Did you blink? If so, you may have missed Omicron springboard us into a hyperdrive tsunami of cases. For the first time during the pandemic, the world reported more than 1 million confirmed cases per day. Omicron leaders, like Denmark and the UK, haven’t peaked yet, and other places are just starting their wave, like Australia and India. Interestingly, South Africa is taking longer to descend than they took to ascend, which is something to keep an eye on.
That sewage data from Boston is absolutely astounding. Do we know if fecal viral load is higher for Omicron than for previous variants? Consequently, do we think that the RNA count in the sewage is directly proportional to cases across waves, or that some sort of correction factor would be needed to compare population case count from sewage results between periods where different variants dominated?
yes sewage data accurately predicted cases by 4-7 days throughout the pandemic. two things i don’t have clarity on (and i wish i remembered to include it in this post!): 1. is this adjusted for increased viral load with omicron? not sure. and 2. does the change in omicron symptoms to GI influence waste water numbers? not sure.
Jan 3, 2022·edited Jan 3, 2022Liked by Katelyn Jetelina
Happy new subscriber here! Wonderful post. Many thanks. Heartened to see the hospitalized vaxxed are trending older and/or with more co-morbidities but it Makes me wonder whether you think we need to start fourth shots for people (like my parents in the 75+ crowd) who were boosted as early as first week if September and don’t have great ability to mount robust tell etc response
Can you please please at some point discuss the true risk for children under 5 who are not likely to be vaccine eligible for a while. I know we want everyone to take this seriously on a population level so we don’t want to compare it to flu but how dangerous is it for each susceptible kid?
-How does it really compare to other (respiratory) infections in this age group?
-What is the true prevalence of MISC by age groups?
There is so much noise and it is hard to really know what most kid’s individual risk is. This group seems forgotten. It is not possible to keep them cooped up for more than 2 years and with how contagious omicron is, every kid will likely get this.
Please please please share your thoughts or any resources you think is reliable. My heart fell out of my chest this morning when I dropped my kids off at school knowing the will get covid.
Here's a quote from Dr J's most recent post, called something like *There is Good News*
In children under 5 years old, the overall risks of ED visit and hospitalization for Omicron were 3.89% and 0.96% respectively, significantly lower than 21.01% and 2.65% in the matched Delta cohort. The running hypothesis (confirmed in 6 lab studies) is that this is the case because Omicron doesn’t infect the lungs as efficiently; rather, it infects the upper respiratory system much more.
Upper respiratory infections are hard on babies and toddlers though. There's been lots of croup and bronchiolitis. Fortunately, kids usually recover well from those.
Clearly too soon to know long-term risk from Omicron. But important observation on the pediatric hospitalizations. Omicron seems to infect the upper airway, and these upper-airway infections are harder on babies and toddlers. Lots of hospitalizations for croup and bronchiolitis. Any breathing problem is scary for parents and kids, and warrants medical attention, but these kids do recover well. Croup is also a common complication from other viral infections like RSV. So this would put COVID for this age group somewhere more serious than the common cold, but in the range of other viral infections of childhood we've learned to deal with.
It might be that we don't actually know yet. Good science requires good data. Good data does not grow on trees. (Actually if you are studying deforestation data could grow on trees... Perhaps I am barking up the wrong tree on this one.)
Thank you again for your time, knowledge, and experience. I wish I could corner some of my “people” and have them hear you. So many people are still contriving such absurd conspiracy theories that I’m sickened by it. How can they ignore what is happening across the GLOBE?!
I will continue to spread the information provided in hopes that I’ll reach someone before C19 comes them. 🌈❤️
If you actually read the article from the economist "Some Nordic nations have experienced almost no excess deaths at all. The exception is Sweden, which imposed some of the continent’s least restrictive social-distancing measures during the first wave." but you don't...
That’s not the article in question. That’s a rather dated one from August of 2021. However, one *could* argue that 2020 excess deaths skewed the data to give Sweden an advantage in 2021.
This is the part I don't get. If you try to get 4 or 5 people to work together to plot something, it usually doesn't work, so how in the world could all the world leaders been in on it?
Jan 4, 2022·edited Jan 4, 2022Liked by Katelyn Jetelina
The University of Michigan also has a great graph showing co-morbidity and age for its vaccinated and unvaccinated patients. I feel lucky to live in a college town during this pandemic. https://www.uofmhealth.org/coronavirus/covid19-numbers
The advantage of your catbird YLE seat inspires a question I've not heard addressed: Are there any reports or statistics on incidents of DUAL infection--with both Delta and Omicron?
