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Molecular benchmarks of a SARS-CoV-2 epidemic.

ABSTRACT: A pressing concern in the SARS-CoV-2 epidemic and other viral outbreaks, is the extent to which the containment measures are halting the viral spread. A straightforward way to assess this is to tally the active cases and the recovered ones throughout the epidemic. Here, we show how epidemic control can be assessed with molecular information during a well characterized epidemic in Iceland. We demonstrate how the viral concentration decreased in those newly diagnosed as the epidemic transitioned from exponential growth phase to containment phase. The viral concentration in the cases identified in population screening decreased faster than in those symptomatic and considered at high risk and that were targeted by the healthcare system. The viral concentration persists in recovering individuals as we found that half of the cases are still positive after two weeks. We demonstrate that accumulation of mutations in SARS-CoV-2 genome can be exploited to track the rate of new viral generations throughout the different phases of the epidemic, where the accumulation of mutations decreases as the transmission rate decreases in the containment phase. Overall, the molecular signatures of SARS-CoV-2 infections contain valuable epidemiological information that can be used to assess the effectiveness of containment measures.

SUBMITTER: Jonsson H

PROVIDER: S-EPMC8206085 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Molecular benchmarks of a SARS-CoV-2 epidemic.

Jonsson Hakon H Magnusson Olafur T OT Melsted Pall P Berglund Jonas J Agustsdottir Arna B AB Eiríksdottir Berglind B Fridriksdottir Run R Garðarsdottir Elisabet Eir EE Georgsson Gudmundur G Gretarsdottir Olafia S OS Guðmundsson Kjartan R KR Gunnarsdottir Thora Rosa TR Eggertsson Hannes H Gylfason Arnaldur A Holm Hilma H Jensson Brynjar O BO Jonasdottir Aslaug A Jonsson Frosti F Josefsdottir Kamilla S KS Thordardottir Marianna M Kristinsson Karl G KG Kristjánsson Þórður Þ Magnusdottir Droplaug N DN Roux Louise le LL Saemundsdottir Jona J Sigurdsson Asgeir A Sigmundsdottir Gudrun G Sveinbjornsson Gardar G Rognvaldsson Solvi S Eiriksson Ogmundur O Magnusson Magnus Karl MK Sveinsdottir Kristin Eva KE Sveinsdottir Maney M Thorarensen Emil Aron EA Thorbjornsson Bjarni B Löve Arthur A Norddahl Gudmundur L GL Jonsdottir Ingileif I Sulem Patrick P Masson Gisli G Moller Alma A Gudnason Thorolfur T Kristjansson Mar M Helgason Agnar A Gudbjartsson Daniel F DF Thorsteinsdottir Unnur U Stefansson Kari K

Nature communications 20210615 1

A pressing concern in the SARS-CoV-2 epidemic and other viral outbreaks, is the extent to which the containment measures are halting the viral spread. A straightforward way to assess this is to tally the active cases and the recovered ones throughout the epidemic. Here, we show how epidemic control can be assessed with molecular information during a well characterized epidemic in Iceland. We demonstrate how the viral concentration decreased in those newly diagnosed as the epidemic transitioned f ...[more]

PMID: 34131116

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Project description:BackgroundIndia was one of the countries to institute strict measures for Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the early phase. Since, then, the epidemic growth trajectory was slow before registering an explosion of cases due to local cluster transmissions.MethodsWe estimated the growth rate and doubling time of SARS-CoV-2 for India and high burden states using crowdsourced time series data. Further, we also estimated the Basic Reproductive Number (R0) and Time-dependent Reproductive number (Rt) using serial intervals from the data. We compared the R0 estimated from five different methods and R0 from SB was further used in the analysis. We modified standard Susceptible-Infectious-Recovered (SIR) models to SIR/Death (SIRD) model to accommodate deaths using R0 with the sequential Bayesian method for simulation in SIRD models.ResultsOn average, 2.8 individuals were infected by an index case. The mean serial interval was 3.9 days. The R0 estimated from different methods ranged from 1.43 to 1.85. The mean time to recovery was 14 ± 5.3 days. The daily epidemic growth rate of India was 0.16 [95% CI; 0.14, 0.17] with a doubling time of 4.30 days [95% CI; 3.96, 4.70]. From the SIRD model, it can be deduced that the peak of SARS-CoV-2 in India will be around mid-July to early August 2020 with around 12.5% of the population likely to be infected at the peak time.ConclusionThe pattern of spread of SARS-CoV-2 in India is suggestive of community transmission. There is a need to increase funds for infectious disease research and epidemiologic studies. All the current gains may be reversed if air travel and social mixing resume rapidly. For the time being, these must be resumed only in a phased manner and should be back to normal levels only after we are prepared to deal with the disease with efficient tools like vaccines or medicine.Key points.QuestionWhat are the estimates of infectious disease parameters of early phase of novel SARS-CoV-2 epidemic in India?FindingsIncidence pattern SARS-CoV-2 shows possible evidence of community transmission. However, the estimated Basic Reproductive Number (R0) is relatively lower than those observed in high burden regions (range 1.43-1.85). Our simulation using susceptible-infectious-recovered/death model shows that peak of SARS-CoV-2 in India is farther than currently projected and is likely to affect around 12.5% of population.MeaningThe lower estimated R0 is indicative of the effectiveness of early social distancing measures and lockdown. Premature relaxation of the current control measures may result in large numbers of cases in India.

Dataset Information

Molecular benchmarks of a SARS-CoV-2 epidemic.

Publications

Molecular benchmarks of a SARS-CoV-2 epidemic.

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