Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

Park, Sang Woo; Sun, Kaiyuan; Abbott, Sam; Sender, Ron; Bar-On, Yinon M.; Weitz, Joshua S.; Funk, Sebastian; Grenfell, Bryan T.; Backer, J.A.; Wallinga, Jacco; Viboud, Cécile; Dushoff, Jonathan

doi:10.1073/pnas.2221887120

Cited by 16 publications

(19 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…* lineages cocirculating in Brazil by estimating the R RI from the observed frequencies of variants in the country from November 2023 to January 2024 as described elsewhere (Ito et al, 2021). The probability mass function of the generation time of Omicron was modeled by discretizing the gamma distribution with α=4.03 and θ=0.737, so that the gamma distribution has the same mean (2.97) and variance (2.19) as the log-normal distribution estimated by Park et al (Park et al, 2023). SARS-CoV-2 lineages observed in each country region were counted using half-month bins.…”

Section: Methodsmentioning

confidence: 99%

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023

Arantes,

Ito,

Gomes

et al. 2024

Preprint

View full text Add to dashboard Cite

Recombination plays a crucial role in the evolution of SARS-CoV-2. The Omicron XBB* recombinant lineages are a noteworthy example, as they have been the dominant SARS-CoV-2 variant worldwide in the first half of 2023. Since November 2023, a new recombinant lineage between Omicron subvariants XBB and BA.2.86, designated XDR, has been detected mainly in Brazil. In this study, we reconstructed the spatiotemporal dynamics and estimated the absolute and relative transmissibility of the XDR lineage. The XDR lineage displayed a recombination breakpoint in the ORF1a coding region, and the most closely related sequences to the 5 and 3 ends of the recombinant correspond to JD.1.1 and JN.1.1 lineages, respectively. The first XDR sequences were detected in November 2023 in the Northeastern Brazilian region, and their prevalence rapidly surged from <1% to 25% by February 2024. The Bayesian phylogeographic analysis supports that the XDR lineage likely emerged in the Northeastern Brazilian region around late October 2023 and rapidly disseminated within and outside Brazilian borders from mid-November onwards. The median effective reproductive number of the XDR lineage in Brazil during the initial expansion phase was estimated to be around 1.5. In contrast, the average relative instantaneous reproduction numbers of XDR and JN* lineages were estimated to be 1.37 and 1.29 higher than that of co-circulating XBB* lineages. In summary, these findings support that the recombinant lineage XDR arose in the Northeastern Brazilian region in October 2023, shortly after the first detection of JN.1 sequences in the country. In Brazil, the XDR lineage exhibited a higher transmissibility level than its parental XBB.* lineages and is spreading at a rate similar to or slightly faster than the JN.1* lineages.

show abstract

Section: Methodsmentioning

confidence: 99%

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023

Arantes,

Ito,

Gomes

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…wild-type-like). During exponential growth, the incubation periods of the recently infected infectors (also known as the backward incubation period in [ 5 , 11 ]) tend to be shorter than the true incubation period (also known as the forward incubation period in [ 5 , 11 ]). Without adjusting for the outbreak dynamics, the overall observed incubation period will be shorten and, hence, shortening the generation intervals.…”

Section: Methodsmentioning

confidence: 99%

“…Without adjusting for the outbreak dynamics, the overall observed incubation period will be shorten and, hence, shortening the generation intervals. The relationship between the observed (backward) and the true (forward) incubation period can be expressed as [ 5 ]: where b ( τ ) is the backward incubation period and f ( τ ) is the forward incubation period τ time since infection, and r is the exponential growth rate if r > 0 and exponential decline if r < 0. We parameterised our model by f ( τ ) to generate the b ( τ ) of the infectors and simulate the different outbreak dynamics.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response

Pung,

Russell,

Kucharski

2024

PLoS Comput Biol

View full text Add to dashboard Cite

The epidemiological characteristics of SARS-CoV-2 transmission have changed over the pandemic due to emergence of new variants. A decrease in the generation or serial intervals would imply a shortened transmission timescale and, hence, outbreak response measures would need to expand at a faster rate. However, there are challenges in measuring these intervals. Alongside epidemiological changes, factors like varying delays in outbreak response, social contact patterns, dependence on the growth phase of an outbreak, and effects of exposure to multiple infectors can also influence measured generation or serial intervals. To guide real-time interpretation of variant data, we simulated concurrent changes in the aforementioned factors and estimated the statistical power to detect a change in the generation and serial interval. We compared our findings to the reported decrease or lack thereof in the generation and serial intervals of different SARS-CoV-2 variants. Our study helps to clarify contradictory outbreak observations and informs the required sample sizes under certain outbreak conditions to ensure that future studies of generation and serial intervals are adequately powered.

show abstract

“…Then q Ai ( t )and q I ( t ) are represented by the following formula: where g ( j ) is the probability mass function of generation time distribution and l is the day when the probability of generating new infections becomes negligibly small. Park et al estimated the Omicron strains’ mean generation time to be 3.0 using within-household transmission data (62). The generation time distribution they estimated was a lognormal distribution with a log mean of 0.98 and a log standard deviation of 0.47, of which the mean is 2.97, and the variance is 2.19.…”

Section: Introductionmentioning

confidence: 99%

Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineages dissemination in Brazil in 2023

Arantes,

Gomes,

Ito

et al. 2023

Preprint

View full text Add to dashboard Cite

The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron VOC that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n =11,065 sequences) with epidemiological data of Severe Acute Respiratory Infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB*+F486P, XBB*+F486P+F456L, and XBB*+F486P+ F456L+L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil’s epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB*+F486P+F456L+L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead.

show abstract

Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

Cited by 16 publications

References 44 publications

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023

Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response

Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineages dissemination in Brazil in 2023

Contact Info

Product

Resources

About