Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar.

Autor: Andriamandimby SF; Virology Unit, Institut Pasteur de Madagascar, Madagascar. Electronic address: soafy@pasteur.mg., Brook CE; Department of Ecology and Evolution, University of Chicago, United States., Razanajatovo N; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Randriambolamanantsoa TH; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Rakotondramanga JM; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Rasambainarivo F; Department of Ecology and Evolutionary Biology, Princeton University, United States., Raharimanga V; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Razanajatovo IM; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Mangahasimbola R; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Razafindratsimandresy R; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Randrianarisoa S; Department of Veterinary Sciences and Medicine, University of Antananarivo, Madagascar., Bernardson B; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Rabarison JH; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Randrianarisoa M; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Nasolo FS; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Rabetombosoa RM; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Ratsimbazafy AM; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Raharinosy V; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Rabemananjara AH; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Ranaivoson CH; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Razafimanjato H; Virology Unit, Institut Pasteur de Madagascar, Madagascar., Randremanana R; Virology Unit, Institut Pasteur de Madagascar, Madagascar; Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Madagascar., Héraud JM; Virology Unit, Institut Pasteur of Dakar, Senegal., Dussart P; Virology Unit, Institut Pasteur de Madagascar, Madagascar.
Jazyk: angličtina
Zdroj: Epidemics [Epidemics] 2022 Mar; Vol. 38, pp. 100533. Date of Electronic Publication: 2021 Nov 29.
DOI: 10.1016/j.epidem.2021.100533
Abstrakt: As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (C t ) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-C t value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on C t value, suggesting that C t value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level C t distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional C t distributions across three regions in Madagascar. We find that C t -derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of C t values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.
(Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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