Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark

Ito, Kimihito; Piantham, Chayada; Nishiura, Hiroshi

doi:10.3934/mbe.2022418

Cited by 36 publications

(32 citation statements)

References 16 publications

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“…This result is consistent with previous findings that support the higher infectiousness of Delta compared to Gamma (Du et al, 2022; Y. Liu & Rocklöv, 2022) and of Omicron (BA.1) compared to Delta (Nishiura et al, 2021; Suzuki et al, 2022; Ito et al, 2022; Ito et al, 2022a; Du et al, 2022). Using epidemiological and phylodynamics models, we estimate that the average Re of Omicron was ∼3 times higher than that of Delta.…”

Section: Discussionsupporting

confidence: 93%

“…Of note, the average relative Re of Omicron w.r.t. Delta in Amazonas (∼3) was roughly comparable to that estimated in other settings with different infection and vaccination histories like South Africa, Denmark, the UK, the United States of America, and India (∼2-5) (Nishiura et al, 2021; Suzuki et al, 2022; Ito et al, 2022a; Ito et al, 2022b; Du et al, 2022). The Omicron outbreak in Amazonas also had a similar duration from the onset of case growth to their peaks (∼30 days) than that observed in other populations with different immune landscapes (Washburne et al, 2022; van Dorp et al, 2022).…”

Section: Discussionsupporting

confidence: 73%

“…The generation time of Gamma and Delta were assumed to follow a gamma distribution having a mean of 4.7 and a standard deviation of 3.3 (Hart et al, 2022). The generation time of Omicron was assumed to follow a gamma distribution having a mean of 2.8 and a standard deviation of 1.98 (Ito et al, 2022a). We use Delta as the baseline variant to calculate the relative Re of Gamma and Omicron.…”

Section: Methodsmentioning

confidence: 99%

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Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity

Arantes

Bello

Nascimento

et al. 2022

Preprint

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The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively, with variable impact according to the immune population landscape. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4,128 patients collected in Amazonas between July 1st, 2021 and January 31st, 2022 and investigated the lineage replacement dynamics using a phylodynamic approach. The VOCs Delta and Omicron displayed similar patterns of phylogeographic spread but significantly different epidemic dynamics. The Delta and Omicron epidemics were fueled by multiple introduction events, followed by the successful establishment of a few local transmission lineages of considerable size that mainly arose in the Capital, Manaus. The VOC Omicron spread and became dominant much faster than the VOC Delta. We estimate that under the same epidemiological conditions, the average Re of Omicron was ~3.3 times higher than that of Delta and the average Re of the Delta was ~1.3 times higher than that of Gamma. Furthermore, the gradual replacement of Gamma by Delta occurred without an upsurge of COVID-19 cases, while the rise of Omicron fueled a sharp increase in SARS-CoV-2 infection. The Omicron wave displayed a shorter duration and a clear decoupling between the number of SARS-CoV-2 cases and deaths compared with previous (B.1.* and Gamma) waves in the Amazonas state. These findings suggest that the high level of hybrid immunity (infection plus vaccination) acquired by the Amazonian population by mid-2021 was able to limit the spread of the VOC Delta and was also probably crucial to curb the number of severe cases, although not the number of VOC Omicron new infections.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 73%

Section: Methodsmentioning

confidence: 99%

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Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity

Arantes

Bello

Nascimento

et al. 2022

Preprint

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“…27 Previous studies have reported different GTs for different variants of SARS-CoV-2. [28][29][30][31] Zhang et al 28 reported a mean GT of 2.9 days for B.1.617.2, while Hart et al 29 reported a mean intrinsic GT of 4.7 days and a mean household GT of 3.2 days for this variant. Ito et al 30 reported a reduction in mean GT for the Omicron variant BA.1 compared with the delta variant B.1.617.2 (GT for BA.1 = 0.44 to 0.46 times delta), and similar results were reported by Manica et al 31 .…”

