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RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Find COVID-19 Vaccines
BCSnob 01/18/22 02:01pm Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

There has been some news reports indicating "leaders" are now suggesting we should just let Omicron run its course through the population to help develop "herd immunity". This study was performed in "transgenic mice overexpressing human ACE2 (K18-hACE2)"; mice modified to have analogous responses to SAS-CoV-2 as humans. The key finding in this study was that infection with Delta provided immunity against Omicron; however, infection with Omicron did not provide immunity against Delta. These data suggest that using infection by the milder Omicron (instead of vaccination) as a means to provide population wide immunity against future SARS-CoV-2 variants may not work. The question we should be asking these leaders and the population is, do we want to be part of a population wide experiment to determine if the results in humans match what is found in these mice. Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination MedRxiv preprint 17 Jan 2022 SARS-CoV-2 Delta and Omicron strains are the most globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease, Omicron infection causes less severe disease, mostly upper respiratory symptoms. The question arises whether rampant spread of Omicron could lead to mass immunization, accelerating the end of the pandemic. Here we show that infection with Delta, but not Omicron, induces broad immunity in mice. While sera from Omicron-infected mice only neutralize Omicron, sera from Delta-infected mice are broadly effective against Delta and other VOCs, including Omicron. This is not observed with the WA1 ancestral strain, although both WA1 and Delta elicited a highly pro-inflammatory cytokine response and replicated to similar titers in the respiratory tracts and lungs of infected mice as well as in human airway organoids. Pulmonary viral replication, pro-inflammatory cytokine expression, and overall disease progression are markedly reduced with Omicron infection. Analysis of human sera from Omicron and Delta breakthrough cases reveals effective cross-variant neutralization induced by both viruses in vaccinated individuals. Together, our results indicate that Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals.
BCSnob 01/18/22 07:01am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

....wow. Interesting. I wonder if where the swab is applied to collect the sample for PCR testing is critical.....with Omicron infection detection? ie. Nose? Mouth saliva? Throat? In the NBA study samples from the nostrils and throat were combined for each patient. The data reported here represent a convenience sample including team staff, players, arena staff, and others affiliated with the NBA. The retrospective study includes samples collected between July 5th, 2021, and January 10th, 2022. Clinical samples were obtained by combined swabs of the anterior nares and oropharynx for each patient administered by a trained provider.
BCSnob 01/18/22 06:47am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

