Background
-
Exhaustively identify transmission chains;
-
Provide strong evidence that community transmission has been eliminated;
-
Identify and manage any reintroductions of disease when control measures are lifted;
-
Address constraints such as limited testing capacity; and
-
Identify broader response priorities that are critical to enhanced surveillance.
Methods
-
Group 1: Patients with pneumonia presenting to hospitals
-
Group 2: Patients presenting with acute respiratory symptoms (fever and cough and/or other acute respiratory illness symptoms such as runny nose, sore throat) for testing in the community (e.g. at primary care or specific respiratory/COVID clinics and testing facilities)
-
Group 3: Asymptomatic community members, including those who may be at higher risk of unprotected exposure (e.g. supermarket and delivery workers, transport workers [18], essential service staff).
-
The estimated number of cases in the community within the same transmission chain as the detected case, at the time the case is detected through the surveillance system.
-
The sensitivity and efficiency of testing these groups for a range of testing capacities and varying weekly cumulative incidence of COVID-19 and non-COVID-19 respiratory symptoms in the population under surveillance. Efficiency was assessed by considering the number of tests required per case detected, and the number of cases missed, under different scenarios.
-
The feasibility of surveillance and system requirements for increasing testing and follow-up.
-
Default transmission scenario, with limited or no containment measures and an assumed reproductive number of 2.2 when cases occur [22].
-
Low transmission scenario, with some containment measures in place and therefore a reproductive number of 1.2
-
Random sampling of presentations in each group.
-
Weekly cumulative incidence of the syndromic surveillance case definition ranging from 2 to 6% of the population under surveillance: this range was chosen based on several data sources, namely, in the absence of control measures 3% (peak), 2% (winter) and 1% (outside winter) fever and cough weekly cumulative incidence in line with Australian syndromic surveillance data (FluTracking) [27], and weekly acute respiratory symptoms (cold or flu-like symptoms as defined previously) incidence of 6% in winter (June) [28]. With social distancing measures, incidence of fever and cough has been shown to decrease by 40% [29], a finding also seen in Australian data [30].
-
Testing rates of 30% [28], 50% and 100% in all patients with symptoms.
-
Weekly cumulative incidence of COVID-19 ranging between 0.01 and 0.5%, based on reporting levels across high- and low-transmission settings with high test coverage [31].
Results
Gains from early detection
Efficiency of testing
Testing of those with respiratory symptoms in the community
Weekly point prevalence of non-COVID-19 ARI /fever and cough | Total non- COVID-19 ARI/ fever and cough presentations per week | Number of patients tested per week | 0.01% COVID-19 prevalence (100 cases in total) | 0.1% COVID-19 prevalence (1000 cases in total) | 0.5% COVID-19 prevalence (5000 cases in total) | |||
---|---|---|---|---|---|---|---|---|
% all (COVID-19 and non-COVID-19) ARI/fever and cough tested | Number of COVID-19 ARI/fever and cough cases in population not tested | % all (COVID-19 and non-COVID-19) ARI/fever and cough tested | Number of COVID-19 ARI/fever and cough cases in population not tested | % all (COVID-19 and non-COVID-19) ARI/fever and cough tested | Number of COVID-19 ARI/fever and cough cases in population not tested | |||
2% | 20,000 | 15,000 | 75% | 25 | 71% | 286 | 60% | 2000 |
