SARS-CoV-2 Infection

Table 1. Table 1. Study Participants in Targeted Testing or Population Screening for SARS-CoV-2, According to Timing.

Figure 2. Figure 2. Distribution of Targeted Testing and Population Screening for SARS-CoV-2 and Percentages of Positive Results, According to Age and Sex. Shown is the distribution according to age and sex among all the participants in the study who were targeted for testing for the presence of SARS-CoV-2 (Panel A), among those who participated in the open invitation of the population screening (Panel B), and among those who participated in the random sample (Panel C). Also shown are the percentages of participants who tested positive stratified according to sex in the targeted-testing group (Panel D) and in the population-screening group (Panel E). In addition, the percentage of participants who tested positive in the population screening is shown according to sampling date in the open invitation (black) and the random sampling (red) (Panel F). The solid blue curve in Panel F indicates the logistic-regression line, and the dashed lines indicate the 95% confidence intervals (CI) of the logistic regression. The logistic-regression slope corresponds to a change of −2% (95% CI, −5 to 1) in the infection rate per day. The vertical bars indicate 95% confidence intervals for age groups (in Panels D and E) and for individual dates (in Panel F).

On April 4, 2020, among the 9199 persons who were targeted for testing, 1221 (13.3%) tested positive for SARS-CoV-2. Through population screening, positive results were reported for 100 of 13,080 participants (0.8%; 95% confidence interval [CI], 0.6 to 1.0); positive test results were reported for 87 of 10,797 persons (0.8%; 95% CI, 0.6 to 1.0) who accepted the open invitation for testing and 13 of 2283 persons (0.6%; 95% CI, 0.3 to 0.9) who were invited at random (Table 1 and Figure 2). The percentage of infected participants that was determined through population screening remained stable for the 20-day duration of screening (Figure 2F).

Sample collection for population screening began on March 13, and the first positive test results were communicated to the Icelandic health authorities on March 15 (Fig. S2). Because of this timing and rapid changes in the definition of high-risk areas by the Icelandic authorities, we report the targeted testing in two phases: early-phase testing (January 31 through March 15) and later-phase testing (March 16 through 31).

Initiation of Testing

In the early targeted testing, 65.0% of the participants who tested positive for SARS-CoV-2 had recently traveled outside Iceland. In the later phase, 15.5% had recently traveled outside the country (Table 1 and Fig. S3). Similarly, the proportion of participants in the population screening and who had recently traveled outside the country also fell rapidly during the study period. Overall, 23.0% of those with positive test results through population screening had recently traveled, in contrast to 8.7% of those who tested negative.

Of the participants who tested positive from the early targeted-testing phase and who had traveled, 86.1% had visited areas designated as being at high risk by the end of February (China and the Alps mountain regions in Austria, Italy, and Switzerland), whereas only 1 of the participants with a positive test identified through population screening had traveled to a high-risk area. The quarantining of persons arriving from these high-risk regions accounted for the very low proportion of participants in the population-screening group who had recently traveled. On the other hand, 12 of 87 participants (13.8%) with positive tests in the screening group had recently traveled to the United Kingdom, as compared with 1.8% of those who tested negative, which suggests relatively early spread of the virus in the U.K. population.

In the early phase of targeted testing, 40.1% of the participants who tested positive reported having had contact with a known infected person, as compared with 60.2% in the later phase of targeted testing. However, only 6.9% of the participants in the population-screening group reported having had contact with an infected person, probably because infected persons and their contacts were in isolation and therefore not eligible for the population screening.

Symptoms of Disease

Among the participants with positive results for SARS-CoV-2, symptoms of Covid-19 were reported by 93% of those in the overall targeted-testing group and by 57% of those in the overall population-screening group. However, 29% of participants who tested negative in the overall population-screening group also reported having symptoms. Reports of symptoms became less common among participants in the population screening during the study period (Fig. S4).

