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Omicron - COVID-19 Variant (B.1.1529) a "Variant of Concern" & BA.2 sub-variant, XE

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  • John Burn-Murdoch
    @jburnmurdoch

    NEW: first thread of 2022 is an Omicron situation update, starting with a detailed look at UK hospitals, before going international.

    Let’s start with severity, and the most important chart:

    Despite steep rises in cases and patients, the number on ventilators has barely risen.



    6:17 AM · Jan 4, 2022·Twitter Web App
    ...

    John Burn-Murdoch
    @jburnmurdoch
    ·
    Jan 4

    We also continue to track "excess ICU pressure" — total number of people in ICU, for any reason, Covid or otherwise, compared to past winters:

    Latest data show that the number of people in London ICUs has fallen in recent weeks, and is not following the same path as last winter.

    "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
    -Nelson Mandela

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      • South Africa offers clues to life after Omicron
        ...

        Joseph Cotterill in Johannesburg 8 HOURS AGO
        ...
        President Cyril Ramaphosa’s government has said the country’s fourth Covid-19 wave has peaked.Total excess deaths attributed to Omicron are about 10,000, compared with about 110,000 excess deaths during the previous, Delta-driven wave.
        ...
        Excess natural deaths last year, for example, were more than 200,000, mostly ascribed to coronavirus and far beyond South Africa’s official pandemic death toll of just over 90,000 people. The country’s total population is 60m.

        “That is pretty sobering,” said Tom Moultrie, professor of demography at the University of Cape Town, who tallies the excess death figures with a team of scientists. “We have possibly had a low-mortality situation in South Africa with Omicron by virtue of the burden we have suffered.”

        Peak hospital admissions in South Africa’s Omicron wave were about two-thirds of the Delta peak. But this figure hides an important nuance that underlines the mild or moderate nature of many cases compared with past waves, Friedland said.

        “A new category of patients emerged, which we had not seen in the past three waves — something we have classified as incidental Covid,” he said. During the Delta wave, nearly all of the positive patients in Netcare hospitals had acute respiratory problems. This time it was about a third.
        ...
        South Africa is also showing that Omicron waves may not fade as rapidly as they emerge. The proportion of tests that come back positive is now far below peaks of 40 per cent in some areas. But in Gauteng, positive test rates have only just fallen below 20 per cent.

        “I think that it is premature either to say it is the end of the world or a ‘nothingburger’,” Moultrie said. “The uncomfortable truth is somewhere between that. It is a lesson in sobriety.”

        Decoupling of community transmission and hospital cases gives lessons for the future as fourth wave peaks
        "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
        -Nelson Mandela

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        • Dr. Eric Legome runs two Mount Sinai Health System emergency sites in New York City.



          “Of all the patients we have with Omicron, the vast, vast majority are going home,” Legome said. Of those hospitalized, “It tends to be the patients who would be admitted otherwise: You’re 90 years old, you have underlying pulmonary disease, heart failure, you have a hip replacement, you don’t get along well at baseline and then you have Omicron on top of that and you just can’t get out of bed. It’s that type that we’re seeing more of,” he said.

          _____________________________________________

          Ask Congress to Investigate COVID Origins and Government Response to Pandemic.

          i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed

          "...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party

          (My posts are not intended as advice or professional assessments of any kind.)
          Never forget Excalibur.

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            • And spreads stunningly fast, as the video point out.

              PROS AND CONS OF OMICRON While legacy media and Public Health Agencies continue to stoke fear over Omicron, new data is painting a different picture of the overwhelmingly mild variant. But there’s a catch; it appears to be able to efficiently escape vaccine protection. #Omicron #PROSNCONS POSTED: January 7, 2022


              PROS AND CONS OF OMICRON
              While legacy media and Public Health Agencies continue to stoke fear over Omicron, new data is painting a different picture of the overwhelmingly mild variant. But there’s a catch; it appears to be able to efficiently escape vaccine protection.
              #Omicron #PROSNCONS
              POSTED: January 7, 2022

              _____________________________________________

              Ask Congress to Investigate COVID Origins and Government Response to Pandemic.

              i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed

              "...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party

              (My posts are not intended as advice or professional assessments of any kind.)
              Never forget Excalibur.

