Estimating Generation Time Of Omicron - Revision history

Alex: /* Abstract */

2022-08-09T12:38:58Z

Abstract

← Older revision		Revision as of 06:38, 9 August 2022
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	We then consider alternative possible explanations for the observed pattern of growth.		We then consider alternative possible explanations for the observed pattern of growth.

			Additional note (opinion): it is possible that a lower generation time for Omicron is part of the explanation for the observed relationship between $$g_\O(t)$$ and $$g_\Delta(t)$$, but it seems unlikely that the generation time of Omicron during this period was quite as low as 2.12 days, given what we know about the the viral load of Omicron as a function of time (e.g., [https://dash.harvard.edu/handle/1/37370587 Hay et al, Jan 2022] observe 4.52 days from first possible detection to peak viral concentration). Some possible reasons for this discrepancy are given in the limitations section below.

	Note that here and throughout, confidence intervals only show statistical variation within the given model. It is possible there are larger sources of error due to an incorrect modelling assumption, as discussed in limitations below.		Note that here and throughout, confidence intervals only show statistical variation within the given model. It is possible there are larger sources of error due to an incorrect modelling assumption, as discussed in limitations below.

Alex: /* Generation Time of the Omicron Variant based on case counts in England in 2021 */

2022-01-29T10:30:21Z

Generation Time of the Omicron Variant based on case counts in England in 2021

← Older revision		Revision as of 04:30, 29 January 2022
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	= Generation Time of the Omicron Variant based on case counts in England in 2021 =		= Generation Time of the Omicron Variant based on case counts in England in 2021 =

	Alex Selby ~~/ [[File:Email.png~~]] / [https://twitter.com/alexselby1770 @alexselby1770]		[[About_Me \|Alex Selby]] / [https://twitter.com/alexselby1770 @alexselby1770]

	= Abstract =		= Abstract =

Alex: /* Abstract */

2022-01-08T00:14:14Z

Abstract

← Older revision		Revision as of 18:14, 7 January 2022
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	There has been speculation that part of the advantage the Omicron variant has over Delta is that it has a significantly shorter generation period. It is important to establish whether or not this is the case because models of the epidemic with this as a default assumption will make substantially different predictions from those without. This will have implications for policies, such as those aimed at combatting virus spread and allocating hospital resources. A shorter generation time would mean, for example, that Omicron's transmission advantage is lower than it otherwise would be which in turn would mean that restrictions (NPIs, reduction of contacts) ought to have a disproportionately successful effect on reducing spread. It would also suggest that a person's infectious period typically starts earlier and is shorter than otherwise expected, which would have implications for contact tracing and quarantine. Another consequence of a lower generation time is that we would expect the epidemic, if unmitigated by restrictions, to be over more quickly than it otherwise would be.		There has been speculation that part of the advantage the Omicron variant has over Delta is that it has a significantly shorter generation period. It is important to establish whether or not this is the case because models of the epidemic with this as a default assumption will make substantially different predictions from those without. This will have implications for policies, such as those aimed at combatting virus spread and allocating hospital resources. A shorter generation time would mean, for example, that Omicron's transmission advantage is lower than it otherwise would be which in turn would mean that restrictions (NPIs, reduction of contacts) ought to have a disproportionately successful effect on reducing spread. It would also suggest that a person's infectious period typically starts earlier and is shorter than otherwise expected, which would have implications for contact tracing and quarantine. Another consequence of a lower generation time is that we would expect the epidemic, if unmitigated by restrictions, to be over more quickly than it otherwise would be.

	In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 (or, more precisely, $$1+0.483$$) is that the generation time of Omicron is much smaller than that of Delta.		In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 (or, more precisely, $$1+0.483\theta_\Delta$$ - see below) is that the generation time of Omicron is much smaller than that of Delta.

