key: cord-0967683-2f94sctn
authors: Dimeglio, Chloé; Loubes, Jean-Michel; Migueres, Marion; Sauné, Karine; Trémeaux, Pauline; Lhomme, Sébastien; Ranger, Noémie; Latour, Justine; Mansuy, Jean-Michel; Izopet, Jacques
title: Influence of vaccination and prior immunity on the dynamics of Omicron BA.1 and BA.2 sub-variants
date: 2022-03-17
journal: J Infect
DOI: 10.1016/j.jinf.2022.03.014
sha: 03cb43c169ea6f3c3332dd568b7496204c70ec83
doc_id: 967683
cord_uid: 2f94sctn

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Our discretized version of a susceptible infectious and recovered (SIR)-type model has been shown well suited to studies on the spread of SARS-CoV-2 (2,3).

The model includes a diffusion/transmission coefficient 0 that varies with the likelihood of contagion, and two reduction coefficients ̂ and ̂ that describe the impact of public health measures on virus transmission. Values of ̂ and ̂ were estimated in previous studies (2, 3) . It also takes into account a parameter 1 describing the proportion of the 1 variant in urban Toulouse, and a similar We set 0 ( ) = 5.9 for the Delta variant at its peak, based on WHO international data (4) . First elements showed that 0 ( 1 ) could reach 10 (5). We estimated the initial model settings using data collected by Toulouse Virology Laboratory ( Table 1 ).

The nucleic acids in nasopharyngeal swab samples collected at Toulouse University Hospital were extracted with the MGI extraction system and tested using the ThermoFisher TaqPath RT-PCR assay. Supplementary S1) ( Figure 1C ). The proportion, 2 , of BA.2 variant increased from 5.5% at the end of January 2022 to 39.9% on February 21, 2022 ( Table 1 ). The rate of positive RT-PCR tests should have doubled between February 1 and 21 if the vaccine/immunity efficacy for BA.2 is close to 23%, the same as that for BA.1 ( Figure 1B) . However the percentage of positive RT-PCR tests decreased from 44% on February 4 to 19.6% on February 21 (weeks 5-7, Table 1 ). Correcting the model parameters to bring the predicted data in line with the observed data (Equation 2, Supplementary S1) gave a vaccine/immunity coefficient of 92.8% ( Figure 1C ). We conclude that the increase in the proportion of BA.2 has not led to a faster spread of the virus;

which seems to indicate that the immunity induced by BA.1 infection is effective against BA.2.

Further studies are needed to determine the contributions of the vaccine booster and a BA.1 infection to protection against BA.2.

The authors have no conflict of interest to declare. 

Breakthrough infections with SARS-CoV-2 omicron despite mRNA vaccine booster dose

Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2. Viruses

Quantifying the impact of public health protection measures on the spread of SARS-CoV-2

Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at

Omicron variant and booster COVID-19 vaccines

Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Viruses

Effectiveness of Covid-19 Vaccines against the B.1.617.2 (Delta) Variant

Influence of immune escape and nasopharyngeal virus load on the spread of SARS-CoV-2 Omicron variant

Antibody evasion properties of SARS-CoV-2 Omicron sublineages

Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households

Figure 1: Daily dynamics of SARS-CoV-2 infection

Assuming that the Omicron BA.1 sub-variant is as sensitive as Delta to vaccination/previous immunity B. Assuming that the Omicron BA.2 sub-variant is as sensitive as BA.1 to vaccination/previous immunity C. Real daily dynamics of SARS-CoV-2 infection

The English text was edited by Dr Owen Parkes.