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                • Has omicron already peaked in Florida? Here’s what one doctor says
                  Dr. Scott Gottlieb expects cases to drop this week

                  Brenda Argueta, Digital Journalist
                  Published: January 10, 2022, 7:48 AM

                  ORLANDO, Fla. – As the demand for COVID-19 tests remains high, the former head of the Food and Drug Administration said things should start improving soon in Florida.

                  “But if you look what’s happening across the East Coast right now, in New York City, Washington, D.C., Maryland, probably Florida as well, have already peaked, maybe Delaware, Rhode Island,” said Dr. Scott Gottlieb, former FDA commissioner and a Pfizer board member. “You’re going to start to see that in the statistics this week, you’re going to start to see those curves, those epidemic curves, bend down.”

                  His comments echo the latest modeling from the University of Florida, which also show cases will likely peak soon since omicron spread so rapidly in the community.
                  ...
                  As the demand for COVID-19 tests remains high, the former head of the Food and Drug Administration said things should start improving soon in Florida.


                  ---------------------------------------------------------------------------------------------
                  From the link above:

                  COVID-19 MODELS
                  UPDATED PROJECTIONS FOR OMICRON WAVE IN FLORIDA


                  Jan. 5, 2022: UF researchers updated their model projecting how a.n omicron-driven surge may unfold in Florida over the next few weeks and months. (This version supersedes the model information published Dec. 17, 2021.
                  ...
                  The main finding is that the omicron wave is estimated to peak earlier than previously reported, in mid-January.



                  The figure above shows the reported and modeled cases per day in Florida through May 2022. The projected winter/spring surge reflects the increased infectiousness and immune escape of the omicron variant. The black line shows past actual reported COVID-19 cases, and the yellow line shows the projected reported cases per day.

                  ...

                  "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
                  -Nelson Mandela

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                  • January 11, 2022
                    4:51 AM CST
                    Last Updated 7 hours ago
                    Africa

                    South African studies suggest Omicron has higher 'asymptomatic carriage'

                    JOHANNESBURG, Jan 11 (Reuters) -
                    ...
                    In the Ubuntu study evaluating the efficacy of Moderna's (MRNA.O) COVID-19 vaccine in people living with HIV, 31% of 230 participants undergoing screening tested positive, with all 56 samples available for sequencing analysis verified to be Omicron.

                    "This is in stark contrast to the positivity rate pre-Omicron, which ranged from less than 1% to 2.4%," the researchers said in a statement.

                    In a subgroup of the Sisonke trial evaluating the efficacy of Johnson & Johnson's (JNJ.N) COVID-19 vaccine, the mean asymptomatic carriage rate rose to 16% during the Omicron period from 2.6% during the Beta and Delta outbreaks.

                    "The Sisonke study included 577 subjects previously vaccinated, ... with results suggesting a high carriage rate even in those known to be vaccinated," the researchers said.

                    They added that the "higher asymptomatic carriage rate is likely a major factor in the rapid and widespread dissemination of the variant, even among populations with high prior rates of coronavirus infection".
                    ...
                    "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
                    -Nelson Mandela

                    Comment



                    • Head of COVID response for UCSF's ER dept.: 'I have not intubated a single COVID patient during this Omicron surge'

                      Amy Graff,SFGATE
                      Jan. 10, 2022
                      Updated: Jan. 11, 2022 9:06 a.m.

                      On Saturday, in response to hospitals begging for relief from a massive staffing crisis, the California Department of Public Health announced that most hospitals and skilled nursing facilities can bring COVID-positive and exposed staff back to work without testing or quarantines. The staffers must be asymptomatic, are required to wear N95 masks and are encouraged to work with patients who are already COVID-positive as much as possible.

                      This news might come as a surprise to people who have been reading dire warnings about omicron and some public health officials’ pleas to cancel plans and stay home. Many public health officials have argued these measures are necessary to prevent hospitals from being overwhelmed with COVID patients. Indeed, for the past few weeks, San Francisco hospitals have been in dire straits. But it’s not because people are sick — it’s because of staffing shortages driven by overly strict state quarantine rules, the director of COVID response at UCSF's emergency department said.

