The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0–3.3 Days Can Be Explained by Immune Evasion

Abstract

Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa’s provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2–3.4 days) and 2.7 days (95% CI: 2.3–3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log–linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2–10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5–4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8–2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.

The changing impact of vaccines in the COVID-19 pandemic

“…For example, it is estimated that the first case of Omicron in South Africa occurred on approximately October 9, 2021 (16). It was first identified on November 9, 2021 and reported to the WHO two weeks later, after identification of its numerous amino acid changes (17). Two days later it was classified as a variant of concern.…”

“…Assuming all vaccinated individuals receive a variant-specific booster series and all unvaccinated individuals receive a variant-specific primary series, a variant-chasing vaccine strategy could avert over 40% of deaths if it is rolled out on a large scale within 5 days from introduction of the new variant, and has a 20-day window in which it would avert more deaths than the same coverage levels with currently available vaccines. The date of introduction of a new variant into a population is impossible to know, but Omicron’s first case was estimated to occur a month before it was first detected (16; 17). Using this lag-time, if it takes 30 days to identify a new variant, the percentage of deaths a variant-chasing vaccine strategy could avert would fall to below 20%, before considering the time it would take to develop and deploy a vaccine after identification.…”

COVID-19 Vaccine: Between Myth and Truth

“…Preliminary data indicate increased transmissibility and risk of reinfection, with the number of cases caused by the Omicron variant increasing in almost all South African provinces. Studies from South Africa and the UK reported doubling times of 3.38 days and 2–2.5 days, respectively, with the basic reproduction number (R0) above 3 and an estimated weekly increase in the Omicron-to-Delta ratio in the range of 7.2–10.2, which was considerably higher than the increase in the ratio of Delta to Alpha (estimated to be in in the range 2.5–4.2) [ 107 , 108 ]. However, the current limited and preliminary evidence suggests that Omicron has a less severe clinical presentation, presenting as a mild disease with predominantly upper respiratory symptoms such as muscle aches and fatigue for 1 to 2 days, headache, itchy throat, slight cold, or mild cough [ 109 , 110 ].…”

Acceptance of COVID 19 vaccine among sub-Sahara African (SSA): a comparative study of residents and diaspora dwellers

“…Many countries have experienced their second, third and fourth waves in terms of cases and resultant deaths. [1][2][3][4] The outbreak of the new Omicron variant in different countries [5][6][7] is of global concern, [8] as it threatens the return to normalcy and the ongoing COVID-19 vaccination programmes. Non-pharmaceutical interventions to minimise the spread of infections included travel restrictions, lockdowns, physical distancing, regular handwashing and wearing of face masks.…”