This is so exhausting and just demoralizing. We can all be vaccinated and three are boosted and our waiting on CDC approval for our 14 year old guy. Daughter was positive and had super mild case thankfully. No one else in our house got it and I am still so scared of this virus. My kids schools are mask optional ( can’t even) and they are going in them. I teach children with severe learning differences and they have to see my mouth in order to learn and clear masks fog, but I do my best. The anxiety is really not healthy but how do we take all the news and process the risk? So grateful for your knowledge, honesty, and humble reporting. Feel like a pinball bouncing from hope to despair. This is hard
Cities are shockingly higher than the states: Chicago is at 1141 per 100,000! My local area Virginia Beach is at 603 per 100,000 with 21% test positivity over 7 days but yesterday's positivity was 32%! AND testing is all but impossible to find, of any kind!
Big question though for you: what about 11 year old that turned 12, so they only got the small dose first two shots but now should they still wait the 5 months for a booster? Is there any information for these families? I have friends whose pediatricians are just as clueless and it seems both frustrating and shocking that no one considered this issue, ESPECIALLY when we saw the little kids' doses fail for 2-5 year olds, so it's not out of the question what tested well for 5-11 may quickly not be enough for 12 year olds.
I've long thought testing sewage at international airports would be a good way to do disease surveillance. It seems the sewage testing underway at some larger cities suggests this could be doable at airports.
I'm disillusioned by the lack of vaccine for the under 5 crowd. I've kept my children so isolated, and we can't stay like this indefinitely. Is there any sense in exposing them to this variant, given that it's supposed to be mild, to build up their immunity in case the next variant is more virulent? Or will the next variant more than likely not responded to Omicron antibodies? I know that this is not the ideal way to gain immunity, but without a vaccine, my hands feel tied.
Question on transmission. This question is predicated on a conversation I had online with some NBA fans: you've mentioned before omicron seemingly ignores prior immunity, especially in unvaxxed individuals. Has there been any record of someone getting omicron twice yet? I know things are still sort of early compared to when it arrived, just curious if this has been detected.
Like EC below, I am aware that those who had an earlier infection (Alpha, Beta, Delta) are more likely to get infected with Omicron than the earlier types, but I don't think Omicron has existed long enough to count as a reinfection of the same strain twice since I believe the definition is still 90 days between.
I hope to hear more about this as well. My current understanding is omicron is more likely to infect the vaccinated and previously-infected because there isn't a great "fit" of the immune protection offered from those and omicron. That shouldn't lead to omicron being more able to re-infect those who have had omicron, but I wouldn't be surprised to learn it's more complicated than that.
Despite all our precautions, our family is Covid positive. We’ve been isolating a lot as our three year old has high and complex needs and obviously, no vaccination. Now that she’s caught Covid, will she have sufficient immunity to be able to again join in activities we ended such as her beloved kinder gymnastics classes? If so, how long might it last?
It's disappointing that we chose to call these medical options "vaccines" because they really aren't the same. You can _still_ get COVID, it's just less likely to kill you or put you in the hospital. Yeah -- I know. Mutations are to blame (for the most part), but that's somewhat beside the point: when you get the hepatitis A VACCINE, you wont get hepatitis (A, at least) Of course, I recognize that no vaccine is 100% effective, but we have eradicated other viruses by using the "vaccine approach" where you have some form of immune response in most people and consequently they WONT GET THE VIRUS at all. COVID is not like that.
So maybe, the way the "coronapocalypse" (as I like to call it) ends is written on the wall: we all eventually will get some form of COVID-19. Those who choose to remain unvaccinated will eventually develop immunity or suffer more serious consequence (hospitalization, financial doom, lifelong health issues, and/or death) while those of us who are vaccinated (and have pushed the "Easy" button, so to speak) develop a much milder form of it that our body fights off.
We will produce a better immune response than many of today's vaccines. To wit: I'm vaccinated, but no booster _yet_. I got Omicron last month and have since recovered (10 days quarantine). My GF, who had the original virus back in Feb of 2020, was unaffected despite us living in close proximity, sleeping together unmasked every day, and not wearing masks at home. There was no point in me masking up because she was told to quarantine like me because I tested positive. But she never got sick.
So perhaps all these "breakthrough infections" are a good thing in the long run - bringing us closer to the holy grail of herd immunity and teaching the unvaccinated a potentially painful lesson in the real life consequences of your freedom to make bad choices.