This study directly measured infectious viral loads (swab samples were used to infect cell lines with the virus) from original strain (WT) in unvaccinated patients, from Delta in vaccinated and unvaccinated patients, and Omicron in vaccinated patients. Unvaccinated patients had higher Delta infectious viral loads than vaccinated patients. Vaccinated patients had similar infectious viral loads from Delta and Omicron. Infectious viral load in unvaccinated and vaccinated patients infected with SARS-CoV-2 WT, Delta and Omicron MedRxiv preprint 11Jan2022 Background Viral load (VL) is one determinant of secondary transmission of SARS-CoV-2. Emergence of variants of concerns (VOC) Alpha and Delta was ascribed, at least partly, to higher VL. Furthermore, with parts of the population vaccinated, knowledge on VL in vaccine breakthrough infections is crucial. As RNA VL is only a weak proxy for infectiousness, studies on infectious virus presence by cell culture isolation are of importance. Methods We assessed nasopharyngeal swabs of COVID-19 patients for quantitative infectious viral titres (IVT) by focus-forming assay and compared to overall virus isolation success and RNA genome copies. We assessed infectious viral titres during the first 5 symptomatic days in a total of 384 patients: unvaccinated individuals infected with pre-VOC SARS-CoV-2 (n= 118) or Delta (n= 127) and vaccine breakthrough infections with Delta (n= 121) or Omicron (n=18). Findings Correlation between RNA copy number and IVT was low for all groups. No correlation between IVTs and age or sex was seen. We observed higher RNA genome copies in pre-VOC SARS-CoV-2 compared to Delta, but significantly higher IVTs in Delta infected individuals. In vaccinated vs. unvaccinated Delta infected individuals, RNA genome copies were comparable but vaccinated individuals have significantly lower IVTs, and cleared virus faster. Vaccinated individuals with Omicron infection had comparable IVTs to Delta breakthrough infections. Interpretation Quantitative IVTs can give detailed insights into virus shedding kinetics. Vaccination was associated with lower infectious titres and faster clearance for Delta, showing that vaccination would also lower transmission risk. Omicron vaccine breakthrough infections did not show elevated IVTs compared to Delta, suggesting that other mechanisms than increase VL contribute to the high infectiousness of Omicron. IVT = infectious viral titer VL = viral load URT = upper respiratory tract The two key parameters when assessing VL are either RNA genome copies, often expressed in cycle threshold (Ct) values, or infectious virus that can only be assessed by virus isolation in cell culture. Although the process of human-to-human transmission is complex, VL can serve as a proxy, with higher VL posing a greater risk for onward transmission. In several epidemiological studies, higher viral load expressed as viral RNA was associated with an increased secondary transmission in household settings(3, 4). Shedding of infectious SARS-CoV-2 in the URT starts on average two days prior to the beginning of symptoms and gradually declines up to 8 days post onset of symptoms. Even though viral RNA could be detected afterwards, in most studies infectious virus was not detected in respiratory samples collected from immunocompetent individuals later than 8 days post onset of symptoms (5-9). What has not been published, yet, for Omicron is a correlation between viral loads and rates of secondary transmission. However, the viral load data above from Omicron and the earlier onset of PCR detection (see study from NBA samples) suggests that patients with Omicron could be infectious a day or two after exposure to an infectious person and before the onset of symptoms or PCR positive test.
BCSnob 01/14/22 01:41pm Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Any bleeding edge research (in preprint) on Omicron pathogenicity.... specifically, the contagious viral shedding period? This is not quite what you're looking for but it does compare the PCR data from first positive to what might be considered PCR negative for both Delta and Omicron in fully vaccinated people (NBA personnel). The authors estimated durations of infections from the peak PCR values and the time to clearance. The estimated time frames for these fully vaccinated patients range from 9.41-12.4 days for Delta and 8.9-10.9 days for Omicron. What is not evaluated in this study is when someone is contagious (proven to infect someone else) relative to when they are PCR positive or the peak in the amount of RNA detected by PCR. Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant MedRxiv preprint 14 Jan 2022 Background. The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and escape from prior immunity. Defining the time course of Omicron viral proliferation and clearance is crucial to inform isolation protocols aiming to minimize disease spread. Methods. We obtained longitudinal, quantitative RT-qPCR test results using combined anterior nares and oropharyngeal samples (n = 10,324) collected between July 5th, 2021 and January 10th, 2022 from the National Basketball Association's (NBA) occupational health program. We quantified the fraction of tests with PCR cycle threshold (Ct) values <30, chosen as a proxy for potential infectivity and antigen test positivity, on each day after first detection of suspected and confirmed Omicron infections, stratified by individuals detected under frequent testing protocols and those detected due to symptom onset or concern for contact with an infected individual. We quantified the duration of viral proliferation, clearance rate, and peak viral concentration for individuals with acute Omicron and Delta variant SARS-CoV-2 infections. Results. A total of 97 infections were confirmed or suspected to be from the Omicron variant and 107 from the Delta variant. Of 27 Omicron-infected individuals testing positive =1 day after a previous negative or inconclusive test, 52.0% (13/25) were PCR positive with Ct values <30 at day 5, 25.0% (6/24) at day 6, and 13.0% (3/23) on day 7 post detection. Of 70 Omicron-infected individuals detected =2 days after a previous negative or inconclusive test, 39.1% (25/64) were PCR positive with Ct values <30 at day 5, 33.3% (21/63) at day 6, and 22.2% (14/63) on day 7 post detection. Overall, Omicron infections featured a mean duration of 9.87 days (95% CI 8.83-10.9) relative to 10.9 days (95% CI 9.41-12.4) for Delta infections. The peak viral RNA based on Ct values was lower for Omicron infections than for Delta infections (Ct 23.3, 95% CI 22.4-24.3 for Omicron; Ct 20.5, 95% CI 19.2-21.8 for Delta) and the clearance phase was shorter for Omicron infections (5.35 days, 95% CI 4.78-6.00 for Omicron; 6.23 days, 95% CI 5.43-7.17 for Delta), though the rate of clearance was similar (3.13 Ct/day, 95% CI 2.75-3.54 for Omicron; 3.15 Ct/day, 95% CI 2.69-3.64 for Delta). Conclusions. While Omicron infections feature lower peak viral RNA and a shorter clearance phase than Delta infections on average, it is unclear to what extent these differences are attributable to more immunity in this largely vaccinated population or intrinsic characteristics of the Omicron variant. Further, these results suggest that Omicron's infectiousness may not be explained by higher viral load measured in the nose and mouth by RT-PCR. The substantial fraction of individuals with Ct values <30 at days 5 of infection, particularly in those detected due to symptom onset or concern for contact with an infected individual, underscores the heterogeneity of the infectious period, with implications for isolation policies.
BCSnob 01/14/22 12:45pm Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Terminally ill patient gets Covid-19 and dies. What caused this death? COPD patient gets Covid-19 and dies. What caused this death? 90 year old patient gets Covid-19 and dies. What caused this death? Would they have lived longer if they didn’t get Covid-19? Those who want to play down the risks of getting Covid-19 (for whatever reason, perhaps anti-vax) are using the presence of comorbidities as the reason for death and having Covid-19 is irrelevant. Here’s another question. Are those who are going to the hospital because of increased severity of their comorbidities and then finding out they have Covid-19; having increased severity of their comorbidities because of Covid-19 or was it just a coincidence? An asymptomatic viral infection is still a viral infection which weakens the body, causes physiological changes the patient doesn't recognize (no outward symptoms), and likely makes one more susceptible to issues from underlying conditions. Chest CT Findings in Cases from the Cruise Ship Diamond Princess with Coronavirus Disease (COVID-19) Radiol Cardiothorac Imaging. 2020 Apr; 2(2) This retrospective study comprised 104 cases (mean age, 62 years ± 16 standard deviation, range, 25–93 years) with COVID-19 confirmed with reverse-transcription polymerase change reaction findings. CT images were reviewed, and the CT severity score was calculated for each lobe and the entire lung. CT findings were compared between asymptomatic and symptomatic cases. Of 104 cases, 76 (73%) were asymptomatic, 41 (54%) of which had lung opacities on CT. Twenty-eight (27%) cases were symptomatic, 22 (79%) of which had abnormal CT findings.
BCSnob 01/13/22 01:21pm Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