                      After reviewing the charts of every COVID-positive patient at UCSF hospitals on Jan. 4, Dr. Jeanne Noble, an associate professor of emergency medicine at UCSF, determined that 70% of them were in the hospital for other reasons.

                      "The real COVID crisis that our hospitals are facing is a severe staffing shortage that is compromising the quality of our care," Noble said Friday, shortly before the policy change was announced.
                      ...
                      "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
                      -Nelson Mandela

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                        • Effectiveness of COVID-19 vaccines against Omicron or Delta infection

                          Sarah A. Buchan, Hannah Chung, Kevin A. Brown, Peter C. Austin, Deshayne B. Fell, Jonathan B. Gubbay, View ORCID ProfileSharifa Nasreen, Kevin L. Schwartz, Maria E. Sundaram, Mina Tadrous, Kumanan Wilson, Sarah E. Wilson, Jeffrey C. Kwong

                          doi: https://doi.org/10.1101/2021.12.30.21268565

                          This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

                          ABSTRACT

                          Background The incidence of SARS-CoV-2 infection, including among those who have received 2 doses of COVID-19 vaccines, has increased substantially since Omicron was first identified in the province of Ontario, Canada.

                          Methods

                          Applying the test-negative design to linked provincial data, we estimated vaccine effectiveness against infection (irrespective of symptoms or severity) caused by Omicron or Delta between November 22 and December 19, 2021. We included individuals who had received at least 2 COVID-19 vaccine doses (with at least 1 mRNA vaccine dose for the primary series) and used multivariable logistic regression to estimate the effectiveness of two or three doses by time since the latest dose.

                          Results

                          We included 3,442 Omicron-positive cases, 9,201 Delta-positive cases, and 471,545 test-negative controls. After 2 doses of COVID-19 vaccine, vaccine effectiveness against Delta infection declined steadily over time but recovered to 93% (95%CI, 92-94%) ≥7 days after receiving an mRNA vaccine for the third dose. In contrast, receipt of 2 doses of COVID-19 vaccines was not protective against Omicron. Vaccine effectiveness against Omicron was 37% (95%CI, 19-50%) ≥7 days after receiving an mRNA vaccine for the third dose.

                          Conclusions

                          Two doses of COVID-19 vaccines are unlikely to protect against infection by Omicron. A third dose provides some protection in the immediate term, but substantially less than against Delta. Our results may be confounded by behaviours that we were unable to account for in our analyses. Further research is needed to examine protection against severe outcomes.
                          ...
                          Funding Statement

