Dating First Cases of COVID-19

David L. Roberts, Jeremy S. Rossman, Ivan Jarić wrote . . . . . . . . .

Abstract

Questions persist as to the origin of the COVID-19 pandemic. Evidence is building that its origin as a zoonotic spillover occurred prior to the officially accepted timing of early December, 2019. Here we provide novel methods to date the origin of COVID-19 cases. We show that six countries had exceptionally early cases, unlikely to represent part of their main case series. The model suggests a likely timing of the first case of COVID-19 in China as November 17 (95% CI October 4). Origination dates are discussed for the first five countries outside China and each continent. Results infer that SARS-CoV-2 emerged in China in early October to mid-November, and by January, had spread globally. This suggests an earlier and more rapid timeline of spread. Our study provides new approaches for estimating dates of the arrival of infectious diseases based on small samples that can be applied to many epidemiological situations.

Author summary

While the COVID-19 pandemic continues, questions still persist as to its origins. Evidence is building that its origin as a zoonotic spillover occurred before the officially accepted timing of early December, 2019. We date the origin of COVID-19 cases from 203 countries and territories using a model from conservation science. We use a method that was originally developed to date the timing of extinction, and turn it to date the timing of origination using case dates rather than sighting events. Our results suggest that the virus emerged in China in early October to mid-November, 2019 (the most likely date being November 17), and by January, 2020, had spread globally. This suggests a much earlier and more rapid spread than is evident from confirmed cases. In addition, our study provides a new approach for estimating dates of the arrival of infectious diseases in new areas that can be applied to many different situations in the future.


Introduction

Uncertainty still persists around the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting COVID-19 disease. While an origin as a zoonotic spillover in the Huanan Seafood Market, Wuhan, sometime during early December, 2019, has been proposed [1], this has been called into question [2–4]. This uncertainty arises due to both the presence of earlier potential COVID-19 cases, and the fact that most phylogenetic analyses put the most recent ancestor at between mid-November and early December, 2019 [5].

Uncertainty around origination dates extends beyond the suggested zoonotic overspill in China to all countries where SARS-CoV-2 has spread. For example, in France the first case of COVID-19 was recorded as January 25, 2020, however a recent retrospective review of medical records from patients in intensive care unit (ICU) with both influenza-like illness (ILI) symptoms and pulmonary ground-glass opacity admitted between December 2, 2019, and January 16, 2020, (14 patients of 58) identified one patient as having COVID-19 who had been presented to the emergency ward on December 27 [6]. In the United States, SARS-CoV-2 RNA was detected through retrospective RT-PCR testing of a woman who had become ill on January 31, 2020, and died on the February 6, 2020, over 3 weeks before the first recognised case on February 26 [7].

Here we repurpose extinction models from conservation science to estimate the potential for earlier cases than has been reported of COVID-19 in 203 countries and territories. Further, we examine exceptionally early cases to determine the likelihood that these cases contributed to the country’s current infection or if they were isolated outbreaks that did not lead to the current lineage of cases. As such we specifically date the origin of cases that resulted in the virus taking hold in each country.

Within the discipline of conservation science, a number of models have been developed to infer or date extinction events based on a series of sightings of a species. Interest lies in determining whether a species still persists, having not been sighted for a period of time. If it is assumed the species is extinct, interest then lies in determining when extinction occurred. The application of these models has been proposed in a number of areas beyond extinction modelling to determine end points, particularly the Optimal Linear Estimation (OLE) method developed by Roberts and Solow [8], including geological stratigraphy [9], archaeology [10], phenological studies [11], and phylogenetics [12]. Based on a series of COVID-19 cases, interest lies in dating the original case. Such a knowledge is critical for our understanding of the spread of this disease.

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