key: cord-0856871-dp9loyeu
authors: Mercer, Tim R.; Salit, Marc
title: Testing at scale during the COVID-19 pandemic
date: 2021-05-04
journal: Nat Rev Genet
DOI: 10.1038/s41576-021-00360-w
sha: 4d603c1ef9f0bcc58a50e66cfae11acf67aff67a
doc_id: 856871
cord_uid: dp9loyeu

Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which hundreds of millions of individuals have been tested to date. The unprecedented scale of testing has driven innovation in the strategies, technologies and concepts that govern testing in public health. This Review describes the changing role of testing during the COVID-19 pandemic, including the use of genomic surveillance to track SARS-CoV-2 transmission around the world, the use of contact tracing to contain disease outbreaks and testing for the presence of the virus circulating in the environment. Despite these efforts, widespread community transmission has become entrenched in many countries and has required the testing of populations to identify and isolate infected individuals, many of whom are asymptomatic. The diagnostic and epidemiological principles that underpin such population-scale testing are also considered, as are the high-throughput and point-of-care technologies that make testing feasible on a massive scale.

On 7 January 2020, a new coronavirus was detected by metatranscriptomic sequencing of lung fluid from a patient with pneumonia-like symptoms in Wuhan, China 1,2 . On 10 January 2020, the assembled reference genome of this new coronavirus, termed severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), was published, and within 2 weeks the first diagnostic tests to detect the virus were issued 3, 4 . To date, hundreds of millions of individuals have been tested for the presence of SARS-CoV-2 (ref. 5 ), leading to widespread public awareness of and debate regarding diagnostic concepts and technologies.

Testing for the presence of SARS-CoV-2 is typically performed for one of two reasons. First, a symptomatic patient might be tested to inform their clinical treatment. Such diagnostic testing is focused on therapeutic care and is typically performed in a well-controlled clinical setting, and the test results are usually interpreted alongside the patient's history and symptoms. Second, testing might be performed to identify infectious individuals in a population, who are then isolated to prevent the onward infection of others. Such screening is focused on public health outcomes and aims to reduce viral transmission through a population. Individuals who are not symptomatic might be tested, and testing might need to be performed on a massive scale. These two different uses of testing have different requirements and priorities, and a test that is useful in clinical diagnosis can be ill-suited for population-scale screening.

The observation that countries with high testing rates were able to effectively control SARS-CoV-2 transmission during the initial stages of the pandemic 6 supported the proposal that screening could help to limit viral transmission. Accordingly, widespread testing rapidly gained traction as an intervention that might avoid both the immediate economic costs of lockdown and the societal costs of social distancing measures. Accordingly, many countries implemented population-scale testing to monitor and reduce viral transmission. However, despite the promise of this approach, obtaining reliable test results on such a massive scale is difficult and unprecedented, and has been achieved with differing outcomes and success 7 . Nonetheless, the COVID-19 pandemic has transformed the role of population-scale screening. With ongoing investment and innovation, large-scale testing is likely to become a common feature of public health.

This Review focuses on the use of testing as a tool to screen populations for individuals infected with SARS-CoV-2. We discuss the changing role of such testing in the COVID-19 pandemic: the initial use of genomic epidemiology to monitor the spread of viral strains around the world; the containment of disease outbreaks using contact tracing; and the massive screening programmes that aim to suppress community transmission (Table 1; fig. 1 ). We also consider the testing strategies and technologies used to address the challenges of population-scale testing. We finally discuss findings from large-scale testing programmes that have measured the exposure of entire populations Lockdown The closure of non-essential businesses and activities, along with requiring individuals to remain within their homes, in an effort to reduce population mobility and contact and thereby reduce viral transmission.

Testing at scale during the COVID-19 pandemic Genomic epidemiology of SARS-CoV-2 During replication and transmission, viral genomes accumulate mutations that can be used to define distinct variants. Whole-genome sequencing can identify these mutations and trace the transmission of variants between individuals, populations and countries around the world. This genomic epidemiology approach was used to monitor past outbreaks of Ebola virus and Zika virus infection [8] [9] [10] and has been widely used to reconstruct the spread of SARS-CoV-2. One of these SARS-CoV-2 strains, termed 'B.1' , was initially transmitted to Italy, where it caused an outbreak in Lombardy before further circulating across Europe and onwards to the USA, where it seeded an outbreak in New York City 11 . This chain of transmission around the globe was reconstructed by the tracking of four mutations in the SARS-CoV-2 B.1 strain. The SARS-CoV-2 viral genome quickly diversified into different strains following the initial zoonotic transmission of the ancestral virus. During its initial spread, thousands of viral genomes were rapidly sequenced by research laboratories worldwide and shared in open-access databases such as the EpiCoV database from GISAID 12 and the Our World in Data COVID-19 dataset. These sequences, along with metadata (including location, date and method of sampling) and tools such as Nextstrain 13 , could then be used to track the spread of SARS-CoV-2 strains 14 .

Genomic epidemiology has also been widely used to reconstruct the routes by which SARS-CoV-2 is introduced into and spreads within countries [15] [16] [17] [18] [19] . These studies show that SARS-CoV-2 is typically introduced into a country several times 20 . Subsequent transmission is stochastic, wherein a small number of infected individuals are responsible for the majority of secondary infections in 'superspreader' events 21, 22 . Genomic epidemiology studies also reveal the routes of transmission into and across a country, and their results have informed public health containment measures such as regional lockdowns, quarantines and travel restrictions 23 .

