Spread of SARS-CoV-2 in the Icelandic Population

Abstract

BACKGROUNDDuring the current worldwide pandemic, coronavirus disease 2019 was first diagnosed in Iceland at the end of February. However, data are limited on how SARS-CoV-2, the virus that causes Covid-19, enters and spreads in a population. METHODSWe targeted testing to persons living in Iceland who were at high risk for infection (mainly those who were symptomatic, had recently traveled to high-risk countries, or had contact with infected persons). We also carried out population screening using two strategies: issuing an open invitation to 10,797 persons and sending random invitations to 2283 persons. We sequenced SARS-CoV-2 from 643 samples. RESULTSAs of April 4, a total of 1221 of 9199 persons (13.3%) who were recruited for targeted testing had positive results for infection with SARS-CoV-2. Of those tested in the general population, 87 (0.8%) in the open-invitation screening and 13 (0.6%) in the random-population screening tested positive for the virus. In total, 6% of the population was screened. Most persons in the targeted-testing group who received positive tests early in the study had recently traveled internationally, in contrast to those who tested positive later in the study. Children under 10 years of age were less likely to receive a positive result than were persons 10 years of age or older, with percentages of 6.7% and 13.7%, respectively, for targeted testing; in the population screening, no child under 10 years of age had a positive result, as compared with 0.8% of those 10 years of age or older. Fewer females than males received positive results both in targeted testing (11.0% vs. 16.7%) and in population screening (0.6% vs. 0.9%). The haplotypes of the sequenced SARS-CoV-2 viruses were diverse and changed over time. The percentage of infected participants that was determined through population screening remained stable for the 20-day duration of screening. CONCLUSIONSIn a population-based study in Iceland, children under 10 years of age and females had a lower incidence of SARS-CoV-2 infection than adolescents or adults and males. The proportion of infected persons identified through population screening did not change substantially during the screening period, which was consistent with a beneficial effect of containment efforts. (Funded by deCODE Genetics-Amgen.

Introductions and early spread of SARS-CoV-2 in France

“…All other sequences from Northern France fall in clade G (defined by a single non-synonymous mutation, D614G (A23403G) in the Spike, Figure 2), and this includes sequences captured during the steep increase of reported cases in many strongly affected regions (Figure 1). While a more thorough sampling will be needed to confirm this observation, it suggests that, unlike what is observed for many other European countries (Gudbjartsson, Helgason et al 2020, Zehender, Lai et al 2020), the French outbreak has been mainly seeded by one or several variants of this clade. This clade can be further classified into lineages, albeit supported again by only 1 to 3 substitutions (putatively named G1, G2, G3, G3a, G3b), and the diversity of the sequence from Northern France is spread out, with most regions represented in the different lineages.…”

“…In addition, pauci or asymptomatic cases are scarcely represented here. As the earliest representative of clade G (HF1463) had no history of travel or contact with returning travelers, we can infer that the virus was silently circulating in France in February, a scenario compatible with the large proportion of mild or asymptomatic diseases (Li, Pei et al 2020), and observations in other European countries (Gudbjartsson, Helgason et al 2020, Onder, Rezza et al 2020). While this is also compatible with the time to the most recent common ancestor estimate for clade G (Figure 2), the current sampling clearly prevents reliable inference for the timing of introduction in France.…”

A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing

“…By contrast, Abbott Labs (one example of many new diagnostic technologies developed in the past few months) has developed a diagnostic test capable of returning results in as little as 5 minutes for a positive result and 13 minutes for a negative result 57 . However, it is worth noting that the maximum number of diagnostic results an Abbot device could complete running 24 hours a day is roughly between 111 tests and 126 tests depending on the number of positive results 58,59 .…”

Revealing COVID-19 Transmission by SARS-CoV-2 Genome Sequencing and Agent Based Modelling

“…Our prospective SARS-CoV-2 genome sequencing has been instrumental in not only defining local transmission events and clusters, but enabling 68% of the cases for which no epidemiological links had been identified to be assigned to known epidemiological clusters, thereby allowing more efficient public health follow-up. The fine scale resolution provided by the genomic analyses presented in this study will become increasingly important for the containment of local outbreaks by enabling identification of secondary cases and providing context for cases of community transmission without clear epidemiological links 20 .…”

“…Our clinical specimens originated from a mixture of private and public pathology providers, thus our sample likely represented a general population with a spectrum of clinical disease. We relied on an average sequence depth greater than 200 to ensure quality of short read mapping and genome comparisons in line with previous reports 20,25 , although further optimisation of may be required for sustainable and cost-effective SARS-CoV-2 surveillance.…”