Why should the fact that covid vaccines don't give 100% protection be grounds for not calling them vaccines? Few if any vaccines give 100% protection against the virus they're designed to fight. The way we eliminate viruses using vaccines that aren't 100% effective by vaccinating enough people that we achieve herd immunity: When somebody gets infected by the virus, those they come in contact with are sufficiently immunized that the virus does not spread very much. Maybe the sick person does not infect anyone at all, or maybe they give a couple people infections that are brief and mild -- and those people have a smaller change than the original person of passing the virus on to anyone else. In other words R0, transmission rate, gets lower than one: The average infected person infects less than one other person. The virus finally dies out. At the end there is only 1 infected person in the population -- he or she does not manage to infect anyone -- poof, end of viruses career.
I guess we have a difference of opinions here. _if_ my thesis is correct, that "all of us will eventually get Covid-19 and develop a better immune response that prevents us from getting it again", then I'd rather have a higher transmission rate.
I was sick with Omicron for about a week (give or take). I've felt worse with the flu, but a couple of days were _bad_. That said, I've had the two shot (Moderna) combo, but no booster. Being big on science, that wasn't intentional -- I went to get the booster at a local pharmacy on a whim and didn't have an appointment, they didn't have the staff to do it. So, I decided it could wait. Now I'll wait even longer since I've just had it and recovered. I still expect to get a booster at some future time. But I do wonder, since I've had the "real deal", will it even matter?
There's lots of info out there about how infections compare to vaccination in the amount and kind of immunity they confer. There's also info about the effectiveness of vaccinations in combination with breakthrough infections. Why not read up on this stuff, instead of speculating out loud? Earlier posts on the present blog cover this topic well and clearly.
Natural infection does not always provide any immunity. The fact that you had been vaccinated in the past should help with that. In general I would say, the more protection the better. You can always try to get a quantitative antibody test to see just how good your protection is.
Given this reference below sent by friend RH, i have to wonder if it is perhaps nothing more than one or more advantageous recombination(s) in a person or people who had two concurrent strains.
I can see labeling something that behaves very differently and needs different approaches as being “deviant" from a treatment and public information standpoint. It may help with those functions.
Certainly, there are people suggesting a labeling change for Omicron, with suggestions varying from taxonomic relabeling to public designation changing from CoVID-19 to CoVID-21 if it continues to pan out as having less health impact on a number of people while being more infectious.
From a genetics and evolutionary standpoint, though, i see the trends which are occurring as being not at all unexpected from a viral survival, spread, and replication aspect, so for species or subspecies designations, especially in such a genetically active disease, i would rather be a lumper than a splitter taxonomically. We humans are far too inclined to split species easily in designations when impact upon us (or similarity to us) is involved. That is just my paleontology and E&E education speaking, of course, but that strikes me as being applicable.
Cooccurrence of N501Y, P681R and other key mutations in SARS-CoV-2 Spike
Abstract
Analysis of circa 4.2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences on Global Initiative on Sharing All Influenza Data (GISAID) shows the spike mutations N501Y (common to Alpha, Beta, Gamma, Omicron variants) and P681R (central to Delta variant spread) have cooccurred 3,678 times between 17 October 2020 and 1 November 2021. In contrast, the N501Y+P681H combination is present in Alpha and Omicron variants and circa 1.1 million entries. Two-thirds of the 3,678 cooccurrences were in France, Turkey or US (East Coast), and the rest across 62 other countries. 55.5% and 4.6% of the cooccurrences were Alpha Q.4 and Gamma P.1.8 sub-lineages acquiring P681R; 10.7% and 3.8% were Delta B.1.617.2 lineage and AY.33 sub-lineage acquiring N501Y; remaining 10.2% were in other variants. Despite the selective advantages individually conferred by N501Y and P681R, the N501Y+P681R combi-nation counterintuitively did not outcompete other variants in every instance. Although a relief to worldwide public health efforts, in vitro and in vivo studies are urgently required in the absence of a strong in silico explanation for this phenomenon. This study demonstrates a pipeline to analyse combinations of key mutations from public domain information in a systematic manner and provide early warnings of spread.
That sewage data from Boston is absolutely astounding. Do we know if fecal viral load is higher for Omicron than for previous variants? Consequently, do we think that the RNA count in the sewage is directly proportional to cases across waves, or that some sort of correction factor would be needed to compare population case count from sewage results between periods where different variants dominated?
yes sewage data accurately predicted cases by 4-7 days throughout the pandemic. two things i don’t have clarity on (and i wish i remembered to include it in this post!): 1. is this adjusted for increased viral load with omicron? not sure. and 2. does the change in omicron symptoms to GI influence waste water numbers? not sure.