The maintenance of a sufficient distance between individuals to prevent airborne transmission of a virus. Superspreader a single individual who infects many other individuals. 82, 122 Although this table distinguishes between pandemic phases for clarity, in practice the different phases, testing modes and their aims often overlap and might also differ between different countries and times. NGS, next-generation sequencing; REACT, real-time assessment of community transmission; RT-qPCR, reverse transcription-quantitative polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

www.nature.com/nrg 0123456789();:

Despite the usefulness of genomic epidemiology, the data should be interpreted with caution. Although infection with different strains can rule out a chain of transmission between two individuals, infections by the same strain do not necessarily prove a direct link in the chain of transmission 24 Fig. 1 | changes in modes of testing across a generalized cOViD-19 infectious course. a | Shedding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome (yellow shading) typically increases rapidly following infection and peaks at the presentation of symptoms (although many patients can be asymptomatic) before gradually declining. Levels of viral proteins (red shading) also rapidly increase, albeit within a narrower window. In response to infection, the body produces IgM (green shading) and IgG (blue shading) antibodies, which persist for weeks to months. b | The SARS-CoV-2 RNA genome can be detected by molecular assays, such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR), before the development of symptoms. Serological tests can detect reactive IgG and IgM, which indicate past infection with SARS-CoV-2. c | Assay sensitivity is dependent on both technical performance aspects and viral load. A test might not detect viral RNA even when an individual is infectious (false negative, red shaded area) or, alternatively, might detect persistent viral RNA after an individual is no longer infectious (false positive), which demonstrates that test positivity correlates poorly with infectivity. Owing to the rapid increase in viral shedding, only a narrow window exists wherein a more sensitive assay (test B) will outperform a less sensitive assay (test A). Note that this figure illustrates a generalized COVID-19 infectious course, and in practice the relative duration of detectability and analyte abundance differ considerably between individuals. NAAT, nucleic acid antigen testing; NGS, next-generation sequencing. Nature reviews | Genetics 0123456789();: other pathogenic viruses, the SARS-CoV-2 genome accumulates mutations slowly and the amount of viral sampling and sequencing has differed widely between countries. Low strain diversity, rapid disease spread and non-representative sampling can confound the results of genomic epidemiology studies, and our understanding of SARS-CoV-2 spread and evolution was especially unclear during the early stages of the COVID-19 pandemic 11, 25 .

The RNA genome of SARS-CoV-2 can be directly detected by nucleic acid assays such as reverse transcriptionquantitative polymerase chain reaction (RT-qPCR) tests, whereas the presence of viral proteins can be detected by an antigen test (box 1). The detection of these analytes requires that a sample contains sufficient viral genome copies or levels of viral proteins that exceed the limit of detection for a given assay ( fig. 2 ). However, the abundance of these viral analytes varies dramatically between different anatomical locations and different stages of infection 26 . Thus, the ability to detect SARS-CoV-2 is ultimately framed by the biology of the virus. Indeed, the sensitivity of tests for detecting SARS-CoV-2 can be as dependent on the time and site sampled as it is on the technical performance of the assay 27 .

The viral load of SARS-CoV-2 changes dramatically during the course of infection 28, 29 . Viral genome abundance rapidly increases following infection, and patients can become infectious and begin shedding viral particles 3-5 days before the development of COVID-19 symptoms 30 . During these early stages of infection, a nasopharyngeal sample (which requires a long swab to sample the back of the nasal cavity) generally provides the highest reported viral RNA abundance 31, 32 . However, other, less invasive options, including oral swabs, nasal swabs or saliva tests, also have detectable levels of viral analytes and can reduce exposure of the health-care workers performing the sampling 33 .

Viral load typically declines gradually following the onset of symptoms. During the later stages of infection, samples from the lower respiratory tract (such as sputum, bronchoalveolar lavage fluid or tracheal secretions) can yield high viral titres. Even after the cessation of all symptoms, persistent viral RNA can be detected for several weeks. However, efforts to isolate replication-competent virus from this persistent RNA have been unsuccessful, and these recovered individuals are generally considered to be non-infectious 34 .

The response of an individual to the test result is a key factor in the effectiveness of testing programmes, and the interpretation of test results should consider both the probability of infection and any pre-existing risk factors 35 (box 2; fig. 2 ). Whereas a positive test result indicates the presence of infection and the need for isolation to prevent further transmission of the virus, a negative test result does not rule out the possibility of it being a false-negative finding 36 . If individuals are falsely reassured by receiving a negative test result, they might ignore other protection strategies and increase the risk of onward transmission of the virus 37 .

Following viral infection, the body mounts a humoral immune response that includes the production of antibodies that target SARS-CoV-2 antigens [38] [39] [40] . These antibodies directly bind to the spike protein and thereby neutralize viral action, as well as recruiting further immune responses to clear the virus. The levels

Reverse transcription-quantitative polymerase chain reaction a method of severe acute respiratory syndrome coronavirus 2 (sars-Cov-2) genome detection based on measuring the amplification of RdRP, E, N or S gene fragments using fluorescent probes 135 . although reverse transcription-quantitative polymerase chain reaction (rt-qPCr) can provide a quantitative measure of viral abundance, it is most commonly used to detect viral presence above a quantitative cycle threshold chosen to minimize false positives. rt-qPCr is the current standard for population-scale testing 135 . although this technique is theoretically capable of detecting very low quantities of the sars-Cov-2 genome, its sensitivity in real-world clinical practice is only 50-70% 26, 136, 137 . the high specificity of rt-qPCr (~99%) can be further enhanced by targeting multiple loci. as rt-qPCr is typically conducted in large, centralized laboratories, efficient sample collection is critical to minimize reporting delays. rt-qPCr benefits from standardized operating procedures and a well-established supply chain.