                          This work was supported by the Canadian Immunization Research Network (CIRN) through a grant from the Public Health Agency of Canada and the Canadian Institutes of Health Research (CNF 151944). This project was also supported by funding from the Public Health Agency of Canada, through the Vaccine Surveillance Reference Group and the COVID-19 Immunity Task Force.
                          ...
                          Background The incidence of SARS-CoV-2 infection, including among those who have received 2 doses of COVID-19 vaccines, has increased substantially since Omicron was first identified in the province of Ontario, Canada. Methods Applying the test-negative design to linked provincial data, we estimated vaccine effectiveness against infection (irrespective of symptoms or severity) caused by Omicron or Delta between November 22 and December 19, 2021. We included individuals who had received at least 2 COVID-19 vaccine doses (with at least 1 mRNA vaccine dose for the primary series) and used multivariable logistic regression to estimate the effectiveness of two or three doses by time since the latest dose. Results We included 3,442 Omicron-positive cases, 9,201 Delta-positive cases, and 471,545 test-negative controls. After 2 doses of COVID-19 vaccine, vaccine effectiveness against Delta infection declined steadily over time but recovered to 93% (95%CI, 92-94%) ≥7 days after receiving an mRNA vaccine for the third dose. In contrast, receipt of 2 doses of COVID-19 vaccines was not protective against Omicron. Vaccine effectiveness against Omicron was 37% (95%CI, 19-50%) ≥7 days after receiving an mRNA vaccine for the third dose. Conclusions Two doses of COVID-19 vaccines are unlikely to protect against infection by Omicron. A third dose provides some protection in the immediate term, but substantially less than against Delta. Our results may be confounded by behaviours that we were unable to account for in our analyses. Further research is needed to examine protection against severe outcomes. ### Competing Interest Statement K.W. is CEO of CANImmunize and serves on the data safety board for the Medicago COVID-19 vaccine trial. The other authors declare no conflicts of interest. ### Funding Statement This work was supported by the Canadian Immunization Research Network (CIRN) through a grant from the Public Health Agency of Canada and the Canadian Institutes of Health Research (CNF 151944). This project was also supported by funding from the Public Health Agency of Canada, through the Vaccine Surveillance Reference Group and the COVID-19 Immunity Task Force. This study was also supported by ICES, which is funded by an annual grant from the Ontario Ministry of Health (MOH). J.C.K. is supported by Clinician-Scientist Award from the University of Toronto Department of Family and Community Medicine. P.C.A. is supported by a Mid-Career Investigator Award from the Heart and Stroke Foundation. This work was supported by Public Health Ontario. This study was also supported by ICES, which is funded by an annual grant from the Ontario Ministry of Health (MOH) and the Ministry of Long-Term Care (MLTC). This study was supported by the Ontario Health Data Platform (OHDP), a Province of Ontario initiative to support Ontarios ongoing response to COVID-19 and its related impacts. The study sponsors did not participate in the design and conduct of the study; collection, management, analysis and interpretation of the data; preparation, review or approval of the manuscript; or the decision to submit the manuscript for publication. Parts of this material are based on data and/or information compiled and provided by the Canadian Institute for Health Information (CIHI) and by Cancer Care Ontario (CCO). However, the analyses, conclusions, opinions and statements expressed herein are solely those of the authors, and do not reflect those of the funding or data sources; no endorsement by ICES, MOH, MLTC, OHDP, its partners, the Province of Ontario, CIHI or CCO is intended or should be inferred. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Section 45 of PHIPA authorizes ICES to collect personal health information, without consent, for the purpose of analysis or compiling statistical information with respect to the management of, evaluation or monitoring of, the allocation of resources to or planning for all or part of the health system. Projects that use data collected by ICES under section 45 of PHIPA, and use no other data, are exempt from REB review. The use of the data in this project is authorized under section 45 and approved by ICES Privacy and Legal Office. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The dataset from this study is held securely in coded form at ICES. While legal data sharing agreements between ICES and data providers (e.g., healthcare organizations and government) prohibit ICES from making the dataset publicly available, access may be granted to those who meet pre-specified criteria for confidential access, available at www.ices.on.ca/DAS (email: das@ices.on.ca).
                          "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
                          -Nelson Mandela

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                          • Omicron much weaker coronavirus variant than Delta, new study says — but some still urge caution


                            Alexander Nazaryan
                            Senior White House Correspondent
                            Wed, January 12, 2022, 12:51 PM·


                            WASHINGTON — The Omicron variant of the coronavirus is much less likely to cause hospitalization and death than the earlier Delta variant, a study released by the Centers for Disease Control and Prevention finds, confirming to a dramatic degree predictions some virologists have been making since the now dominant variant first appeared in Southern Africa.

                            The findings provided “key insight” into how the newest variant operates, CDC Director Dr. Rochelle Walensky said as she introduced the data, which came from a study of both Omicron and Delta infections throughout Southern California. The study found that, as compared to the Delta variant, Omicron resulted in a 91 percent drop in the risk of death, while the risk of hospitalization was halved. For those who did require hospitalization from Omicron, risk of being admitted to an intensive care unit — signaling more serious disease — was reduced by three-fourths.

                            CDC

                            Omicron infection is “associated with substantially reduced risk of severe clinical endpoints and shorter durations of hospital stay” compared to Delta, the authors found.
                            ...
                            The Omicron variant of the coronavirus is much less likely to cause hospitalization and death than the earlier Delta variant, a study released by the CDC finds, confirming predictions some virologists have been making since Omicron first appeared in southern Africa.
                            "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
                            -Nelson Mandela

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