Happy new subscriber here! Wonderful post. Many thanks. Heartened to see the hospitalized vaxxed are trending older and/or with more co-morbidities but it Makes me wonder whether you think we need to start fourth shots for people (like my parents in the 75+ crowd) who were boosted as early as first week if September and don’t have great ability to mount robust tell etc response
Can you please please at some point discuss the true risk for children under 5 who are not likely to be vaccine eligible for a while. I know we want everyone to take this seriously on a population level so we don’t want to compare it to flu but how dangerous is it for each susceptible kid?
-How does it really compare to other (respiratory) infections in this age group?
-What is the true prevalence of MISC by age groups?
There is so much noise and it is hard to really know what most kid’s individual risk is. This group seems forgotten. It is not possible to keep them cooped up for more than 2 years and with how contagious omicron is, every kid will likely get this.
Please please please share your thoughts or any resources you think is reliable. My heart fell out of my chest this morning when I dropped my kids off at school knowing the will get covid.
Thank you
Here's a quote from Dr J's most recent post, called something like *There is Good News*
In children under 5 years old, the overall risks of ED visit and hospitalization for Omicron were 3.89% and 0.96% respectively, significantly lower than 21.01% and 2.65% in the matched Delta cohort. The running hypothesis (confirmed in 6 lab studies) is that this is the case because Omicron doesn’t infect the lungs as efficiently; rather, it infects the upper respiratory system much more.
Upper respiratory infections are hard on babies and toddlers though. There's been lots of croup and bronchiolitis. Fortunately, kids usually recover well from those.
Clearly too soon to know long-term risk from Omicron. But important observation on the pediatric hospitalizations. Omicron seems to infect the upper airway, and these upper-airway infections are harder on babies and toddlers. Lots of hospitalizations for croup and bronchiolitis. Any breathing problem is scary for parents and kids, and warrants medical attention, but these kids do recover well. Croup is also a common complication from other viral infections like RSV. So this would put COVID for this age group somewhere more serious than the common cold, but in the range of other viral infections of childhood we've learned to deal with.
Thank you so much for the feedback.
It might be that we don't actually know yet. Good science requires good data. Good data does not grow on trees. (Actually if you are studying deforestation data could grow on trees... Perhaps I am barking up the wrong tree on this one.)
...username checks out. :)
Thank you again for your time, knowledge, and experience. I wish I could corner some of my “people” and have them hear you. So many people are still contriving such absurd conspiracy theories that I’m sickened by it. How can they ignore what is happening across the GLOBE?!
I will continue to spread the information provided in hopes that I’ll reach someone before C19 comes them. 🌈❤️
I've been saying the same thing. How can people ignore what is happening across the globe, indeed!?
https://twitter.com/prof_freedom/status/1473635587299151877?s=20
If you actually read the article from the economist "Some Nordic nations have experienced almost no excess deaths at all. The exception is Sweden, which imposed some of the continent’s least restrictive social-distancing measures during the first wave." but you don't...
https://www.businessinsider.com/sweden-covid-no-lockdown-strategy-failed-higher-death-rate-2021-8
That’s not the article in question. That’s a rather dated one from August of 2021. However, one *could* argue that 2020 excess deaths skewed the data to give Sweden an advantage in 2021.
The quote did come from the original article, I was sending you some additional information. (here is the original : https://www.economist.com/graphic-detail/coronavirus-excess-deaths-tracker) It is very interesting, and your tweeter misrepresented the info as all "misinformers" do.
This is the part I don't get. If you try to get 4 or 5 people to work together to plot something, it usually doesn't work, so how in the world could all the world leaders been in on it?
The University of Michigan also has a great graph showing co-morbidity and age for its vaccinated and unvaccinated patients. I feel lucky to live in a college town during this pandemic. https://www.uofmhealth.org/coronavirus/covid19-numbers
The advantage of your catbird YLE seat inspires a question I've not heard addressed: Are there any reports or statistics on incidents of DUAL infection--with both Delta and Omicron?
