ABSTRACT
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 Brazils 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.
ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved since its introduction to the human population in 2019. Natural selection selects variants with higher effective reproduction numbers, increasing the overall transmissibility of the circulating viruses. In order to establish effective control measures for a new variant, it is crucial to know its transmissibility and replacement time course in early phases of the variant replacement. In this paper, we conduct retrospective prediction tests of the variant replacement from Alpha to Delta in England. Our method firstly estimated the relative reproduction number, the ratio of the reproduction number of a variant to that of another, from partial observations up to a given time point. Secondly, the replacement time course after the time point was predicted based on the estimates of relative reproduction number. Thirdly, the estimated relative reproduction number and the predicted time course were evaluated by being compared to those estimated using the entire observations. We found that it is possible to estimate the relative reproduction number of Delta with respect to Alpha when the frequency of Delta was more than or equal to 0.25. Using these relative reproduction numbers, predictions targeting on 1st June 2021, the date when the frequency of Delta reached 0.90, had maximum absolute prediction errors of 0.015 for frequencies of Delta and 0.067 for the average relative reproduction number of circulating viruses with respect to Alpha. These results suggest that our method allows us to predict the time course of variant replacement in future from partial datasets observed in early phases of variant replacement.
ABSTRACT
The Omicron variant is the most transmissible variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) we had so far. The BA.1 and BA.2 sublineages of Omicron are circulating in Europe and it is urgent to evaluate the transmissibility of these sub-lineages. Using a mathematical model describing trajectories of variant frequencies that assumes a constant ratio in generation times and a constant ratio in effective reproduction numbers among variants, trajectories of variant frequencies in Denmark from November 22, 2021 to February 26, 2022 were analyzed. We found that the generation times of Omicron BA.1 and BA.2 are 0.60 (95%CI: 0.59-0.62) and 0.51 (95%CI: 0.50-0.52) of the length of that of Delta, respectively. We also found that the effective reproduction number of Omicron BA.1 is 1.99 (95% CI: 1.98-2.02) times and that of Omicron BA.2 is 2.51 (95% CI: 2.48- 2.55) times larger than the effective reproduction number of Delta. The generation times of Omicron BA.2 is 0.85 (95% CI:0.84-0.86) the length of that of BA.1 and that the effective reproduction number of Omicron BA.2 is 1.26 (95% CI:1.25-1.26) times larger than that of Omicron BA.1. These estimates on the ratio of generation times and the ratio of effective reproduction numbers has epidemiologically important implications. The duration of quarantine for people who contacted with an Omicron BA.1 and BA.2 patient can be reduced to 60% and 51% of that for Delta, respectively. The control measures against Omicron BA.1 and BA.2 need to reduce contacts between infectious and susceptible people respectively by 50% (95% CI: 49-50%) and 60% (95% CI: 60-61%) compared to that against Delta to achieve the same effect on their control.
ABSTRACT
Using numbers of SARS-CoV-2 variants detected in Japan, the relative instantaneous reproduction numbers of the R.1, Alpha, and Delta variants with respect to other strains circulating in Japan were estimated at 1.245, 1.437, and 1.948, respectively. The numbers can vary within 1.190-1.319 for R.1, 1.335-1.580 for Alpha, and 1.703-2.30 for Delta depending on the assumed serial interval distributions. The frequency of the Delta is expected to take over the Alpha in Japan around July 12, 2021.
ABSTRACT
The B.1.1.7 strain, also referred to as Alpha variant, is a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Alpha variant is considered to possess higher transmissibility compared to the strains previously circulating in England. This paper proposes a new method to estimate the selective advantage of a mutant strain over another strain using the time course of strain frequencies and the distribution of the serial interval of infections. This method allows the instantaneous reproduction numbers of infections to vary over calendar time. The proposed method also assumes that the selective advantage of a mutant strain over previously circulating strains is constant. Applying the method to SARS-CoV-2 sequence data from England, the instantaneous reproduction number of the B.1.1.7 strain was estimated to be 26.6-45.9% higher than previously circulating strains in England. This result indicates that control measures should be strengthened by 26.6-45.9% when the B.1.1.7 strain is newly introduced to a country where viruses with similar transmissibility to the preexisting strain in England are predominant.