No such correlation can be determined from that data. Nowhere in the data does it (for example) differentiate in "deaths with Covid" vs. "deaths due to Covid". You can have covid and die of a cancer and its all recorded the same "Covid Case". Here is data from Minnesota: Clicky What is your hypothesis for the change in deaths overtime, if not Covid-19? Have deaths due to cancer increased since the beginning of the year? What is being claimed in the opinion website you linked (not simply raw MN data as you imply) is that the deaths could have been due to the comorbidities; where the real question is would they have died now from their comorbidities if they had not gotten covid-19. This question is addressed by looking at excess mortality. Excess mortality during the Coronavirus pandemic
BCSnob 01/13/22 11:26am Around the Campfire
RE: Is this forum dying?

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BCSnob 01/13/22 10:24am Forum Posting Help and Support
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

I’ve not found studies on the temporal progression of viral shedding due to omicron. I have seen comments (hypotheses) that since omicron starts replicating higher up in the lungs than delta it becomes contagious earlier after initial infection than with delta.
BCSnob 01/13/22 10:01am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Some good news. Vaccines Elicit Highly Cross-Reactive Cellular Immunity to the SARS-CoV-2 Omicron Variant MedRxiv Preprint 2Jan2022 The highly mutated SARS-CoV-2 Omicron (B.1.1.529) variant has been shown to evade a substantial fraction of neutralizing antibody responses elicited by current vaccines that encode the WA1/2020 Spike immunogen1, resulting in increased breakthrough infections and reduced vaccine efficacy. Cellular immune responses, particularly CD8+ T cell responses, are likely critical for protection against severe SARS-CoV-2 disease2-6. Here we show that cellular immunity induced by current SARS-CoV-2 vaccines is highly cross-reactive against the SARS-CoV-2 Omicron variant. Individuals who received Ad26.COV2.S or BNT162b2 vaccines demonstrated durable CD8+ and CD4+ T cell responses that showed extensive cross-reactivity against both the Delta and Omicron variants, including in central and effector memory cellular subpopulations. Median Omicron-specific CD8+ T cell responses were 82-84% of WA1/2020-specific CD8+ T cell responses. These data suggest that current vaccines may provide considerable protection against severe disease with the SARS-CoV-2 Omicron variant despite the substantial reduction of neutralizing antibody responses. While most studies of antibody responses show evasion by omicron which is partially restored by boosting (see quote below), this study of memory cells show vaccination continues to show protection against omicron. Analysis of SARS-CoV-2 Omicron Neutralization Data up to 2021-12-22 BioRxiv preprint 7Jan2022 Two definitive statements can be made from the aggregation of the early data on Omicron virus neutralization data. Sera from individuals who have been vaccinated twice or infected once show generally more than a 19x fold drop of titers, whereas people who have been vaccinated three times or have been vaccinated + infected show an average of approximately 7x fold drop of titers.
BCSnob 01/13/22 08:56am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Life (multiple issues at home and at work) has prevented me from having the time to focus on the posted preprints since Jan 1. It'll get even busier once our 60+ ewes start lambing. I have a little time now.
BCSnob 01/13/22 08:34am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

I agree The ratios you posted are from averages over the last 28 days of data; over those last 28 days the ratios were increasing. Also, “fully vaccinated” includes all vaccines (1 shot of J&J, 2 shots of either mRNA, and any of these boosted) and any duration of time since being fully vaccinated. Other data indicates there are wide differences in the protection afforded within the category of “fully vaccinated”; however, fully vaccinated is by far better against omicron than not fully vaccinated.
BCSnob 01/13/22 07:52am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

I could not copy the graphs from the news article but here are links to their sources. Look at the graphs of weekly rates by vaccination status (second configurable graph at this link) NYC Dept of Health Covid Data This report from Washington State Department of Health has multiple graphs comparing cases, hospitalization, deaths by vaccination status from several age groups. Take a close look at the difference between fully vaccinated and unvaccinated for the last time points in these plots. The ratios are much higher than the average ratios reported for the last 28days.
BCSnob 01/12/22 12:22pm Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Look at the graphs (from the New York City Department of Health, Washington Department of Health) in this recent news article While the estimated vaccine efficacy is dependent upon the variables I listed; the numbers in the graphs in the news article do not distinguish these variables; only vaccinated vs not fully vaccinated. These numbers are easy to interpret the benefits of full vaccination against omicron
BCSnob 01/12/22 11:26am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

and equal opportunity to the vaccinated and non vaccinated alike - . If this was actually true the vaccine effectiveness against infection would be 0% not the reported 50% to 90% (depending upon number of doses, vaccine manufacturer, and time since last dose).
BCSnob 01/12/22 10:47am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

