Table 1 Modes of testing during different phases of the COVID-19 pandemic

Zoonotic transmission

De novo genome assembly

NGS

Identify causative agent

12 Dec. 2019: first case of pneumonia reported in Wuhan, China

11 Jan. 2020: SARS-CoV-2 reference genome published

^1,2

Global spread

Genomic epidemiology

NGS

Identify chains of transmission

13 Jan. 2020: international transmission of SARS-CoV-2 to Thailand

2 Feb. 2020: first dispatch of RT–qPCR laboratory diagnostic kits

30 Mar. 2020: whole viral genome sequences uploaded to the GISAID database

⁴

Outbreak

Testing and contact tracing

RT–qPCR, NGS

Contain local outbreaks

21 Feb. 2020: entire town of Vo’, Italy, tested for SARS-CoV-2

30 Apr. 2020: contact tracing of outbreak in Itaewo, South Korea

^46,62

Community transmission

Population-scale testing

RT–qPCR, NGS, point-of-care testing, sample pooling, serology

Reduce viral reproduction number

27 Feb. 2020: SARS-CoV-2 detected in Netherlands sewage

1 May 2020: serology testing scheme (REACT) measures viral transmission in the UK

11 Jun. 2020: population testing in Iceland detects less than 50% of infected individuals

11 Oct. 2020: entire population of Qingdao, China, undergoes pooled testing

31 Oct. 2020: Slovakia tests all citizens using lateral flow tests

3 Nov. 2020: antigen testing of symptomatic residents in Liverpool, UK

^{55,63,65,66,75,95}

Regional or seasonal outbreak

Surveillance testing and environmental testing

RT–qPCR, NGS

Detect outbreaks and monitor emerging variants

23 Apr. 2020: SARS-CoV-2 detected in a domestic mink population

14 Dec. 2020: new SARS-CoV-2 strain (B.1.1.7) emerges in the UK

^82,122