This is so exhausting and just demoralizing. We can all be vaccinated and three are boosted and our waiting on CDC approval for our 14 year old guy. Daughter was positive and had super mild case thankfully. No one else in our house got it and I am still so scared of this virus. My kids schools are mask optional ( can’t even) and they are going in them. I teach children with severe learning differences and they have to see my mouth in order to learn and clear masks fog, but I do my best. The anxiety is really not healthy but how do we take all the news and process the risk? So grateful for your knowledge, honesty, and humble reporting. Feel like a pinball bouncing from hope to despair. This is hard
Cities are shockingly higher than the states: Chicago is at 1141 per 100,000! My local area Virginia Beach is at 603 per 100,000 with 21% test positivity over 7 days but yesterday's positivity was 32%! AND testing is all but impossible to find, of any kind!
Big question though for you: what about 11 year old that turned 12, so they only got the small dose first two shots but now should they still wait the 5 months for a booster? Is there any information for these families? I have friends whose pediatricians are just as clueless and it seems both frustrating and shocking that no one considered this issue, ESPECIALLY when we saw the little kids' doses fail for 2-5 year olds, so it's not out of the question what tested well for 5-11 may quickly not be enough for 12 year olds.
I've long thought testing sewage at international airports would be a good way to do disease surveillance. It seems the sewage testing underway at some larger cities suggests this could be doable at airports.
I'm disillusioned by the lack of vaccine for the under 5 crowd. I've kept my children so isolated, and we can't stay like this indefinitely. Is there any sense in exposing them to this variant, given that it's supposed to be mild, to build up their immunity in case the next variant is more virulent? Or will the next variant more than likely not responded to Omicron antibodies? I know that this is not the ideal way to gain immunity, but without a vaccine, my hands feel tied.
Just seen a news report on the variant you mention here. Thank God for you.
Question on transmission. This question is predicated on a conversation I had online with some NBA fans: you've mentioned before omicron seemingly ignores prior immunity, especially in unvaxxed individuals. Has there been any record of someone getting omicron twice yet? I know things are still sort of early compared to when it arrived, just curious if this has been detected.
Like EC below, I am aware that those who had an earlier infection (Alpha, Beta, Delta) are more likely to get infected with Omicron than the earlier types, but I don't think Omicron has existed long enough to count as a reinfection of the same strain twice since I believe the definition is still 90 days between.
I hope to hear more about this as well. My current understanding is omicron is more likely to infect the vaccinated and previously-infected because there isn't a great "fit" of the immune protection offered from those and omicron. That shouldn't lead to omicron being more able to re-infect those who have had omicron, but I wouldn't be surprised to learn it's more complicated than that.
Great question!
Despite all our precautions, our family is Covid positive. We’ve been isolating a lot as our three year old has high and complex needs and obviously, no vaccination. Now that she’s caught Covid, will she have sufficient immunity to be able to again join in activities we ended such as her beloved kinder gymnastics classes? If so, how long might it last?
About Ohio & Indiana: how do we know whether the high hospitalization rate is due to Delta vs due to Omicron + low vaccination rate?
OK; so I'll play devil's advocate here:
It's disappointing that we chose to call these medical options "vaccines" because they really aren't the same. You can _still_ get COVID, it's just less likely to kill you or put you in the hospital. Yeah -- I know. Mutations are to blame (for the most part), but that's somewhat beside the point: when you get the hepatitis A VACCINE, you wont get hepatitis (A, at least) Of course, I recognize that no vaccine is 100% effective, but we have eradicated other viruses by using the "vaccine approach" where you have some form of immune response in most people and consequently they WONT GET THE VIRUS at all. COVID is not like that.
So maybe, the way the "coronapocalypse" (as I like to call it) ends is written on the wall: we all eventually will get some form of COVID-19. Those who choose to remain unvaccinated will eventually develop immunity or suffer more serious consequence (hospitalization, financial doom, lifelong health issues, and/or death) while those of us who are vaccinated (and have pushed the "Easy" button, so to speak) develop a much milder form of it that our body fights off.
We will produce a better immune response than many of today's vaccines. To wit: I'm vaccinated, but no booster _yet_. I got Omicron last month and have since recovered (10 days quarantine). My GF, who had the original virus back in Feb of 2020, was unaffected despite us living in close proximity, sleeping together unmasked every day, and not wearing masks at home. There was no point in me masking up because she was told to quarantine like me because I tested positive. But she never got sick.
So perhaps all these "breakthrough infections" are a good thing in the long run - bringing us closer to the holy grail of herd immunity and teaching the unvaccinated a potentially painful lesson in the real life consequences of your freedom to make bad choices.