Age and Viral Susceptibility

The mean (±SD) age of persons who were targeted for testing overall (40.3±18.4 years) was similar to the mean age (39.7±18.0 years) in the overall population-screening group (Figure 2A through 2C). In the two data sets, those who tested positive were older and had a narrower age distribution than the full-participant data set (Table 1). Of the 564 children under the age of 10 years in the targeted testing group, 38 (6.7%) tested positive, in contrast to positive test results in 1183 of 8635 persons who were 10 years of age or older (13.7%). In analyses involving participants up to 20 years of age, we observed a gradual increase with older age in the percentage who tested positive (Fig. S5). In the population-screening group, the difference was even more marked: none of the 848 children under the age of 10 years tested positive, as compared with 100 of 12,232 persons (0.8%; 95% CI, 0.7 to 1.0) 10 years of age or older.

Sex and Viral Susceptibility

In the overall targeted-testing and population-screening groups, more females were tested than males (60.5% and 55.1%, respectively) (Table 1). However, in the targeted testing, the percentage of males who tested positive was greater than that of females (16.7% vs. 11.0%), for an odds ratio of 1.66 (95% CI, 1.47 to 1.87). In the population screening, the relative difference between the sexes was similar (0.9% vs. 0.6%), for an odds ratio of 1.55 (95% CI, 1.04 to 2.30) (Figure 2D and Fig. S6).

Viral Haplotypes

Figure 3. Figure 3. Distribution of Variants across the SARS-CoV-2 Genome, a Median-Joining Network of Haplotypes, and Cumulative Counts from Targeted Testing and Population Screening. Panel A shows the distribution of variants across the SARS-CoV-2 genome. The genes of SARS-CoV-2 are E (envelope small membrane protein), M (membrane protein), N (nucleoprotein), S (spike protein), and ORFs (open reading frames) 10, 1ab, 3a, 6, 7a, 7b, and 8. The different subsets that were considered included all variants, variants only observed in Iceland, and variants that were determined by the variant effect predictor to have a low effect (synonymous variants), a moderate effect (missense variants), or a high effect (loss-of-function variants). Panel B shows a median-joining network of 802 haplotypes from 1547 SARS-CoV-2 sequences (of which 513 are from Iceland). Each circle represents a different sequence type, in which the size of the circle reflects the number of carrier hosts, and the lines between circles represent one or more mutations that differentiate the sequence types. Circles are colored according to the regions where samples were obtained. The principal clades are outlined and labeled, with the number of sequences from Icelanders shown in parentheses. Haplotypes from clade A are not outlined. Panel C shows the cumulative counts of SARS-CoV-2 haplotypes from targeted testing and population screening as a function of sampling date. A2a* refers to all A2a haplotypes except A2a1, A2a2, and A2a3. The dashed vertical line indicates the start of the population screening.

Table 2. Table 2. Distribution of SARS-CoV-2 Haplotypes, According to Timing of Diagnosis and Internationally Imported or Local Transmission.

We sequenced SARS-CoV-2 RNA extracted from 643 samples; of these samples, we obtained coverage of more than 90% of the SARS-CoV-2 genome from 581 samples and more than 67% from 605 samples. We called 409 sequence variants, 291 of which were not found in the GISAID database (Figure 3A). (GISAID accession numbers are provided in the Supplementary Appendix.) We used clade-informative mutations (Table S3) to assign haplotypes to persons: 518 from the targeted-testing group and 59 from the population-screening group (Table 2, Figure 3C, and Fig. S7).

Geographic Viral Origin

To shed further light on the geographic origin of the SARS-CoV-2 infections in residents of Iceland, we generated a median-joining network of 1547 complete viral sequences (513 from complete viral genomes from Icelanders and 1034 from other populations around the world) (Figure 3B). Several viral lineages have emerged during the 3 to 4 months since the original outbreak in China, with an average of five mutations separating the lineages from the founding haplotype from Wuhan (the central haplotype of clade A). Although the sequencing efforts vary considerably among populations, it is clear that the geographical distribution of clades is highly structured. Thus, A and B haplotypes are common in East Asia, whereas the B1a haplotype appears to be at the center of the outbreak on the West Coast of the United States, and A2a and its descendants are almost exclusively found in European populations.

Composition of Haplotypes

The haplotypes of SARS-CoV-2 infections observed in Iceland cluster into several diverse clades (Figure 3B). To estimate the number of introductions of the SARS-CoV-2 virus to Iceland, we searched for infected persons who had traveled internationally or had an unknown source of infection. This led us to 363 persons for whom viral genomes had been sequenced. These genomes clustered into 42 distinct clades, which provided a lower boundary on the number of individual introductions.