	The above relationship between characteristics of Delta and of Omicron is inferred from variant case counts only. If we go further and make use of previous estimates of characteristics of Delta, then we can estimate those of Omicron. In this article we consider the generation time distribution of Delta from [https://www.medrxiv.org/content/10.1101/2021.10.21.21265216v1 Hart et al, Oct 2021]. Combined with the above linear relationship, these suggest that the generation time of Omicron is 46% (38% - 60%) that of Delta, or 2.12 (1.75 - 2.77) days, and that the relative transmissibility in England in December 2021, $$R_t(\O)/R_t(\Delta)$$, was 2.28 (2.03 - 2.68), lower than some early estimates that did not consider a different generation time.		The above relationship between characteristics of Delta and of Omicron is inferred from variant case counts only. If we go further and make use of previous estimates of characteristics of Delta, then we can estimate those of Omicron. In this article we consider the generation time distribution of Delta from [https://www.medrxiv.org/content/10.1101/2021.10.21.21265216v1 Hart et al, Oct 2021]. Combined with the above linear relationship, these suggest that the generation time of Omicron is 46% (38% - 60%) that of Delta, or 2.12 (1.75 - 2.77) days, and that the relative transmissibility in England in December 2021, $$R_t(\O)/R_t(\Delta)$$, was 2.28 (2.03 - 2.68), lower than some early estimates that did not consider a different generation time.

Alex: /* Abstract */

2022-01-07T19:28:03Z

Abstract

← Older revision		Revision as of 13:28, 7 January 2022
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	There has been speculation that part of the advantage the Omicron variant has over Delta is that it has a significantly shorter generation period. It is important to establish whether or not this is the case because models of the epidemic with this as a default assumption will make substantially different predictions from those without. This will have implications for policies, such as those aimed at combatting virus spread and allocating hospital resources. A shorter generation time would mean, for example, that Omicron's transmission advantage is lower than it otherwise would be which in turn would mean that restrictions (NPIs, reduction of contacts) ought to have a disproportionately successful effect on reducing spread. It would also suggest that a person's infectious period typically starts earlier and is shorter than otherwise expected, which would have implications for contact tracing and quarantine. Another consequence of a lower generation time is that we would expect the epidemic, if unmitigated by restrictions, to be over more quickly than it otherwise would be.		There has been speculation that part of the advantage the Omicron variant has over Delta is that it has a significantly shorter generation period. It is important to establish whether or not this is the case because models of the epidemic with this as a default assumption will make substantially different predictions from those without. This will have implications for policies, such as those aimed at combatting virus spread and allocating hospital resources. A shorter generation time would mean, for example, that Omicron's transmission advantage is lower than it otherwise would be which in turn would mean that restrictions (NPIs, reduction of contacts) ought to have a disproportionately successful effect on reducing spread. It would also suggest that a person's infectious period typically starts earlier and is shorter than otherwise expected, which would have implications for contact tracing and quarantine. Another consequence of a lower generation time is that we would expect the epidemic, if unmitigated by restrictions, to be over more quickly than it otherwise would be.

	In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 is that the generation time of Omicron is much smaller than that of Delta.		In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 (or, more precisely, $$1+0.483$$) is that the generation time of Omicron is much smaller than that of Delta.

	The above relationship between characteristics of Delta and of Omicron is inferred from variant case counts only. If we go further and make use of previous estimates of characteristics of Delta, then we can estimate those of Omicron. In this article we consider the generation time distribution of Delta from [https://www.medrxiv.org/content/10.1101/2021.10.21.21265216v1 Hart et al, Oct 2021]. Combined with the above linear relationship, these suggest that the generation time of Omicron is 46% (38% - 60%) that of Delta, or 2.12 (1.75 - 2.77) days, and that the relative transmissibility in England in December 2021, $$R_t(\O)/R_t(\Delta)$$, was 2.28 (2.03 - 2.68), lower than some early estimates that did not consider a different generation time.		The above relationship between characteristics of Delta and of Omicron is inferred from variant case counts only. If we go further and make use of previous estimates of characteristics of Delta, then we can estimate those of Omicron. In this article we consider the generation time distribution of Delta from [https://www.medrxiv.org/content/10.1101/2021.10.21.21265216v1 Hart et al, Oct 2021]. Combined with the above linear relationship, these suggest that the generation time of Omicron is 46% (38% - 60%) that of Delta, or 2.12 (1.75 - 2.77) days, and that the relative transmissibility in England in December 2021, $$R_t(\O)/R_t(\Delta)$$, was 2.28 (2.03 - 2.68), lower than some early estimates that did not consider a different generation time.

Alex: /* Abstract */

2022-01-07T01:11:30Z

Abstract

← Older revision		Revision as of 19:11, 6 January 2022
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	In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 is that the generation time of Omicron is much smaller than that of Delta.		In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 is that the generation time of Omicron is much smaller than that of Delta.