Next-generation sequencing (NGs) was instrumental in the identification and assembly of the sars-Cov-2 genome 1,2 and can also be used for high-throughput testing to identify mutations in the viral genome. as only a small amount of sequencing is required to detect amplified viral complementary DNa (cDNa), thousands of patient samples can be tested in a single sequencing run, which facilitates very large scale testing. each sample is labelled with a unique molecular barcode that can be identified in the output library. such barcoding can occur during initial reverse transcription, cDNa amplification or library preparation. the samples are then pooled and undergo multiplexed sequencing, an advance specific to large-scale testing 138, 139 . emerging findings indicate that NGs can distinguish between different sars-Cov-2 variant strains and can also detect other respiratory viruses (such as influenza viruses) and synthetic rNa internal controls 140 . isothermal nucleic acid amplification assays these assays use various nucleic acid amplification reactions that are conducted at a constant temperature. they generate large amounts of cDNa that can be detected by colorimetric or turbidimetric approaches. examples include loop-mediated isothermal amplification 141, 142 , nicking endonuclease amplification reaction, and recombinase polymerase amplification 143 . these approaches provide simple, rapid and cheap diagnostic tests that can be performed without specialized equipment. a preliminary report states that when reverse transcriptase is included in the reagent mix, this process can be done in a single step 144 ). However, the formation of non-specific products might require additional sequence-specific detection using NGs or CrisPr 145 .

antigen tests are based on antibodies that can bind to the sars-Cov-2 spike protein or nucleocapsid protein. Bound antibodies are detected by use of a simple immunoassay, such as a lateral flow assay, which indicates the presence of viral protein 146 . these cost-effective tests can provide rapid results within 30 min at the point of care, and benefit from cheap and scalable manufacture. Despite these advantages, antigen tests tend to have lower specificity and sensitivity than corresponding nucleic acid-based assays 147, 148 and are therefore usable across a narrower window of the sars-Cov-2 infectious course. serological tests these assays detect the presence of anti-sars-Cov-2 igM and/or igG antibodies produced by the humoral immune response 38 . serological assays can also indicate the extent and duration of immune protection offered by these antibodies, which is critical to understanding the success of vaccination programmes. the sensitivity of serological assays depends on both technical factors and antibody titres, which vary according to the duration and severity of infection, age and sex 149, 150 . serological tests for sars-Cov-2 generally have reported specificities greater than 85%, although false positives can result from cross-reactivity with other coronaviruses 151 . serological tests are particularly useful in epidemiological studies to determine the exposure of a population to sars-Cov-2 (refs [64] [65] [66] of reactive (that is, anti-SARS-CoV-2) IgM antibodies typically increase within a few days of the viral infection and these antibodies persist for weeks, whereas reactive IgG antibodies appear in the middle and later stages of the infection and can remain circulating in the blood for several months 41, 42 . Serological tests can detect reactive antibodies produced in response to viral exposure. As these tests do not directly detect the virus but instead detect the body's response to the virus, they can indicate whether an individual was previously infected with SARS-CoV-2 (ref. 43 ). Serological tests can also indicate the strength and direction of an individual's immune response. However, a positive serological test result does not necessarily indicate a protective immune response, and other anti-SARS-CoV-2 immunoglobulins (for example, IgA and IgE) are often not detected by available serological tests.

The introduction and initial outbreak of SARS-CoV-2 within a country can be contained by testing and contact tracing, wherein all infected individuals and their secondary contacts are identified and isolated. If these secondary exposed individuals are quarantined before they can infect others, further onward transmission of the virus is prevented 44 .

Large-scale contact tracing programmes have been instrumental in halting SARS-CoV-2 transmission in countries such as Vietnam, Taiwan and Japan 6, 45 . Within days of detecting its first case on 20 January 2020, test sensitivity, specificity and disease prevalence influence the interpretation of test results. a,b | In a population with a low prevalence (5% here) of COVID-19 cases, even a highly sensitive and specific test (part a) returns many false-positive results. c,d | By contrast, a high infection prevalence (25% here) increases the likelihood that a positive result is true, despite the test performance remaining unchanged. The positive predictive value (PPV) of a test describes the probability that an individual who tests positive is actually infected 35 , and thus depends on both the specificity of the test and the prevalence of infection. At low prevalence values, the proportion of false-positive results is increased and the PPV is reduced. Even a highly specific test returns mostly false-positive results (and therefore has a low PPV) when the prevalence of infection is low. Adapted from ref. 134 , Springer Nature Limited.

South Korea quickly scaled up the nation's existing network of contact tracers, who had been used in the SARS-CoV outbreak in 2003. These contact tracers used patient interviews as well as medical, mobile phone and credit card transaction records to identify thousands of people linked to an outbreak in Itaewo, a popular nightclub district in Seoul. Subsequent testing identified and isolated hundreds of infected individuals, many of whom were separated by multiple cycles of transmission from the original Itaewo outbreak 46 .

Although simple in concept, contract tracing is often difficult to put into practice because the effectiveness of this approach depends on identifying contacts before they can infect others 47, 48 . Given that individuals can become infectious within days of initial exposure to SARS-CoV-2 and before they develop symptoms, only a narrow window is available within which to identify individuals before they infect others. Therefore, rapid testing is of primary importance for effective contact tracing, and contacted individuals are recommended to pre-emptively isolate themselves while awaiting their test results.

Contact tracing is also laborious and time-consuming, and becomes increasingly difficult in the context of ongoing viral transmission. As more cases are diagnosed, the number of secondary contacts scales non-linearly to increasingly large numbers of people, who must in turn be identified, tested and isolated 49 . This increasing case burden results in delays that further decrease the effectiveness of contact tracing. The use of digital contact tracing using mobile apps and other technologies can help to automate contact tracing approaches and ease this burden, but requires widespread adoption and adherence 50, 51 . Once the case burden exceeds a country's contact tracing capacity, most individuals with secondary cases are contacted too late and tracing has little further effect on viral transmission.

Reducing community transmission. Despite efforts to contain SARS-CoV-2, community transmission has become entrenched in many countries, which has required a shift from contact tracing to the populationscale testing required to detect the large fraction of presymptomatic, mildly symptomatic and asymptomatic individuals who can unwittingly transmit the virus 52,53 . On 31 October 2020, Slovakia became the first country to test its entire population in an attempt to reduce viral transmission [54] [55] [56] . This massive undertaking required thousands of health-care workers to test almost all citizens using a rapid antigen test, following which individuals who tested positive and their close contacts were advised to isolate themselves. Although the effects of this massive testing effort are difficult to distinguish from those of concurrent interventions, a marked reduction in SARS-CoV-2 infections was observed following the effort 57 . However, this reduction was limited to regions with high viral prevalence, and testing seemingly had little effect in regions with a lower viral prevalence 58 .