Why should the fact that covid vaccines don't give 100% protection be grounds for not calling them vaccines? Few if any vaccines give 100% protection against the virus they're designed to fight. The way we eliminate viruses using vaccines that aren't 100% effective by vaccinating enough people that we achieve herd immunity: When somebody gets infected by the virus, those they come in contact with are sufficiently immunized that the virus does not spread very much. Maybe the sick person does not infect anyone at all, or maybe they give a couple people infections that are brief and mild -- and those people have a smaller change than the original person of passing the virus on to anyone else. In other words R0, transmission rate, gets lower than one: The average infected person infects less than one other person. The virus finally dies out. At the end there is only 1 infected person in the population -- he or she does not manage to infect anyone -- poof, end of viruses career.
The vaccines do reduce the R(t) of the virus. Do they reduce it to zero? No. Lets hope they help bring it down below 1 and keep it down.
I guess we have a difference of opinions here. _if_ my thesis is correct, that "all of us will eventually get Covid-19 and develop a better immune response that prevents us from getting it again", then I'd rather have a higher transmission rate.
I was sick with Omicron for about a week (give or take). I've felt worse with the flu, but a couple of days were _bad_. That said, I've had the two shot (Moderna) combo, but no booster. Being big on science, that wasn't intentional -- I went to get the booster at a local pharmacy on a whim and didn't have an appointment, they didn't have the staff to do it. So, I decided it could wait. Now I'll wait even longer since I've just had it and recovered. I still expect to get a booster at some future time. But I do wonder, since I've had the "real deal", will it even matter?
There's lots of info out there about how infections compare to vaccination in the amount and kind of immunity they confer. There's also info about the effectiveness of vaccinations in combination with breakthrough infections. Why not read up on this stuff, instead of speculating out loud? Earlier posts on the present blog cover this topic well and clearly.
Natural infection does not always provide any immunity. The fact that you had been vaccinated in the past should help with that. In general I would say, the more protection the better. You can always try to get a quantitative antibody test to see just how good your protection is.
All of this has been addressed in prior blog posts. Recommend catching up on some reading, then your comments will be better informed.
Did you know that Injectable Polio Vaccine doesn't prevent infection, but only severe disease and paralysis?
A few of our vaccines confer sterilizing immunity, but many do not. They're still extremely useful.
Given this reference below sent by friend RH, i have to wonder if it is perhaps nothing more than one or more advantageous recombination(s) in a person or people who had two concurrent strains.
I can see labeling something that behaves very differently and needs different approaches as being “deviant" from a treatment and public information standpoint. It may help with those functions.
Certainly, there are people suggesting a labeling change for Omicron, with suggestions varying from taxonomic relabeling to public designation changing from CoVID-19 to CoVID-21 if it continues to pan out as having less health impact on a number of people while being more infectious.
From a genetics and evolutionary standpoint, though, i see the trends which are occurring as being not at all unexpected from a viral survival, spread, and replication aspect, so for species or subspecies designations, especially in such a genetically active disease, i would rather be a lumper than a splitter taxonomically. We humans are far too inclined to split species easily in designations when impact upon us (or similarity to us) is involved. That is just my paleontology and E&E education speaking, of course, but that strikes me as being applicable.
https://www.medrxiv.org/content/10.1101/2021.12.25.21268404v2
Cooccurrence of N501Y, P681R and other key mutations in SARS-CoV-2 Spike
Abstract
Analysis of circa 4.2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences on Global Initiative on Sharing All Influenza Data (GISAID) shows the spike mutations N501Y (common to Alpha, Beta, Gamma, Omicron variants) and P681R (central to Delta variant spread) have cooccurred 3,678 times between 17 October 2020 and 1 November 2021. In contrast, the N501Y+P681H combination is present in Alpha and Omicron variants and circa 1.1 million entries. Two-thirds of the 3,678 cooccurrences were in France, Turkey or US (East Coast), and the rest across 62 other countries. 55.5% and 4.6% of the cooccurrences were Alpha Q.4 and Gamma P.1.8 sub-lineages acquiring P681R; 10.7% and 3.8% were Delta B.1.617.2 lineage and AY.33 sub-lineage acquiring N501Y; remaining 10.2% were in other variants. Despite the selective advantages individually conferred by N501Y and P681R, the N501Y+P681R combi-nation counterintuitively did not outcompete other variants in every instance. Although a relief to worldwide public health efforts, in vitro and in vivo studies are urgently required in the absence of a strong in silico explanation for this phenomenon. This study demonstrates a pipeline to analyse combinations of key mutations from public domain information in a systematic manner and provide early warnings of spread.