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.
Highlights
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
We used two methods to assess viral concentration in tested individuals: the cycle threshold (CT) values to detect a PCR product from the qPCR test and the fraction of sequence reads that mapped to the SARS-CoV-2 reference from viral RNA sequencing
One of the difficult challenges in managing containment efforts in an epidemic such as COVID-19 is to figure out at specific points in time where the epidemic is in its trajectory, is gaining or waning? In the work presented here, we show how changes in the viral concentration and in the accumulation of viral mutations can be used to determine the phase of the epidemic instead of counting new cases
Summary
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. 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 first case of COVID19 was diagnosed in Iceland on February 28, the largest number of active infections was on April 4th and on May 5th the first phase of the epidemic was all but over (Fig. 1). The mutations carried by virions from the transmitting host are passed to the receiving host and can be used to track the spread of the virions[6,7,8,9,10,11] This means that there is substantial epidemiological information in the viral concentration and sequence diversity of SARS-CoV-2 infection. Having means to determine where an epidemic such as COVID-19 is in its trajectory is useful for the management of containment efforts
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