The success of population-scale testing can be precisely measured as a reduction in the reproductive number, which indicates the extent of viral transmission through a population (box 2). However, the amount of testing that must be performed to markedly reduce the reproductive number is difficult to evaluate. The fraction of tests that return a positive result can provide some indication as to the adequacy of the testing programme: a low test positivity rate indicates both low viral prevalence and sufficient surveillance capacity, whereas a high test positivity rate suggests that testing is inadequate and that many infected individuals are going undetected 59 (box 2).

For many countries, adequate surveillance mandates a massive amount of testing, requiring huge resources and a collaborative effort across a laboratory enterprise that includes commercial, clinical, government and research organizations 57 . Large coordinated systems are required for safe sample acquisition, transport and custody. In addition, test results must be returned 152 . R depends on the mode, duration and potency of viral infection, as well as the degree of contact between individuals, which is affected by population density, location, mobility and interventions such as social restrictions [153] [154] [155] . R is compounded with each infectious cycle, and models the compounded viral spread or collapse that is characteristic of pandemic waves over time. R > 1 indicates growing viral transmission, whereas R < 1 indicates decreasing viral transmission. For example, in the italian municipality of vo', the sars-Cov-2 R value fell from 2.49 before social lockdown to 0.41 afterwards 62 . Despite its advantages, the R value often does not capture the heterogeneous dynamics of viral transmission, wherein a small number of individuals cause the majority of secondary infections by 'superspreader' events 21 . this high stochasticity under low prevalence is characteristic of sars-Cov-2 transmission, and is distinct from the lower stochasticity observed for other pathogens, such as influenza viruses. test positivity rate the test positivity rate is the proportion of tests that return a positive result, which reflects the level of testing relative to the viral prevalence in a population. a low test positivity rate indicates low viral prevalence and adequate surveillance capacity of the testing scheme; a high test positivity rate indicates high viral prevalence or that testing is biased to symptomatic or selected individuals (positive results represent only a small fraction of the true number of infections). a rising test positivity rate suggests that viral transmission is faster than that seen in confirmed cases. test positivity can be used with other metrics (such as R) to inform intervention strategies. For example, the wHO recommends that test positivity remains less than 5% for at least 2 weeks before public health and social measures are changed 156 . sensitivity sensitivity is the fraction of individuals who are correctly identified as having the condition by a given test. a highly sensitive test returns few false-negative results because few infected individuals escape detection. the sensitivity of a test is often determined under controlled conditions and is solely dependent on test performance. in practice, variables such as sampling and processing errors decrease real-world sensitivity 157 . For example, ineffective swabbing has been cited as a major reason for decreased sensitivity, and some schemes require dual testing of nasopharyngeal and sputum or throat samples to improve performance. specificity the specificity of a test refers to its ability to correctly identify a non-infected individual as not being infected 35 . Highly specific tests return few false-positive results because infection is erroneously diagnosed in few uninfected individuals. tests with low specificity have the disadvantage that many uninfected individuals are erroneously identified as being infected and could potentially have to undergo unnecessary quarantine or receive unnecessary treatment. Low specificity is particularly problematic for large-scale testing schemes, as it can result in overwhelming absolute numbers of false positives.

The fraction of individuals within a population who are affected. This value can indicate the a priori probability that a randomly selected individual from a given population is infected, and is a key determinant of the utility of a screening test.

www.nature.com/nrg 0123456789();: sufficiently rapidly to enable individuals who test positive to isolate themselves before they infect others. Indeed, the speed and frequency of testing is considered as important as test sensitivity in effectively reducing viral transmission 58 . Such massive testing efforts can quickly strain supply chains and infrastructure, and many countries have faced shortages in key reagents 60 that left them unable to implement effective, widespread testing. As a result, testing of health-care workers and symptomatic individuals is often prioritized over testing of asymptomatic individuals. Competition for reagents has often reflected global health inequities, and wide disparities in testing rates are observed between countries 61 . However, containing SARS-CoV-2 transmission is a global challenge, and the global responsibility for sustainable testing must be recognized.

Population-scale testing also provides critical viral prevalence data that have informed our response to the pandemic. On 21 February 2020, the town of Vo' in Italy reported the first death from COVID-19 and quickly entered a complete lockdown for 2 weeks. Researchers were able to test almost every town resident and to quantify the effect of lockdown on reducing the viral reproduction number (box 2), thereby providing early validation of the effectiveness of such interventions used to combat the pandemic 62 .

Population-scale testing enables the rate of viral spread through a population to be measured, aids in the identification of regional hotspots and high-risk subpopulations, and facilitates the calculation of incidence and mortality rates. However, as with any measurement process, such testing is subject to the errors and biases inherent in the assay and sampling processes. Low-sensitivity tests can underestimate viral prevalence, whereas low-specificity tests can overestimate prevalence. For example, an early study conducted in California, USA, was criticized for providing an inflated measure of SARS-CoV-2 prevalence owing to the use of low-specificity serological tests 63 .

Serological assays that detect reactive antibodies can indicate whether an individual was previously infected with SARS-CoV-2. These assays, which are sufficiently cheap to be widely deployed, have been used in some of the largest studies of SARS-CoV-2 spread and immunization 64, 65 . Repeated rounds of serological sampling across large, representative populations in the UK conducted as part of the real-time assessment of community transmission (REACT) study provided ongoing estimates of viral exposure during successive pandemic waves 66 . The REACT investigators measured viral spread through subpopulations in the UK and their data were used to determine the need for regional lockdowns.

Iceland has proved ideal for the study of COVID-19 because more than half of its citizens have been tested for SARS-CoV-2 antibodies, and the clinical outcomes of individuals with a positive test result have been closely monitored 67 . However, despite extensive testing, almost half of infected people in Iceland were not detected, thereby illustrating the limitations of and gaps in even the most widespread population-scale testing schemes 64 . A similar seroprevalence study in Spain found that population-scale testing detected just 9% of infected people during the first pandemic wave, and almost one million infected people were estimated to have gone undetected 65 .