	If we use the generation time distribution of Delta from [https://www.medrxiv.org/content/10.1101/2021.10.21.21265216v1 Hart et al, Oct 2021]~~, then~~ the above linear relationship ~~suggests~~ that the generation time of Omicron is 46% (38% - 60%) that of Delta, or 2.12 (1.75 - 2.77) days, and that the relative transmissibility in England in December 2021, $$R_t(\O)/R_t(\Delta)$$, was 2.28 (2.03 - 2.68), lower than some early estimates that did not consider a different generation time. We then consider alternative possible explanations for the observed pattern of growth.		The above relationship between characteristics of Delta and of Omicron is inferred from variant case counts only. If we go further and make use of previous estimates of characteristics of Delta, then we can estimate those of Omicron. In this article we consider the generation time distribution of Delta from [https://www.medrxiv.org/content/10.1101/2021.10.21.21265216v1 Hart et al, Oct 2021]. Combined with the above linear relationship, these suggest that the generation time of Omicron is 46% (38% - 60%) that of Delta, or 2.12 (1.75 - 2.77) days, and that the relative transmissibility in England in December 2021, $$R_t(\O)/R_t(\Delta)$$, was 2.28 (2.03 - 2.68), lower than some early estimates that did not consider a different generation time.

			We then consider alternative possible explanations for the observed pattern of growth.

	Note that here and throughout, confidence intervals only show statistical variation within the given model. It is possible there are larger sources of error due to an incorrect modelling assumption, as discussed in limitations below.		Note that here and throughout, confidence intervals only show statistical variation within the given model. It is possible there are larger sources of error due to an incorrect modelling assumption, as discussed in limitations below.

Alex: /* Abstract */

2022-01-07T01:02:58Z

Abstract

← Older revision		Revision as of 19:02, 6 January 2022
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	= Abstract =		= Abstract =

	There has been speculation that part of the advantage the Omicron variant has over Delta is that it has a significantly shorter generation period. It is important to establish whether or not this is the case because models of the epidemic with this as a default assumption will make substantially different predictions from those without. A shorter generation time would mean, for example, that Omicron's transmission advantage is lower than it otherwise would be which in turn would mean that restrictions (NPIs, reduction of contacts) ought to have a disproportionately successful effect on reducing spread. It would also suggest that a person's infectious period typically starts earlier and is shorter than otherwise expected, which would have implications for contact tracing and quarantine. Another consequence of a lower generation time is that we would expect the epidemic, if unmitigated by restrictions, to be over more quickly than it otherwise would be.		There has been speculation that part of the advantage the Omicron variant has over Delta is that it has a significantly shorter generation period. It is important to establish whether or not this is the case because models of the epidemic with this as a default assumption will make substantially different predictions from those without. This will have implications for policies, such as those aimed at combatting virus spread and allocating hospital resources. A shorter generation time would mean, for example, that Omicron's transmission advantage is lower than it otherwise would be which in turn would mean that restrictions (NPIs, reduction of contacts) ought to have a disproportionately successful effect on reducing spread. It would also suggest that a person's infectious period typically starts earlier and is shorter than otherwise expected, which would have implications for contact tracing and quarantine. Another consequence of a lower generation time is that we would expect the epidemic, if unmitigated by restrictions, to be over more quickly than it otherwise would be.

	In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 is that the generation time of Omicron is much smaller than that of Delta.		In this article we consider the sequence of Delta and Omicron daily case counts and highlight a particular striking pattern of growth in new cases per day: the daily growth rates, $$g_\Delta(t)$$ and $$g_\O(t)$$ of Delta and Omicron respectively in England from 25 November - 24 December 2021 are related to a good approximation by $$g_\O(t)=0.483+3.391g_\Delta(t)$$ (95% CI for the gradient: 2.788 - 3.663). One possible explanation for the gradient of this line being so much larger than 1 is that the generation time of Omicron is much smaller than that of Delta.

Alex: /* Conclusion */

2022-01-07T00:58:42Z

Conclusion

← Older revision		Revision as of 18:58, 6 January 2022
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	= Conclusion =		= Conclusion =

	We observe some unusual phenomena (Figs. 1-3). One explanation for these is that Omicron has a significantly shorter generation time than Delta. In the opinion of the author, a shorter generation time is likely to be at least part of the explanation.		We observe some unusual phenomena (Figs. 1-3). One explanation for these is that Omicron has a significantly shorter generation time than Delta. In the opinion of the author, a shorter generation time is likely to be at least part of the explanation. A particular policy implication of this is that interventions (reduction in mixing, contacts) are likely to be disproportionately effective against Omicron.