How can omicron be more infectious than the original strain (R0 ~3) but have an R0 less than 3? If you look at the graph here you’ll see the y axis is listed as Rt. Also, the article that has the quote you posted and the graph (see my link) you’ll read about the R value changing over time during a pandemic. This is effective reproduction number, Rt (or Re), as defined the the links I provided earlier (see quote below) not R0. R0 R0 is an estimate of the contagiousness that is a function of human behavior and the biological character of pathogens. R0 is not a measure of the severity of an infectious disease or the rapidity of a pathogen's spread through a population. It is not a biological constant for a specific pathogen.1 It is estimated when there is zero immunity in the population. R0 is a derivative of the following variables—the duration of infectivity after the patient gets infected, the likelihood of transmission of infection per contact between a susceptible person and an infectious individual, and the contact rate. The infectivity of the pathogen and duration of contagiousness are biological constants, but the extent of human-to-human interaction will vary and hence R0 will vary depending on this parameter. This explains the importance of social distancing during the COVID-19 pandemic. It is also to be noted that the R0 value of COVID-19 is higher than that of SARS and MERS. Re Re (effective reproduction number) which also known as Rt, is the number of people in a population who can be infected by an individual at any specific time. While measuring the transmissibility of the virus at any given time during an epidemic we use Re. It changes as the population becomes increasingly immunized, either by individual immunity following infection or vaccination and also as people die. Factors affecting Re include the number of people with infection, the number of susceptible people with whom infected people are in contact, and people's behavior such as social distancing. This is from the first linked article on R0. Vaccination campaigns reduce the proportion of a population at risk for infection and have proven to be highly effective in mitigating future outbreaks (26). This conclusion is sometimes used to suggest that an aim of vaccination campaigns is to remove susceptible members of the population to reduce the R0 for the event to <1. Although the removal of susceptible members from the population will affect infection transmission by reducing the number of effective contacts between infectious and susceptible persons, this activity will technically not reduce the R0 value because the definition of R0 includes the assumption of a completely susceptible population. When examining the effect of vaccination, the more appropriate metric to use is the effective reproduction number (R), which is similar to R0 but does not assume complete susceptibility of the population and, therefore, can be estimated with populations having immune members (16,20,27). Efforts aimed at reducing the number of susceptible persons within a population through vaccination would result in a reduction of the R value, rather than R0 value. In this article the authors use R for effective reproduction number where the authors in the quote above use Rt or Re for effective reproduction number.
BCSnob 01/11/22 07:20pm Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Good background reading on R0 Complexity of the Basic Reproduction Number (R0) I wonder if the low R numbers in your quote are actually Rt (or Re). See R0 and Re of COVID-19: Can We Predict When the Pandemic Outbreak will be Contained? Indian J Crit Care Med 2020;24(11):1125–1127
BCSnob 01/11/22 09:55am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

The original strain of SARS-CoV-2 has an R0 of 2·5, while the delta variant (B.1.617.2) has an R0 of just under 7. Martin Hibberd, professor of emerging infectious diseases at London School of Hygiene & Tropical Medicine (London, UK), reckons omicron's R0 could be as high as 10. Omicron variant and booster COVID-19 vaccines The Lancet 17 Dec 2021 The original Covid-19 virus has R0 around 2-3 (4,5), Delta R0˜5 (5) and Omicron R0˜7.5 (5,6). How Large Fraction of A Population Must be Vaccinated before A Disease is Controlled? ResearchSquare 11 Jan 2022
BCSnob 01/11/22 09:20am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

My question is how can all four get it at the same time? My only speculation would be that they keep two cats in the house, and these cats go from one girl to the next for affection and petting and have the run of the house. Or they all were exposed at the same time: traveled together in the same vehicle with someone infected, when together to the same social gathering, an infected person came to their house, etc.
BCSnob 01/09/22 06:57am Around the Campfire
RE: 2019–2022 CORONAVIRUS PANDEMIC POSTINGS

Omicron is evading previously induced immunity (past vaccinations, and boosting), the extent of evasion is highly dependent upon the details of the previously induced immunity. Two doses of mRNA vaccines are proving to be vastly more effective than the other vaccines; but just 2 doses are very effective against omicron. Boosting with one of the mRNA vaccines restores protection; the level of protection is best after boosting for those who had one of the mRNA vaccines. mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant Cell, 23 Dec 2021 See figures 2 & 3 The level of protection appears to wane over time after boosting; the decrease in protection is lower after boosting with Moderna than with Pfizer. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing: Update on hospitalisation and vaccine effectiveness for Omicron VOC-21NOV-01 (B.1.1.529) UK Health Security Agency 31 Dec 2021 See figure 2
BCSnob 01/09/22 06:53am Around the Campfire
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