Population-scale testing has relied heavily on RT-qPCR, which is performed in large, high-throughput, centralized laboratories with automated equipment by skilled personnel (box 1). These centralized laboratories achieve sensitive and reliable results owing to validated and regu lated oversight of testing procedures. However, samples need to be transported to the testing site, which can often extend the testing turnaround time to several days.

The pooling of several samples enables multiple individuals to be simultaneously tested. Chinese authorities tested more than seven million people in the city of Qingdao in 3 days using a pooling approach, wherein ten samples were combined and tested with a single reaction 68 . If the pool returns a negative test result, then all constituent individual samples are also considered to have a negative result. Only if the pooled test returns a positive result are the constituent samples tested individually to ultimately identify the positive sample or samples. A further innovation divides the samples among overlapping pools, such that any single sample is present in a unique combination of pools 69, 70 . If the unique combination of pools returns a positive result, the individual sample can be identified without requiring an additional round of retesting 71 .

Pooling of patient samples, viral transport media or extracted RNA enables more individuals to be tested with use of fewer reagents. However, the advantages of pooling are limited in the context of a high test positivity rate. If positive samples are common, the majority of pools will return positive results, and most samples still need to be tested individually. In practice, this shortcoming can be mitigated by non-random pooling of samples from shared households or groups, which increases the likelihood that positive samples will be clustered within a small number of pools 72 . Nevertheless, the additional rounds of testing mandated by pooling can incur reporting delays, and the dilution of positive samples within large pools can reduce test sensitivity 73 .

Point-of-care (POC) tests can be performed on-site, such as within a local clinic, workplace or even a patient's home. These tests are typically antigen-based lateral flow assays that can be easily shipped to the site and are sufficiently simple to be performed and interpreted without specialized training or equipment (box 1). These features enable POC tests to be easily and widely distributed to the population without incurring the challenges and delays associated with sample collection and reporting 74 . Decentralization can improve access to testing, enable earlier and more frequent testing, and reduce exposure of health-care workers. Given these advantages, POC tests are widely considered an attractive approach to achieve a massive expansion in testing 75 , and a diverse range of POC tests have been developed that incorporate molecular, antigen-based and serological technologies 76 .

In November 2020, an initial pilot scheme aimed to screen up to half a million people in Liverpool, UK, Nature reviews | Genetics 0123456789();: using rapid, on-site antigen tests 74 . This scheme offered routine and repeated testing to all residents, regardless of symptoms, in a broad effort to achieve populationscale test coverage and reduce viral transmission. This community-led testing scheme identified more than one-third of the infected but mildly symptomatic or asymptomatic individuals in Liverpool 77 . However, despite this achievement, the sensitivity of the antigen tests used in this scheme was markedly lower than that reported in the original test validation studies, and the tests were thought to miss almost one-third of infectious individuals 78 .

The mutations that accumulate in the SARS-CoV-2 genome can alter the viral phenotype and confer a selective advantage that gives rise to new strains. Genomic epidemiology showed that one strain, distinguished by a non-synonymous D614G mutation in the spike protein, first emerged in Europe before expanding to become the predominant strain worldwide 79 owing to a selective fitness advantage conferred by the mutation that increased viral transmissibility 80 .

The integration of genome sequencing within population-scale testing can enable monitoring of the viral strains circulating within a population. Numerous countries have mandated that a proportion of positive samples is subjected to whole-genome sequencing, thereby providing ongoing surveillance of emerging and circulating variants. This sequencing information can identify emergent SARS-CoV-2 variants with differing transmission or pathogenicity, with resistance to antiviral treatment or that are at risk of vaccine escape 81 . In late December 2020, a new SARS-CoV-2 strain known as B.1.1.7 rapidly increased in prevalence throughout the UK, apparently outcompeting existing variants and prompting the rapid imposition of restrictions on travel to other countries 82 . Additional variants that might increase transmissibility and pathogenicity or reduce the efficacy of vaccines have similarly arisen in South Africa (B.1.351) 83 and Brazil (P.1) 84 . As the effect of these variants on the viral phenotype has become apparent, authorities have recognized that global testing will be increasingly needed to monitor the emergence and circulation of new variant SARS-CoV-2 strains.

Variant diversification identified by genomic surveillance is also important to assess the influence of new mutations on the ongoing performance of molecular diagnostic tests 85, 86 . The emergent B.1.1.7 strain harbours a large number of mutations that might prevent the binding of some primers to the spike gene and thereby reduce the sensitivity of RT-qPCR tests 87 (box 1). In response, numerous variant-specific primers have been developed, illustrating that strain diversification will require ongoing updates and validation of testing reagents.

In the early stages of the COVID-19 pandemic, the routes of SARS-CoV-2 transmission were unclear, and viral particles that land on objects and surfaces (fomites) were considered to pose a risk of indirect transmission 88 . Testing of hospital and public surfaces close to infected patients detected the presence of viral RNA, and countries such as China implemented testing of frozen food imports 89, 90 . However, ongoing environmental testing and epidemiological studies suggest that this mode of transmission is uncommon, and that viral transmission is instead primarily caused by contaminated respiratory droplets and aerosols 91 .

Nevertheless, although viral transmission via fomites is rare, the detection of SARS-CoV-2 in environ mental samples can be used to infer its circulation within a community. SARS-CoV-2 can infect the gastrointestinal tract and can be shed at high concentrations in stool, and might be subsequently discharged into wastewater 92 . SARS-CoV-2 RNA can be sensitively detected in untreated municipal wastewater, including settled solids and sludge [93] [94] [95] . Accordingly, many municipalities have started to test sewage for the presence of SARS-CoV-2, similarly to the testing of primary sewage for poliovirus, which has been successfully used to monitor communities for decades 96 .

Retrospective studies show that increases in the concentration of SARS-CoV-2 RNA in raw wastewater are correlated with increases in reported COVID-19 cases 83, 97 . For example, the detection of SARS-CoV-2 in wastewater from New Haven, Connecticut, USA, tracked rates of hospital admissions during early stages of the COVID-19 pandemic 98 . The detection of SARS-CoV-2 RNA in wastewater occurred days before the rise in the numbers of clinical COVID-19 cases at local hospitals and provided a valuable predictor of viral presence 98 .

