@article{fdi:010086415,
  title = {{R}etrospective analysis of {SARS}-{C}o{V}-2 omicron invasion over delta in {F}rench regions in 2021-22 : a status-based multi-variant model},
  author = {{H}aschka, {T}. and {V}ergu, {E}. and {R}oche, {B}enjamin and {P}oletto, {C}. and {O}patowski, {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {SARS}-{C}o{V}-2 is a rapidly spreading disease affecting human life and the economy on a global scale. {T}he disease has caused so far more then 5.5 million deaths. {T}he omicron outbreak that emerged in {B}otswana in the south of {A}frica spread around the globe at further increased rates, and caused unprecedented {SARS}-{C}o{V}-2 infection incidences in several countries. {A}t the start of {D}ecember 2021 the first omicron cases were reported in {F}rance. {M}ethods: {I}n this paper we investigate the spreading potential of this novel variant relatively to the delta variant that was also in circulation in {F}rance at that time. {U}sing a dynamic multi-variant model accounting for cross-immunity through a status-based approach, we analyze screening data reported by {S}ante {P}ublique {F}rance over 13 metropolitan {F}rench regions between 1st of {D}ecember 2021 and the 30th of {J}anuary 2022. {D}uring the investigated period, the delta variant was replaced by omicron in all metropolitan regions in approximately three weeks. {T}he analysis conducted retrospectively allows us to consider the whole replacement time window and compare regions with different times of omicron introduction and baseline levels of variants' transmission potential. {A}s large uncertainties regarding cross-immunity among variants persist, uncertainty analyses were carried out to assess its impact on our estimations. {R}esults: {A}ssuming that 80% of the population was immunized against delta, a cross delta/omicron cross-immunity of 25% and an omicron generation time of 3.5 days, the relative strength of omicron to delta, expressed as the ratio of their respective reproduction rates, ({R}) over cap omicron/({R}) over cap delta, was found to range between 1.51 and 1.86 across regions. {U}ncertainty analysis on epidemiological parameters led to ({R}) over cap omicron/({R}) over cap delta ranging from 1.57 to 2.34 on average over the metropolitan {F}rench regions, weighted by population size. {C}onclusions: {U}pon introduction, omicron spread rapidly through the {F}rench territory and showed a high fitness relative to delta. {W}e documented considerable geographical heterogeneities on the spreading dynamics. {T}he historical reconstruction of variant emergence dynamics provide valuable ground knowledge to face future variant emergence events.},
  keywords = {{M}ulti-variant model ; {SARS}-{C}o{V}-2 ; {O}micron ; {T}ransmissibility ; {FRANCE}},
  booktitle = {},
  journal = {{BMC} {I}nfectious {D}iseases},
  volume = {22},
  numero = {1},
  pages = {815 [13 p.]},
  year = {2022},
  DOI = {10.1186/s12879-022-07821-5},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086415},
}