4% | 40,000 | 15,000 | 37% | 63 | 37% | 634 | 33% | 3333 |
6% | 60,000 | 15,000 | 25% | 75 | 25% | 754 | 23% | 3846 |
2% | 20,000 | 20,000 | 100% | 0 | 95% | 48 | 80% | 1000 |
4% | 40,000 | 20,000 | 50% | 50 | 49% | 512 | 44% | 2778 |
6% | 60,000 | 20,000 | 33% | 67 | 33% | 672 | 31% | 3462 |
2% | 20,000 | 25,000 | 124% | 0 | 119% | 0 | 100% | 0 |
4% | 40,000 | 25,000 | 62% | 38 | 61% | 390 | 56% | 2222 |
6% | 60,000 | 25,000 | 42% | 58 | 41% | 590 | 38% | 3077 |
2% | 20,000 | 30,000 | 149% | 0 | 143% | 0 | 120% | 0 |
4% | 40,000 | 30,000 | 75% | 25 | 73% | 268 | 67% | 1667 |
6% | 60,000 | 30,000 | 50% | 50 | 49% | 508 | 46% | 2692 |
2% | 20,000 | 40,000 | 199% | 0 | 190% | 0 | 160% | 0 |
4% | 40,000 | 40,000 | 100% | 0 | 98% | 24 | 89% | 556 |
6% | 60,000 | 40,000 | 67% | 33 | 66% | 344 | 62% | 1923 |
2% | 20,000 | 60,000 | 299% | 0 | 286% | 0 | 240% | 0 |
4% | 40,000 | 60,000 | 150% | 0 | 146% | 0 | 133% | 0 |
6% | 60,000 | 60,000 | 100% | 0 | 98% | 16 | 92% | 385 |
2% | 20,000 | 70,000 | 348% | 0 | 333% | 0 | 280% | 0 |
4% | 40,000 | 70,000 | 175% | 0 | 171% | 0 | 156% | 0 |
6% | 60,000 | 70,000 | 116% | 0 | 115% | 0 | 108% | 0 |
Row | Prevalence of COVID-19 in those being tested | Number with disease per 10,000 | Sensitivity of pooled test | Exhaustive testing of 10,000 individuals using 1/4 pooling | Exhaustive testing of 10,000 individuals using 1/16 pooling | Percentage cases missed with no pooling (test sensitivity of 99.9%) | |||
---|---|---|---|---|---|---|---|---|---|
Col 1 | Col 2 | Col 3 | Col 4 | Same number of tests used and individuals tested as in column 1 | Same number of tests used and individuals tested as in column 3 | ||||
Total tests needed | Percentage of cases missed | Total tests needed | Percentage of cases missed | ||||||
1 | 0.05% | 5 | 99.90% | 2530 | 0% | 715 | 1% | 75% | 93% |
2 | 0.05% | 5 | 95.00% | 2529 | 5% | 711 | 5% | 75% | 93% |
3 | 0.05% | 5 | 90.00% | 2528 | 10% | 707 | 10% | 75% | 93% |
4 | 0.05% | 5 | 80.00% | 2526 | 20% | 699 | 20% | 75% | 93% |
5 | 0.05% | 5 | 70.00% | 2524 | 30% | 691 | 30% | 75% | 93% |
6 | 0.10% | 10 | 99.90% | 2550 | 0% | 793 | 1% | 75% | 92% |
7 | 0.10% | 10 | 95.00% | 2548 | 5% | 786 | 6% | 75% | 92% |
8 | 0.10% | 10 | 90.00% | 2546 | 10% | 778 | 11% | 75% | 92% |
9 | 0.10% | 10 | 80.00% | 2542 | 20% | 762 | 21% | 75% | 92% |
10 | 0.10% | 10 | 70.00% | 2538 | 30% | 746 | 31% | 75% | 93% |
11 | 1.00% | 100 | 99.90% | 2903 | 2% | 2117 | 7% | 71% | 79% |
12 | 1.00% | 100 | 95.00% | 2884 | 7% | 2045 | 12% | 71% | 80% |
13 | 1.00% | 100 | 90.00% | 2864 | 11% | 1970 | 17% | 71% | 80% |
14 | 1.00% | 100 | 80.00% | 2825 | 21% | 1822 | 26% | 72% | 82% |
15 | 1.00% | 100 | 70.00% | 2785 | 31% | 1673 | 35% | 72% | 83% |
16 | 3.00% | 300 | 99.90% | 3655 | 5% | 4485 | 20% | 63% | 55% |
17 | 3.00% | 300 | 95.00% | 3599 | 9% | 4296 | 24% | 64% | 57% |
18 | 3.00% | 300 | 90.00% | 3541 | 14% | 4103 | 28% | 65% | 59% |
19 | 3.00% | 300 | 80.00% | 3427 | 24% | 3717 | 36% | 66% | 63% |
20 | 3.00% | 300 | 70.00% | 3312 | 33% | 3331 | 44% | 67% | 67% |
Testing of asymptomatic groups with high-risk contacts
Prevalence of asymptomatic COVID-19 infection | Number of tests conducted | Upper 95% confidence limit of prevalence estimate for COVID-19 in asymptomatic population | Number of cases in screened population | Number of COVID-19 asymptomatic infections missed by screening | % of asymptomatic COVID-19 infections in populations that are missed during screening |
---|---|---|---|---|---|
0.79% | 10,000 | 0.98% | 7900 | 7821 | 99.0% |
0.48% | 10,000 | 0.64% | 4800 | 4752 | 99.0% |
0.24% | 10,000 | 0.36% | 2400 | 2376 | 99.0% |
0.16% | 10,000 | 0.26% | 1600 | 1584 | 99.0% |
0.10% | 10,000 | 0.18% | 1000 | 990 | 99.0% |