Environmental testing has the advantage of detecting SARS-CoV-2 across a wide catchment area that encompasses many individuals. This cost-effective approach can provide community data even in the absence of large-scale testing and is unbiased with regard to people who lack access to health care. Environmental testing can also be used to closely monitor closed residential settings, such as colleges, universities, nursing homes and prisons 99 . Despite its potential, wastewater testing faces technical challenges in achieving sufficient sensitivity, in part because variables such as sampling location, type and volume can all affect detection. Rigorous validation and longitudinal monitoring is required for reliable, actionable wastewater testing 100 .

The speed and scale of the COVID-19 pandemic has created unprecedented challenges to ensure the accuracy and reliability of testing. The implementation of population-scale screening is a massive undertaking that requires coordinated input from governmental, commercial and academic organizations. Numerous large programmes, such as the RADx initiative and the X-Prize Challenge, have been established to accelerate population-scale testing 101, 102 .

The unique requirements of the pandemic have also called for modified regulatory regimes that encourage the development of rapid, cheap tests that are well suited to population-scale testing 26 . To expedite access to SARS-CoV-2 testing during the pandemic, many regulatory agencies have responded with expedited authorization of testing devices. For example, the FDA issues Emergency Use Authorizations (EUAs) if devices have a reasonable expectation of being effective (and vari ous other criteria are met) 103 . Although EUAs provide welcome flexibility for commercial and laboratory developers, this approach also increases the risk that these tests could perform unexpectedly when deployed at scale in the field. For example, several poorly performing antigen tests were initially issued EUAs that were ultimately revoked, which required the FDA to independently evaluate these poor-quality tests and subsequently update its performance requirements and advice 104, 105 .

Reference standards can improve quality and standardization across large and diverse testing schemes 106 . The rapid manufacture of synthetic SARS-CoV-2positive controls has enabled molecular assays to be rapidly evaluated even in the context of limited access to patient samples. These positive controls also enable the early detection of defective reagents, such as faulty primers in RT-qPCR tests 107, 108 . Inactivated viral fractions and serum samples have also been used to develop and evaluate the performance of serological tests 109 . Indeed, the proliferation of positive reference controls has been so widespread as to fuel concerns about contamination of testing and environmental surveillance schemes 110, 111 .

The FDA has issued SARS-CoV-2 reference sample panels for the standardized evaluation of diagnostic assays 109 , and numerous other organizations, such as FIND, have launched standardized evaluation programmes 112 . Notably, findings from these standardized evaluations often differ markedly from test performance statistics published in the EUA 101, 113 . The disparity might, in part, be due to the initial validation of test performance in hospitalized patients, who typically have high viral loads and undergo sampling in a well-controlled setting. This approach can render unreliable the estimation of test performance during population-scale screening, where many tested individuals might be presymptomatic or asymptomatic and have low viral or antibody loads 114 . This situation highlights that test validation is an ongoing process and that proficiency testing schemes are required to continually evaluate the performance of individual laboratories 115 .

Surveillance testing SARS-CoV-2 will probably continue to circulate within human populations for many years, with ongoing regional or seasonal outbreaks 29 . Surveillance testing aims to identify these outbreaks early, often by the detection of a symptomatic index case, and to quickly contain their spread through contact tracing and isolation. Genomic epidemiology can distinguish between novel introductions and persistent local circulation, and can trace the source of outbreaks 116 , whereas environmental testing provides ongoing monitoring of large catchment areas.

Routine testing could also become more common in various aspects of life, with testing of closed communities and populations (such as prisons, schools and universities) increasingly common 115, 117, 118 . Given the role of cross-border transport in the rapid spread of SARS-CoV-2, testing might become a standard feature of international travel, with testing of incoming travellers mandatory in many countries that aim to limit reintroduction of SARS-CoV-2 or new variant strains 119, 120 . Global surveillance of circulating SARS-CoV-2 variants using genome sequencing will also become increasingly important to match circulating variants with vaccines, and to monitor vaccine escape and the emergence of antiviral resistance 7 .

Clinical diagnostic testing for SARS-CoV-2 (alongside other respiratory pathogens, such as influenza viruses) is expected to become part of the standard evaluation of patients admitted to hospital with associated symptoms. Currently, the presence of SARS-CoV-2 is sufficient to direct clinical treatment; however, genome sequencing might be required to distinguish between different variant strains if they necessitate differing clinical or containment responses. Although the considerable innovation and investment in testing is likely to also benefit the detection of other infectious diseases and endemic diseases such as cancer, the disruption to national screening programmes as a result of the pandemic is anticipated to increase the case burden of these diseases for many years to come 121 .

Domestic and wild animal populations can also be infected with SARS-CoV-2 and could act as reservoirs for the virus. Spillover viral transmission between human and animal populations can result in changes in selection pressure that accelerate viral adaptation and evolution. Testing has found repeated, independent infections of domestic mink populations in the Netherlands and Denmark, where SARS-CoV-2 accumulated additional mutations before being reintroduced into human populations [122] [123] [124] . This observation has prompted culling of domestic mink populations as a result of fears that they could act as reservoirs for new SARS-CoV-2 strains. In addition, pressure is growing for increased testing of both wild and domestic animal populations to monitor viral prevalence and diversity.

