Karim, S. S. A., & Karim, Q. A. (2021). Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic. The Lancet, 0(0). https://doi.org/10.1016/S0140-6736(21)02758-6

Beaumont, P. (2021, December 17). T-cells in Pfizer Covid jab recipients stay robust against severe illness. The Guardian. https://www.theguardian.com/world/2021/dec/17/t-cells-pfizer-covid-jab-robust-against-severe-illness-south-africa-research

Weaver, M. (2022, January 4). Omicron infections may have plateaued in London, Neil Ferguson says. The Guardian. https://www.theguardian.com/world/2022/jan/04/omicron-infections-may-have-plateaued-in-london-neil-ferguson-says

Bloom, J., & Cobey, S. (2021, December 12). Opinion | A Scientist’s Guide to Understanding Omicron. The New York Times. https://www.nytimes.com/2021/12/12/opinion/covid-omicron-data.html

Dolgin, E. (2021). Omicron is supercharging the COVID vaccine booster debate. Nature. https://doi.org/10.1038/d41586-021-03592-2

Dickson, C. (2021, November 30). B.C. identifies 1st case of omicron variant | CBC News. CBC. https://www.cbc.ca/news/canada/british-columbia/henry-dix-nov30-1.6267987

Campbell, L., Belam, M., & Lock, S. (2021, December 2). Covid live: Germany set to impose restrictions on the unvaccinated; India detects two cases of Omicron variant. The Guardian. https://www.theguardian.com/world/live/2021/dec/02/coronavirus-news-live-south-africa-sees-exponential-increase-in-covid-cases-dominated-by-omicron-variant

Kozlov, M. (2021). Waning COVID super-immunity raises questions about Omicron. Nature. https://doi.org/10.1038/d41586-021-03674-1

Iketani, S., Liu, L., Guo, Y., Liu, L., Huang, Y., Wang, M., Luo, Y., Yu, J., Yin, M. T., Sobieszczyk, M. E., Huang, Y., Wang, H. H., Sheng, Z., & Ho, D. D. (2022). Antibody Evasion Properties of SARS-CoV-2 Omicron Sublineages (p. 2022.02.07.479306). bioRxiv. https://doi.org/10.1101/2022.02.07.479306

Gye, H. (2021, November 29). All adults to be offered booster jabs after 3 months, and over-12s to get second doses. Inews.Co.Uk. https://inews.co.uk/news/politics/covid-booster-jabs-to-be-offered-all-adults-after-3-months-and-over-12s-second-doses-1325151

Lauring, A. S., Tenforde, M. W., Chappell, J. D., Gaglani, M., Ginde, A. A., McNeal, T., Ghamande, S., Douin, D. J., Talbot, H. K., Casey, J. D., Mohr, N. M., Zepeski, A., Shapiro, N. I., Gibbs, K. W., Files, D. C., Hager, D. N., Shehu, A., Prekker, M. E., Erickson, H. L., … Self, W. H. (2022). Clinical severity of, and effectiveness of mRNA vaccines against, covid-19 from omicron, delta, and alpha SARS-CoV-2 variants in the United States: Prospective observational study. BMJ, 376, e069761. https://doi.org/10.1136/bmj-2021-069761

Torjesen, I. (2021). Covid-19: Omicron may be more transmissible than other variants and partly resistant to existing vaccines, scientists fear. BMJ, 375, n2943. https://doi.org/10.1136/bmj.n2943

Zeitung, S. (2021, December 1). Sieben weitere bestätigte Omikron-Fälle in Hessen. Süddeutsche.de. https://www.sueddeutsche.de/gesundheit/gesundheit-frankfurt-am-main-sieben-weitere-bestaetigte-omikron-faelle-in-hessen-dpa.urn-newsml-dpa-com-20090101-211201-99-218296

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

Regev-Yochay, G., Gonen, T., Gilboa, M., Mandelboim, M., Indenbaum, V., Amit, S., Meltzer, L., Asraf, K., Cohen, C., Fluss, R., Biber, A., Nemet, I., Kliker, L., Joseph, G., Doolman, R., Mendelson, E., Freedman, L. S., Harats, D., Kreiss, Y., & Lustig, Y. (2022). 4th Dose COVID mRNA Vaccines’ Immunogenicity & Efficacy Against Omicron VOC (p. 2022.02.15.22270948). medRxiv. https://doi.org/10.1101/2022.02.15.22270948

Smith, L., Potts, H., Amlôt, R., Fear, N. T., Michie, S., & Rubin, J. (2022). How has the emergence of the Omicron SARS-CoV-2 variant of concern influenced worry, perceived risk, and behaviour in the UK? A series of cross-sectional surveys. OSF Preprints. https://doi.org/10.31219/osf.io/rpcu2

Karberg, S., & Friebe, R. (2022, January 18). Virologe Drosten im Interview: „Wie lange geht diese Quälerei noch weiter?“. https://plus.tagesspiegel.de/wissen/virologe-drosten-im-interview-wie-lange-geht-diese-qualerei-noch-weiter-361636.html

Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., Zepeda, S. K., Papa, G., Kemp, S. A., Ikeda, T., Toyoda, M., Tan, T. S., Kuramochi, J., Mitsunaga, S., Ueno, T., … Gupta, R. K. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature, 1–1. https://doi.org/10.1038/s41586-022-04474-x