0.79% | 15,000 | 0.95% | 7900 | 7782 | 98.5% |
0.48% | 15,000 | 0.60% | 4800 | 4728 | 98.5% |
0.24% | 15,000 | 0.33% | 2400 | 2364 | 98.5% |
0.16% | 15,000 | 0.24% | 1600 | 1576 | 98.5% |
0.10% | 15,000 | 0.16% | 1000 | 985 | 98.5% |
0.79% | 20,000 | 0.92% | 7900 | 7742 | 98.0% |
0.48% | 20,000 | 0.59% | 4800 | 4704 | 98.0% |
0.24% | 20,000 | 0.32% | 2400 | 2352 | 98.0% |
0.16% | 20,000 | 0.23% | 1600 | 1568 | 98.0% |
0.10% | 20,000 | 0.15% | 1000 | 980 | 98.0% |
0.79% | 25,000 | 0.91% | 7900 | 7703 | 97.5% |
0.48% | 25,000 | 0.57% | 4800 | 4680 | 97.5% |
0.24% | 25,000 | 0.31% | 2400 | 2340 | 97.5% |
0.16% | 25,000 | 0.22% | 1600 | 1560 | 97.5% |
0.10% | 25,000 | 0.15% | 1000 | 975 | 97.5% |
Test performance and costs versus benefits of pooling
Prevalence | Specificity | PPV | False positive rate | Number with disease in population per 10,000 tested | Number of false positives per 10,000 tested |
---|---|---|---|---|---|
0.0005 | 0.999 | 33.32% | 0.1% | 5 | 10 |
0.0005 | 0.95 | 0.99% | 5.0% | 5 | 500 |
0.0005 | 0.9 | 0.50% | 10.0% | 5 | 1000 |
0.0005 | 0.8 | 0.25% | 20.0% | 5 | 2000 |
0.0005 | 0.7 | 0.17% | 30.0% | 5 | 3000 |
0.001 | 0.999 | 50.00% | 0.1% | 10 | 10 |
0.001 | 0.95 | 1.96% | 5.0% | 10 | 500 |
0.001 | 0.9 | 0.99% | 10.0% | 10 | 1000 |
0.001 | 0.8 | 0.50% | 20.0% | 10 | 2000 |
0.001 | 0.7 | 0.33% | 30.0% | 10 | 3000 |
0.01 | 0.999 | 90.98% | 0.1% | 100 | 10 |
0.01 | 0.95 | 16.79% | 5.0% | 100 | 500 |
0.01 | 0.9 | 9.17% | 10.0% | 100 | 1000 |
0.01 | 0.8 | 4.80% | 20.0% | 100 | 2000 |
0.01 | 0.7 | 3.25% | 30.0% | 100 | 3000 |
0.03 | 0.999 | 96.86% | 0.1% | 300 | 10 |
0.03 | 0.95 | 38.19% | 5.0% | 300 | 500 |
0.03 | 0.9 | 23.60% | 10.0% | 300 | 1000 |
0.03 | 0.8 | 13.38% | 20.0% | 300 | 2000 |
0.03 | 0.7 | 9.34% | 30.0% | 300 | 3000 |
Epidemiological investigation and contact tracing
Indicators of success: monitoring and evaluation of surveillance system performance
System coverage, uptake, and completeness
-
The proportion of those with respiratory symptoms who present for testing on the day of symptom onset.
-
The proportion of those with respiratory symptoms who isolate from time of symptom onset to receipt of a negative test result.
-
Newly reported cases that are tested on the day of symptom onset (target = 100%).
-
The proportion of newly detected cases that have been under quarantine from the time of the exposure event (target = 100%).
-
The proportion of age-specific hospitalised new cases and/or deaths relative to new community-acquired cases in the respective age group (target = 0%) [35].
-
The proportion of cases with complete follow-up of contacts (target = 100%).
-
The proportion of cases with unknown source of transmission (community transmission), with a target of 0%.
-
The proportion of newly reported cases that are importations (i.e. acquired disease outside the surveillance area) and/or known contacts of confirmed cases (target = 100%). This is the mirror of the first indicator (i.e. if all detected cases are in contact of cases or imported cases in travellers, then cases with unknown transmission will be 0%).
Progress towards elimination of community transmission
The indicator of successful elimination of community transmission, given the above system coverage, uptake and completeness indicators have all been met, is that the proportion of new cases that are classified as unknown source of infection (community transmission) is 0% over a 28-day period. This is the definition proposed by a range of experts in Australia and New Zealand, based on a period of 2 incubation periods free of disease following known community transmission, and has also been applied to decisions in Australia around the lifting of internal border controls [37].