	Traditionally, generation times are hard to measure and require careful surveys of people's behaviour, but the above analysis suggests it might be possible to extract some information about comparative generation times between variants from simple case numbers under some circumstances, especially when it looks like the difference is large. It also helped in this case that there was a substantial change in people's behaviour in December 2021 that provided a variation in the growth parameters, which made the inverse problem of finding the relationship between growth parameters well-conditioned.		Traditionally, generation times are hard to measure and require careful surveys of people's behaviour, but the above analysis suggests it might be possible to extract some information about comparative generation times between variants from simple case numbers under some circumstances, especially when it looks like the difference is large. It also helped in this case that there was a substantial change in people's behaviour in December 2021 that provided a variation in the growth parameters, which made the inverse problem of finding the relationship between growth parameters well-conditioned.

Alex: /* Conclusion */

2022-01-07T00:56:45Z

Conclusion

← Older revision		Revision as of 18:56, 6 January 2022
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	= Conclusion =		= Conclusion =

	We ~~have~~ some unusual phenomena (Figs. 1-3)~~, one~~ explanation for ~~which~~ is that Omicron has a significantly shorter generation time than Delta. In the opinion of the author, a shorter generation time is likely to be at least part of the explanation.		We observe some unusual phenomena (Figs. 1-3). One explanation for these is that Omicron has a significantly shorter generation time than Delta. In the opinion of the author, a shorter generation time is likely to be at least part of the explanation.

	Traditionally, generation times are hard to measure and require careful surveys of people's behaviour, but the above analysis suggests it might be possible to extract some information about comparative generation times between variants from simple case numbers under some circumstances, especially when it looks like the difference is large. It also helped in this case that there was a substantial change in people's behaviour in December 2021 that provided a variation in the growth parameters, which made the inverse problem of finding the relationship between growth parameters well-conditioned.		Traditionally, generation times are hard to measure and require careful surveys of people's behaviour, but the above analysis suggests it might be possible to extract some information about comparative generation times between variants from simple case numbers under some circumstances, especially when it looks like the difference is large. It also helped in this case that there was a substantial change in people's behaviour in December 2021 that provided a variation in the growth parameters, which made the inverse problem of finding the relationship between growth parameters well-conditioned.

Alex: /* Conclusion */

2022-01-07T00:55:39Z

Conclusion

← Older revision		Revision as of 18:55, 6 January 2022
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	We have some unusual phenomena (Figs. 1-3), one explanation for which is that Omicron has a significantly shorter generation time than Delta. In the opinion of the author, a shorter generation time is likely to be at least part of the explanation.		We have some unusual phenomena (Figs. 1-3), one explanation for which is that Omicron has a significantly shorter generation time than Delta. In the opinion of the author, a shorter generation time is likely to be at least part of the explanation.

	Traditionally, generation times are hard to measure and require careful surveys of people's behaviour, but the above analysis suggests it might be possible to extract some information about comparative generation times between variants from simple case numbers under some circumstances, especially when it looks like the difference is large.		Traditionally, generation times are hard to measure and require careful surveys of people's behaviour, but the above analysis suggests it might be possible to extract some information about comparative generation times between variants from simple case numbers under some circumstances, especially when it looks like the difference is large. It also helped in this case that there was a substantial change in people's behaviour in December 2021 that provided a variation in the growth parameters, which made the inverse problem of finding the relationship between growth parameters well-conditioned.

	To do this requires a somewhat careful treatment of case counts to remove any consistent anomalous features. This is unlike simple relative growth rates, which rely on $$\log(\O_t/\Delta_t)$$ in which anomalies in $$\O_t$$ and $$\Delta_t$$ tend to cancel out nicely.		To do this requires a somewhat careful treatment of case counts to remove any consistent anomalous features. This is unlike simple relative growth rates, which rely on $$\log(\O_t/\Delta_t)$$ in which anomalies in $$\O_t$$ and $$\Delta_t$$ tend to cancel out nicely.

Alex at 00:51, 7 January 2022

2022-01-07T00:51:42Z

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