Section: Methodsmentioning

confidence: 99%

Effects of wearing FFP2 masks on SARS-CoV-2 infection rates in classrooms

Jarnig

Kerbl

Poppel

2022

Preprint

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Importance: Different mitigation measures are mandated in schools worldwide to control the spread of SARS-CoV-2. The efficacy of most measures, however, has not been investigated thus far. Objective: To investigate the usefulness of FFP-2 masks in classrooms to prevent the spread of SARS-CoV-2. Design: A retrospective comparative cohort study of infection rates (evaluated by PCR screening in school) in students wearing FFP-2 masks continuously and students in sports classes with limited face mask use. Setting: A single-center evaluation comparing classes (middle school: age 10-16 years, 4-year high school: age 14-20 years) with a high sports focus (SF), with regular classes during the Delta and Omicron waves (September 2021-April 2022). Participants: In total, 616 children/families were invited to participate in the comparative evaluation, and 614 (99.7%) followed this invitation by providing relevant information concerning their SARS-CoV-2 infection status. A total of 213 legal guardians (for children < 14 years) and 401 adolescents (14 years and older) reported SARS-CoV-2 infections during the 2021/22 school year. Main Outcomes and Measures: A comparative analysis of cumulative SARS-CoV-2 infection rates in sports and non-sports classes (the 7-day classroom incidence of SARS-CoV-2 infections, and potential secondary infections among school classmates). Results: Cumulative SARS-CoV-2 infection rates were clearly higher in sports classes (with limited mask use) than in non-sports classes (continuous mask use). After the relaxation of the mitigation measures, students in non-sports classes, however, showed a clear catch-up of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (April 30, 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p=0.037, phi=0.09) was detected between classes with a sports focus and those without a sports focus. Conclusions and Relevance: Wearing FFP2 face masks reduces the risk of SARS-CoV-2 infection if strict mitigation measures are applied. Following the relaxation of strict measures, previously protected students show a significant catch-up infection rate. Thus, continuous face mask use postpones rather than avoids SARS-CoV-2 infection in many cases. Therefore, the advantage of reduced transmission must be carefully balanced against the disadvantages associated with mask wearing throughout schools.

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“…The accumulation of genetic changes in S has been related to increased viral transmission compared with previous VOCs [3]. For instance, in Denmark and Italy, it has been estimated that BA.1 had an effective reproduction number (R t ) around two to three times greater than the Delta variant [4,5]. The large number of mutations in S resulted in an enhanced antigenic escape, reflected by the high number of infections among the vaccinated population and a sharp decline in the neutralization titers of reported monoclonal antibodies, as well as in the sera of vaccinated subjects [6,7].…”

Section: Introductionmentioning

confidence: 99%

Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico

Zárate

Taboada

Rosales-Rivera

et al. 2022

Preprint

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The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In Mexico, this subvariant began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in the country. Unlike previous SARS-CoV-2 variants, BA.1 did not acquire local substitutions nor exhibited a geographically distinct circulation pattern in Mexico. However, a regional difference in the speed of the replacement of the Delta variant was observed, as some northern states showed persistence of Delta lineages well into February 2022. Mexican states were divided into four regions (North, Central North, Central South, and Southeast) based on the lineage circulation before the dominance of BA.1 to study possible causes for this difference. For each region, the time to fixation of BA.1, the diversity of Delta sublineages in the weeks preceding BA.1 entry, the population density, and the level of virus circulation during the inter-wave interval were determined. An association between a faster Omicron spread and lower Delta diversity, as well as fewer COVID-19 cases during the Delta-BA.1.x inter-wave period, was observed. For example, the North region exhibited the slowest spread but had the highest diversity of Delta sublineages and the greatest number of inter-wave cases relative to the maximum amount of the virus circulating in the region, whereas the Southeast region showed the opposite. Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics. Nonetheless, if there is a significant difference in the fitness of the variants or the time allowed for the competition is sufficient, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.

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Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark

Cited by 36 publications

References 16 publications

Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity

Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity

Effects of wearing FFP2 masks on SARS-CoV-2 infection rates in classrooms

Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico

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