Population-scale testing has assumed a central role in our efforts to combat the COVID-19 pandemic and will be similarly central to our preparation for future pandemics. Notably, countries such as South Korea and Taiwan that had been affected by SARS outbreaks were able to quickly scale up existing contact tracing and testing schemes, which proved key in containing COVID-19 outbreaks 45, 125 . Many other countries are likely to establish similar national preparation plans that maintain their investment in testing infrastructure and supplies of reagents. The establishment of international genomic surveillance systems to monitor the emergence of novel SARS-CoV-2 strains and the zoonotic transmission of new viruses will enable prompt and appropriate responses, including the development and manufacture of diagnostic tests, and the rapid imposition of travel restrictions and testing requirements 7 . Although some of these preparations are specific to coronaviruses, which have been the source of multiple pandemics in the past two decades 126 , the lessons learned are also applicable to response planning for other viruses with different transmission dynamics, such as influenza viruses and Ebola virus 9 . Nature reviews | Genetics 0123456789();:

Population-scale testing has emerged as a major intervention strategy to manage the COVID-19 pandemic. As community transmission became entrenched within countries, the utility of population-scale testing has been intensely debated. Although widespread testing has been proposed as a solution to suppress and even stop the pandemic, the limitations of and gaps in populationscale testing have also become apparent, and both the cost and the effectiveness of mass testing on reducing viral transmission have been intensely debated.

In the early stages of the pandemic, the main limitations on widespread testing were technical, including insufficient reagents and an unprepared laboratory testing infrastructure. These practical obstacles to the implementation of testing on a massive scale favoured the use of established technologies, which explains why the vast majority of testing for SARS-CoV-2 has been performed by conventional RT-qPCR tests in centralized laboratories. These RT-qPCR tests were developed almost immediately after publication of the reference genome, were quickly scaled up through an existing infrastructure and have generally proved both accurate and reliable. However, with the pandemic ongoing, a new generation of rapid and convenient POC tests have been developed.

With sufficiently broad and frequent community testing, identification and isolation of most infectious individuals was considered possible, thereby arresting the pandemic 127 . However, even the most extensive testing schemes have been found to miss many infectious individuals and to provide only partial population coverage 64, 65 . The rapid infectious course of SARS-CoV-2 and the possibility of its transmission by presymptomatic or asymptomatic individuals blunts the impact of population-scale testing, as many infectious individuals escape detection 128 . In France, for example, models based on health records suggest that most infected people were not tested or quarantined following the first pandemic wave in early 2020, despite the implementation of a nationwide surveillance programme 129 .

The benefits of widespread testing have been widely debated, with researchers arguing that screening of large populations with low infection rates is expensive and ineffective, as most positive results are false positives 130 . Furthermore, the effectiveness of population-scale testing becomes increasingly marginal as viral prevalence falls, and testing alone seems insufficient to eliminate viral transmission. Therefore, researchers have argued that testing should be reserved for symptomatic individuals, traced contacts, closed populations or high-risk groups with an increased probability of infection, where this approach has proven effective, and used in coordination with other interventions, such as targeted regional lockdowns or travel restrictions [131] [132] [133] .

Human populations have experienced many pandemics throughout history; however, this has been the first pandemic in which widespread and routine testing has been available. We have been able to monitor viral transmission and measure viral spread in successive pandemic waves of SARS-CoV-2 infection throughout human populations worldwide. The COVID-19 pandemic has already required unprecedented testing of millions of people, and this information has been critical to understanding viral transmission, informing effective responses and planning for future pandemics. Although population-scale testing has not provided a simple or single technical solution to the pandemic, it has served as an invaluable guide to our response.

Published online xx xx xxxx

A pneumonia outbreak associated with a new coronavirus of probable bat origin

A new coronavirus associated with human respiratory disease in China

Coronavirus and the race to distribute reliable diagnostics

World Health Organization. Molecular assays to diagnose COVID-19: summary table of available protocols

A cross-country database of COVID-19 testing

Response to COVID-19 in Taiwan: big data analytics, new technology, and proactive testing

The COVID-19 testing debacle

Towards a genomicsinformed, real-time, global pathogen surveillance system

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

This work uses genomic epidemiology to describe the initial international spread of SARS-CoV-2 variants

Data, disease and diplomacy: GISAID's innovative contribution to global health

Nextstrain: real-time tracking of pathogen evolution

Phylogenetic network analysis of SARS-CoV-2 genomes

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Genomic epidemiology of SARS-CoV-2 in Guangdong province

Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States

Tracking the COVID-19 pandemic in Australia using genomics

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into northern California

Superspreading events in the transmission dynamics of SARS-CoV-2: opportunities for interventions and control

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Rapid SARS-CoV-2 wholegenome sequencing and analysis for informed public health decision-making in the Netherlands

Phylogenetic interpretation during outbreaks requires caution

Cryptic transmission of SARS-CoV-2 in Washington State

Virological assessment of hospitalized patients with COVID-2019

Rethinking COVID-19 test sensitivity -a strategy for containment

This report determines the initial SARS-CoV-2 transmission dynamics, including infectious and incubation periods and basic reproductive number

SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis

Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period

Viral load of SARS-CoV-2 in clinical samples

Detection of SARS-CoV-2 in different types of clinical specimens

SalivaDirect: a simplified and flexible platform to enhance SARS-CoV-2 testing capacity

Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19)

The interpretation of SARS-CoV-2 diagnostic tests

Interpreting diagnostic tests for SARS-CoV-2

Information and rational decision-making: explanations to patients and citizens about personal risk of COVID-19

Functional SARS-CoV-2-specific immune memory persists after mild COVID-19

The trinity of COVID-19: immunity, inflammation and intervention

Humoral response and PCR positivity in patients with COVID-19 in the New York city region, USA: an observational study

Antibody responses to SARS-CoV-2 in patients with COVID-19

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood

A serological assay to detect SARS-CoV-2 seroconversion in humans

The effect of human mobility and control measures on the COVID-19 epidemic in China

Pandemic preparedness in Taiwan

Coronavirus disease exposure and spread from nightclubs

Impact of delays on effectiveness of contact tracing strategies for COVID-19: a modelling study

Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study

Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

The app credibility gap

Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2)

Slovakia to test all adults for SARS-CoV-2

The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia

On pilot massive COVID-19 testing by antigen tests in Europe. case study: Slovakia

Considerations for diagnostic COVID-19 tests

Test sensitivity is secondary to frequency and turnaround time for COVID-19 surveillance

Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections

Global supply-chain effects of COVID-19 control measures

A locally sustainable approach to COVID-19 testing in Africa

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'

Large-scale testing enabled the measurement of SARS-CoV-2 transmission within an entire town and allowed the impact of interventionists

