Epidemic curve and reproduction number of COVID-19 in Iran

Sahafizadeh, Ebrahim; Sartoli, Samaneh

doi:10.1093/jtm/taaa077

Cited by 25 publications

(17 citation statements)

References 6 publications

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“…Notably, this virus was sampled before the first report of COVID-19 in Iran on February 19th 23 , but our reconstruction suggests that considerable diversification, and hence transmission, already took place prior to this report.…”

Section: Resultsmentioning

confidence: 77%

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

et al. 2020

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Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.

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Section: Resultsmentioning

confidence: 77%

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

et al. 2020

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“…The first confirmed cases of COVID-19 in Iran were reported on February 19, 2020 in Qom [2]. Although the outbreak quickly moved to other provinces of Iran and the basic reproduction number was estimated to be more than four [3], Bushehr was the last province confirmed to be infected in the third week of the outbreak (on March 5, 2020).…”

Section: Introductionmentioning

confidence: 99%

High temperature has no impact on the reproduction number and new cases of COVID-19 in Bushehr, Iran

Sahafizadeh

Sartoli

2020

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Background: COVID-19 was first reported in Iran on February 19, 2020. Bushehr, one of the warmest provinces of Iran, was the last province confirmed to be infected on March 5, 2020. In the beginning of April, Bushehr was announced as a white, coronavirus-free, province. However, increasing the temperature in the next months did not affect the spread of coronavirus and the number of confirmed cases increased during the next months, so that Bushehr was announced as a Red province on June 13, 2020. Methods: This paper aims 1) to estimate the reproduction number of COVID-19 in Bushehr considering COVID-19 reported cases of Bushehr from April to June 12, 2020, using exponential function and SIR epidemic model, and 2) to investigate the impact of temperature on the reproduction number and the spread of coronavirus in Bushehr using the temperature data. Results: The reproduction number was estimated to be 2.564, 2.641 and 2.573 at the beginning of April, May and June 2020 respectively. Regarding the increase in the temperature from April to June, the results showed that not only was the spread of COVID-19 not reduced but it also increased. Conclusion: Data analysis on this study showed that high temperature has no impact on the reproduction number and does not slow down the spread of coronavirus in Bushehr.

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“…In this regard, Sahafizadeh et al estimated the reproduction number of 4.86 in the first week of the outbreak in Iran, while this number declined to <1 since April 7, 2020. 3 After the Nowruz holidays, nearly a month and a half since the first infection, on April 8, 2020, conditional reopening gradually began; little by little social activities resumed. In early times after the closures, the infection rate was still declining, possibly due to the sanitation behavior of a high percentage of people and active screening programs.…”

mentioning

confidence: 99%

“…In this regard, Sahafizadeh et al estimated the reproduction number of 4.86 in the first week of the outbreak in Iran, while this number declined to <1 since April 7, 2020. 3…”

mentioning

confidence: 99%