329494216726

John Burn-Murdoch. (2021, November 25). Five quick tweets on the new variant B.1.1.529 Caveat first: Data here is very preliminary, so everything could change. Nonetheless, better safe than sorry. 1) Based on the data we have, this variant is out-competing others far faster than Beta and even Delta did 🚩🚩 https://t.co/R2Ac4e4N6s [Tweet]. @jburnmurdoch. https://twitter.com/jburnmurdoch/status/1463956686075580421

CNN, I. K. (n.d.). Vaccine inequity and hesitancy made the Omicron variant more likely, scientists say. CNN. Retrieved December 23, 2021, from https://www.cnn.com/2021/11/28/world/omicron-coronavirus-variant-vaccine-inequity-intl-cmd/index.html

ReconfigBehSci. (2021, December 22). RT @chrischirp: Positivity rising steeply too—There are definitely many more people we aren’t catching https://t.co/4xDPwYQtrx [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1473695678610214927

ReconfigBehSci on Twitter: “RT @chrischirp: As well as Tom’s new one (B.1.1.529), C.1.2 seems to be spreading in S Africa—C.1.2 was the one with lots of worrying mut…” / Twitter. (n.d.). Retrieved December 23, 2021, from https://twitter.com/SciBeh/status/1463597407082532864

ReconfigBehSci. (2021, December 16). RT @MadsAlbertsen85: #Omicron update from Denmark. Omicron cases on the 12th of December adjusted up to 20.5% (+2%). Omicron is now having… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1471516083819462670

ReconfigBehSci. (2021, December 11). RT @thehowie: BREAKING: Hospitalizations South Africa Hospitalizations⬆️67% week over week. Gauteng Province⬆️66%. GP⬆️1.6% from yesterd… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1469685234149072897

ReconfigBehSci. (2021, December 9). a rather worrying development- a (local) newspaper “fact checking” the new German health minister simply by interviewing a virologist who happens to have a different view. There’s simply no established “fact” as to the severity of omicron in children at this point in time [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1469037817481334786

Trevor Bedford. (2021, December 11). We find that logistic growth of Omicron sequence fraction looks similar between the UK, the US and Germany with roughly 1% of sequenced cases in all three countries being Omicron on Dec 1. 3/10 https://t.co/De0t2xreU9 [Tweet]. @trvrb. https://twitter.com/trvrb/status/1469784757261127685

Gollub, R. L. (2022). Brain changes after COVID revealed by imaging. Nature. https://doi.org/10.1038/d41586-022-00503-x

ReconfigBehSci. (2021, December 17). RT @EricTopol: No evidence that Omicron is less severe, new @imperialcollege study reports https://ft.com/content/020534b3-5a54-4517-9fd1-167a5db50786 https://t.co/5YYzJ6tVtc [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1472156681098469380

ReconfigBehSci. (2021, November 26). RT @HZiauddeen: 🧵 COVID-19 & B.1.1.529: A chance for govt & others to change their mind and their approach? While we are still gathering d… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464200877888184324

ReconfigBehSci. (2021, December 22). RT @chrishendel: We need increased targeted measures now to slow the spread of #Omicron by @DrSarahHal via @bmj_latest https://t.co/3Tx… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1473987200509521925

Perspective | Even the best-case scenario with omicron will still be bad. (n.d.). Washington Post. Retrieved December 23, 2021, from https://www.washingtonpost.com/outlook/2021/12/21/omicron-mild-cases-numbers/

Covid: Dutch go into Christmas lockdown over Omicron wave. (2021, December 18). BBC News. https://www.bbc.com/news/world-europe-59713503

Nature Portfolio. (2021, October 15). A study in @NatureMedicine indicates that the effectiveness of the Pfizer/BioNTech and Oxford-AstraZeneca vaccines against SARS-CoV-2 infections with symptoms or high viral burden is reduced with the Delta variant compared to the Alpha variant. Https://go.nature.com/3vecpoj https://t.co/XQdnMYguFz [Tweet]. @NaturePortfolio. https://twitter.com/NaturePortfolio/status/1449145321188216836

Prof. Shane Crotty. (2021, October 19). 1/ The regular vaccines give great booster responses against Delta and other variants This was first shown by Moderna, with “original recipe” vaccine booster, compare to Beta booster. Https://nature.com/articles/s41591-021-01527-y https://t.co/g7YDwGIURP [Tweet]. @profshanecrotty. https://twitter.com/profshanecrotty/status/1450489709050744833

ReconfigBehSci [@SciBeh]. (2021, November 26). RT @mvankerkhove: I thank researchers from 🇿🇦 and 🇧🇼 for sharing information with @WHO & the world about B.1.1.529 variant that has been re… [Tweet]. Twitter. https://twitter.com/SciBeh/status/1464196599773642779

ReconfigBehSci. (2021, December 20). RT @thehowie: South Africa Deaths (7 day average) are near double levels of a few weeks ago. They will go up further. They are only 7.5%… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1472991477672419334

Yale researchers develop RNA-based therapy that clears SARS-CoV-2 from mice. (n.d.). EurekAlert! Retrieved January 9, 2022, from https://www.eurekalert.org/news-releases/934454

Purpose of WGS in population epidemiology

1. Surveillance
2. Outbreak Investigation
3. Source attribution
4. Microbial population