Prof. Christina Pagel. (2021, December 7). This is not good news for Scotland (and I suspect England not too far behind) https://t.co/aR26GjPGbj [Tweet]. @chrischirp. https://twitter.com/chrischirp/status/1468232471816855553

Davis, N., & Sample, I. (2021, November 29). UK science advisers brace for hundreds of confirmed Omicron Covid cases. The Guardian. https://www.theguardian.com/world/2021/nov/29/uk-scientific-advisers-brace-confirmed-omicron-covid-cases

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/

Silk, J. (2021, December 3). Hippos with runny noses test positive for COVID-19 at Belgian zoo | DW | 03.12.2021. DW.COM. https://www.dw.com/en/hippos-with-runny-noses-test-positive-for-covid-19-at-belgian-zoo/a-60015051

EMERGENCY STATEMENT ON OMICRON: 15 DECEMBER 2021 | Independent SAGE. (2021, December 15). https://www.independentsage.org/emergency-statement-on-omicron-15-december-2021/

Dr Dan Goyal. (2022, March 15). What’s been happening This Week in Covid? The schism between reality and policy grew even wider this week... Omicron B.2 sent cases soaring and stock markets sinking! #TheWeekInCovid [Tweet]. @danielgoyal. https://twitter.com/danielgoyal/status/1503699425427968001

Mccarthy, C. (2022, February 22). This Fort Worth inventor created a DIY air filter that traps coronavirus particles. Fort Worth Star-Telegram. https://www.star-telegram.com/news/local/crossroads-lab/article258052148.html

(((Howard Forman))). (2022, January 30). New York City Update Cases down 67%. Positive rate down to 3.8%, lowest since 12/12. Hospital census down 33%, lowest since 12/28. New admits lowest since 12/21. Getting closer and closer to pre-Omicron levels. Https://t.co/c6H98PUA0E [Tweet]. @thehowie. https://twitter.com/thehowie/status/1487582265551077387

Julia Raifman. (2022, January 25). How to U-Turn your Omicron decline: Announce the end of mask policies https://t.co/WQGjxXg9fg [Tweet]. @JuliaRaifman. https://twitter.com/JuliaRaifman/status/1486028388590628873

Vaccination of children aged 5 to 11 against Covid-19: Don’thesitate any longer – Académie nationale de médecine | Une institution dans son temps. (2022, January 25). https://www.academie-medecine.fr/vaccination-of-children-aged-5-to-11-against-covid-19-donthesitate-any-longer/?lang=en

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

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

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

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

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

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/

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, 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

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

Purpose of WGS in population epidemiology

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

ReconfigBehSci [@SciBeh]. (2022, January 14). RT @kallmemeg: NEW: @UKHSA Variant Technical Briefing Technical Briefing 34 https://gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings Updated Omicron Risk Assessment https… [Tweet]. Twitter. https://twitter.com/SciBeh/status/1482057283957891075

Danner, C. (2022, January 14). Seriously, Upgrade Your Face Mask. Intelligencer. https://nymag.com/intelligencer/article/why-you-should-upgrade-your-face-mask-to-an-n95.html

Times, T. N. Y. (2020, March 3). Coronavirus in the U.S.: Latest Map and Case Count. The New York Times. https://www.nytimes.com/interactive/2021/us/covid-cases.html

Schlosser, F. (2021, November 29). Omicron—Import Risk. Covid-19 Mobility Project. https://www.covid-19-mobility.org/reports/importrisk_omicron/

Kai Kupferschmidt. (2021, December 1). If you’re curious how likely #omicron is to have spread from South Africa or Botswana to different places, @DirkBrockmann and colleagues have done some interesting calculations based on the world aviation network from 08/2021 You can see that US seems a very likely destination https://t.co/OSnZ6ZNble [Tweet]. @kakape. https://twitter.com/kakape/status/1466107074585239568

Kai Kupferschmidt. (2021, December 1). @DirkBrockmann That percentage number tells you “how likely an infected passenger from South Africa or Botswana travels to each country and exits the airport there”. So: “0.9% in Germany means that out of 1000 such individuals, 9 are expected to have Germany as their final destination.” [Tweet]. @kakape. https://twitter.com/kakape/status/1466107478807097354

🇺🇦 Meaghan Kall. (2022, January 27). NEW: 🏴󠁧󠁢󠁥󠁮󠁧󠁿 Vaccine effectiveness (symptomatic infection) data for BA.2 {Omicron’s more infectious sister} NO difference in VE between Omicron (BA.1) and BA.2 Possibly even higher VE for BA.2 but estimates overlap See full thread 🧵 from @freja_kirsebom https://t.co/bJ7uCn2cGV [Tweet]. @kallmemeg. https://twitter.com/kallmemeg/status/1486821549458001927

Freja Kirsebom. (2022, January 28). Two important updates from our team this week: - Vaccine effectiveness (VE) against symptomatic disease after Omicron BA.2 shows that VE remains unchanged—VE against death after Omicron BA.1 shows VE is 95% at 2+ weeks after booster 1/7 Full report https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1050721/Vaccine-surveillance-report-week-4.pdf [Tweet]. @freja_kirsebom. https://twitter.com/freja_kirsebom/status/1486730977464369160