Of the 157 sequenced virions obtained during the early targeted testing, 143 were in the A2 clade (Table 2 and Fig. S7). By the time we initiated the population screening, all travelers who had returned from ski resorts in the Alps had been requested to self-quarantine and were not eligible for participation, which resulted in a substantially different composition of haplotypes. For example, the A2a2 haplotype, which was most commonly seen in travelers coming from Austria in the early phase of targeted testing, was much less frequent in travelers in the population screening. The A1a haplotype was more common in the general population than in those who received targeted testing, with a total of 23 of 59 haplotypes among participants in the population-screening group, as compared with only 8 of 157 haplotypes in the early-targeted testing.

The composition of haplotypes changed substantially from early targeted testing to later targeted testing. The A2a1 and A2a2 haplotypes, which had collectively made up 103 of 157 haplotypes (65.6%) in the early-targeted testing, were reduced to 115 of 361 haplotypes (31.9%) in the later-targeted testing, mostly because of the increased frequency of the A1a and other A2a-derived haplotypes. This change probably meant that population screening identified clusters of infected persons who seeded infection from areas that had not been designated as high risk, such as the United Kingdom. The relatively high prevalence of A1a and A2a clades in the later-targeted testing group was unsurprising: the targeted testing had been extended to include those who had traveled to additional high-risk areas, and population screening had identified cases that could be used to inform tracking efforts. The A2a3a and A2a2a haplotypes were the two most common haplotypes in Iceland; of the 577 persons who provided samples that were sequenced, the A2a3a haplotype was found in 78 (13.5%) and the A2a2a haplotype was found in 45 (7.8%).

Haplotype Analysis of Contact-Tracing Networks

Figure 4. Figure 4. Overall Clusters in the Contact-Tracing Network, a Network Cluster Including a Novel Domestic Mutation, and Source of Exposure. Panel A shows an overview of all clusters in the contact-tracing network with SARS-CoV-2 haplotypes. Panel B shows a contact-tracing network for a cluster that included a novel domestic mutation (24054C→T). Person T25 carried both the A2a1a strain and the A2a1a+25958 strain. Contact-tracing networks show infected persons as nodes and a connection between two nodes where a transmission of infection or contact has been established. In cases in which the direction of transmission was ambiguous, a bidirectional arrow is shown. Persons who traveled internationally are indicated in boxes representing their travel destination. The colors of nodes represent the haplotype of the viral strain, either as a clade or a clade plus one or more mutations. Additional mutations are represented by a position number beside each node. The labels on the nodes are identifiers given in increasing order of identification (e.g., T6 is the sixth case reported). Red X marks indicate recorded contacts that are inconsistent with the viral haplotypes carried by each person. Panel C shows the type of exposure from contact-tracing data according to the date of isolation and percentage (top graph) and total number (bottom graph). The type of exposure is classified for each positive case into the following categories: family, unknown, social, work (including schools), tourism (reported working domestically in tourism), and travel (international travel).

Haplotype analysis that was based on SARS-CoV-2 sequences overlaid on contact-tracing networks16 showed concordance between the contacts identified by the tracking team and those based on viral sequences (Figure 4A). Of the 369 pairs of persons found through contact tracing, 295 were consistent with the sequence data (i.e., their haplotypes differed by strictly less than 3 mutations).

Figure 4B shows one of the most complex contact-tracing networks, in which clusters of persons returning from Italy or Austria transmitted the virus to persons in Iceland. The figure shows a network of 14 persons who were infected in Iceland. Haplotype analysis showed that these persons were infected by viruses with the A2a1 haplotype, more commonly imported from northern Italy than from Austria (Table 2). This cluster also contained persons with a mutation that was specific to Iceland. The cluster can be traced to a person who had both mutated and wild-type haplotypes; those whom this person infected had only the mutated haplotype. We searched for persons carrying these mutations who were not associated with this cluster and found two who had probably been infected by someone in the cluster through an unknown contact.

Contact Tracing and Exposure Type

We categorized exposure into six categories: family, social, tourism (working in the travel industry in Iceland), work (including schools), travel (international), and unknown and observed a shift in the composition of exposures from international travel and social exposure to familial exposure over time (Figure 4C).