Antibody surveys suggesting vast undercount of coronavirus infections may be unreliable

This population-scale serological study measured the exposure of the Icelandic population to SARS-CoV-2 during the first pandemic wave and assessed the effectiveness of large

Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study

Antibody prevalence for SARS-CoV-2 in England following the first peak of the pandemic

Spread of SARS-CoV-2 in the Icelandic population

Rapid response to an outbreak in Qingdao

Tapestry: a single-round smart pooling technique for COVID-19 testing

A pooled testing strategy for identifying SARS-CoV-2 at low prevalence

Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers

Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests

Assessing the dilution effect of specimen pooling on the sensitivity of SARS-CoV-2 PCR tests

Covid-19: Mass population testing is rolled out in Liverpool

Scaling up COVID-19 rapid antigen tests: promises and challenges

Diagnostics for SARS-CoV-2 infections

Research and analysis. Liverpool COVID-19 community testing pilot: interim evaluation report summary

Covid-19: Lateral flow tests miss over half of cases, Liverpool pilot data show

Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus

Spike mutation D614G alters SARS-CoV-2 fitness

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

This study describes the emergence of SARS-CoV-2 variants with higher estimated reproductive numbers than other variants

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

A recurrent mutation at position 26340 of SARS-CoV-2 is associated with failure of the E Gene quantitative reverse transcription-PCR utilized in a commercial dual-target diagnostic assay

SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations

Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1

Monitoring COVID-19 transmission risks by quantitative real-time PCR tracing of droplets in hospital and living environments

Cold-chain food contamination as the possible origin of COVID-19 resurgence in Beijing

Identifying airborne transmission as the dominant route for the spread of COVID-19

Prolonged presence of SARS-CoV-2 viral RNA in faecal samples

SARS-CoV-2 in wastewater: potential health risk, but also data source

SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community

Estimation of polio infection prevalence from environmental surveillance data

Presence of SARS-coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands

This group shows that detection of the presence of SARS-CoV-2 RNA in wastewater correlated with hospital COVID-19 admissions

COVID-19 containment on a college campus via wastewater-based epidemiology, targeted clinical testing and an intervention

The challenges of informative wastewater sampling for SARS-CoV-2 must be met: lessons from polio eradication

The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing

Rapid scaling up of COVID-19 diagnostic testing in the US -the NIH RADx initiative

COVID-19 molecular diagnostic testing -lessons learned

The promise of directto-consumer COVID-19 testing: ethical and regulatory issues

The promise and peril of antibody testing for COVID-19

Diagnostics and the coronavirus: don't let the standards slip

Comparative performance of SARS-CoV-2 detection assays using seven different primer-probe sets and one assay kit

Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets

SARS-CoV-2 reference panel comparative data

Contamination of SARS-CoV-2 RT-PCR probes at the oligonucleotide manufacturer

Delayed laboratory response to COVID-19 caused by molecular diagnostic contamination

SARS-CoV-2 diagnostic pipeline

Buyer beware: inflated claims of sensitivity for rapid COVID-19 tests

Are seroprevalence estimates for severe acute respiratory syndrome coronavirus 2 biased?

INSTAND report on extra external quality assessment scheme group no. 340 virus genome detection SARS-CoV-2

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

The missing piece -SARS-CoV-2 testing and school reopening

Assessment of SARS-CoV-2 screening strategies to permit the safe reopening of college campuses in the US

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak

Impact of international travel and border control measures on the global spread of the novel 2019 coronavirus outbreak

The impact of the COVID-19 pandemic on cancer deaths due to delays in diagnosis in England, UK: a national, population-based, modelling study

This group uses whole-genome sequencing to show SARS-CoV-2 transmission between minks and humans

SARS-CoV-2 infection in farmed minks, the Netherlands

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

Response to COVID-19 in South Korea and implications for lifting stringent interventions

Origin and evolution of pathogenic coronaviruses

Population-scale testing can suppress the spread of COVID-19

Asymptomatic transmission, the Achilles' heel of current strategies to control COVID-19

Underdetection of COVID-19 cases in France threatens epidemic control

COVID-19 mass testing programmes

Asymptomatic transmission of COVID-19

Diagnostic tool or screening programme? Asymptomatic testing for SARS-CoV-2 needs clear goals and protocols

Estimating the effects of nonpharmaceutical interventions on COVID-19 in Europe

Coronavirus antibody tests have a mathematical pitfall

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in

Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR

LAMP-Seq: population-scale COVID-19 diagnostics using combinatorial barcoding

HiDRA-seq: high-throughput SARS-CoV-2 detection by RNA barcoding and amplicon sequencing

Swab-Seq: a high-throughput platform for massively scaled up SARS-CoV-2 testing

Loop-mediated isothermal amplification of DNA

A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples

DNA detection using recombination proteins

A single and two-stage, closed-tube, molecular test for the 2019 novel coronavirus (COVID-19) at home, clinic, and points of entry

CRISPR-Cas12-based detection of SARS-CoV-2

Evaluation of a rapid diagnostic assay for detection of SARS-CoV-2 antigen in nasopharyngeal swabs

Low performance of rapid antigen detection test as frontline testing for COVID-19 diagnosis

Evaluation of rapid antigen test for detection of SARS-CoV-2 virus

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance

Developing antibody tests for SARS-CoV-2

Clinical performance of two SARS-CoV-2 serologic assays

Complexity of the basic reproduction number (R0)

The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 131 countries

Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China

Early dynamics of transmission and control of COVID-19: a mathematical modelling study

World Health Organization. Considerations for implementing and adjusting public health and social measures in the context of COVID-19

SARS-CoV2 testing: the limit of detection matters

The authors contributed equally to all aspects of the article.

The authors declare no competing interests.

Nature Reviews Genetics thanks Z. Kozlakidis, R. S. Vincenzo, J. Hay and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

GisAiD: https://www.gisaid.org/ Nextstrain: https://nextstrain.org/ Our world in Data COviD-19 dataset: https://ourworldindata. org/coronavirus-testing