key: cord-0814141-yoviku4m
authors: Gitman, Melissa R.; Shaban, Maryia V.; Paniz-Mondolfi, Alberto E.; Sordillo, Emilia M.
title: Laboratory Diagnosis of SARS-CoV-2 Pneumonia
date: 2021-07-15
journal: Diagnostics (Basel)
DOI: 10.3390/diagnostics11071270
sha: 64e11a44a3cc971c446acb45b08d1a079741f6bc
doc_id: 814141
cord_uid: yoviku4m

The emergence and rapid proliferation of Coronavirus Disease-2019, throughout the past year, has put an unprecedented strain on the global schema of health infrastructure and health economy. The time-sensitive agenda of identifying the virus in humans and delivering a vaccine to the public constituted an effort to flatten the statistical curve of viral spread as it grew exponentially. At the forefront of this effort was an exigency of developing rapid and accurate diagnostic strategies. These have emerged in various forms over the past year—each with strengths and weaknesses. To date, they fall into three categories: (1) those isolating and replicating viral RNA in patient samples from the respiratory tract (Nucleic Acid Amplification Tests; NAATs), (2) those detecting the presence of viral proteins (Rapid Antigen Tests; RATs) and serology-based exams identifying antibodies to the virus in whole blood and serum. The latter vary in their detection of immunoglobulins of known prevalence in early-stage and late-stage infection. With this review, we delineate the categories of testing measures developed to date, analyze the efficacy of collecting patient specimens from diverse regions of the respiratory tract, and present the up and coming technologies which have made pathogen identification easier and more accessible to the public.

The illness now known as Coronavirus Disease-2019, or COVID-19, was first described in mid-December 2019 when the Wuhan health authorities detected a cluster of cases of atypical pneumonia [1] . As Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the cause of COVID-19, spread globally, the need for rapid, accurate diagnostic testing was recognized. In this review, we discuss the direct and indirect methods that are currently employed for diagnosis of SARS-CoV-2 infection. Although this virus is relatively new, a plethora of publications have appeared in the last year, and a comprehensive review of all available data is beyond the scope of this paper. We present a brief overview of the virus and available testing options.

Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses [2] . A part of the Coronaviridae family, Betacoronavirus genus, SARS-CoV-2 is the seventh coronavirus known to infect humans [3] . Understanding the structure and genomic architecture of the virus is important, as this is the basis of the targets for the various diagnostic tests. The SARS-CoV-2 virion is roughly spherical and 60-140 nm in diameter [4] . A viral membrane contains the spike (S) glycoprotein, giving the virus its characteristic corona or crown-like appearance [5] . The spike protein features two functional subunits [6] : S1, containing the receptor-binding domain (RBD) that mediates binding to the host cell surface receptor angiotensin-converting enzyme-2 

Throughout the pandemic, the populations who meet criteria for testing have evolved as the testing capacity has expanded. Initially, only patients with symptoms compatible with COVID-19 who had traveled to Wuhan, China, were eligible to be tested. As the pandemic progressed and local community transmission was recognized, rapid diagnosis of potentially SARS-CoV-2-infected individuals became crucial in order to cut off chains of transmission, and the requirement for travel was eliminated. As more diagnostic assays became available, screening of potentially exposed but asymptomatic patients became more widespread. Screening in facilities such as nursing homes and other communal living settings has become an indication for testing [9] . Other groups for whom screening of asymptomatic individuals has now been implemented include schools, travelers, healthcare workers, and those with potential exposure to individuals diagnosed with COVID-19 [10] . The Infectious Diseases Society of America (IDSA) has designed an algorithm to assist in the decision of whom to test that stresses the importance of testing symptomatic individuals and lists others who may meet criteria such as recently exposed or pre-procedural and testing available [11] . 

Throughout the pandemic, the populations who meet criteria for testing have evolved as the testing capacity has expanded. Initially, only patients with symptoms compatible with COVID-19 who had traveled to Wuhan, China, were eligible to be tested. As the pandemic progressed and local community transmission was recognized, rapid diagnosis of potentially SARS-CoV-2-infected individuals became crucial in order to cut off chains of transmission, and the requirement for travel was eliminated. As more diagnostic assays became available, screening of potentially exposed but asymptomatic patients became more widespread. Screening in facilities such as nursing homes and other communal living settings has become an indication for testing [9] . Other groups for whom screening of asymptomatic individuals has now been implemented include schools, travelers, healthcare workers, and those with potential exposure to individuals diagnosed with COVID-19 [10] . The Infectious Diseases Society of America (IDSA) has designed an algorithm to assist in the decision of whom to test that stresses the importance of testing symptomatic individuals and lists others who may meet criteria such as recently exposed or pre-procedural and testing available [11] .

Nasopharyngeal (NP) swabs are the preferred specimen for direct detection of SARS-CoV-2 according to both the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) guidelines.

However, several significant barriers are associated with collection of NP swab specimens for SARS-CoV-2 detection, including the requirement for collection by a trained provider, the use of personal protective equipment (PPE) due to triggering of reflex cough/sneeze during collection, patient discomfort, and potential harm, including a case of a Cerebral Spinal Fluid (CSF) leak due to improper collection [11, 12] . Additionally, supply chain disruption resulting in scarcity of the flocked swabs and transport media used for collection of NP specimens has been a concern, particularly during the pandemic surge. As a result, alternate upper respiratory tract specimen types have been evaluated such as anterior nares or nasal swabs. Pere et al. compared NP swabs and nasal swabs in 44 consecutive patients. They detected four false negatives in the nasal swab group (9.1%) and there were no additional positives found in the nasal swab group not detected in the NP swab group [13] .

Saliva is another alternative specimen type that has been considered for SARS-CoV-2 diagnostic testing. Advantages of this specimen type include ease of collection, minimal patient discomfort, and improved safety for both patients and providers. As collection of saliva does not provoke a cough/sneeze reflex, guidelines do not require special provider PPE for aerosol exposure. Furthermore, since flocked collection swabs and transport media are not required, reliance on the material supply chain is minimized. In an initial proof of concept, To et al. collected saliva from known positive patients and demonstrated that SARS-CoV-2 could be detected in specimens collected from 11 of the 12 tested [14] . Wyllie et al. compared paired samples of saliva and NP swabs from 70 in-patients with a known diagnosis of COVID-19. At days 1-5 after diagnosis, more patients tested positive from saliva (81%) than NP specimens. (71%). Overall, viral load was higher in saliva than in the paired NP swab specimens (5.58 vs. 4.93 mean log copies per mL) [15] . Conversely, a study of paired NP and saliva samples from 91 patients found NP swab specimens to be slightly more sensitive in the first week and 20% more sensitive if collected in the second week of illness or later [16] . The suitability of saliva for detection of SARS-CoV-2 may reflect overall viral dynamics, since both upper respiratory tract contents as well as lower respiratory secretions driven by the mucociliary airway epithelium combine in the oral cavity. Of note, a recent study from Huang et al. demonstrated higher RNA expression of the ACE2 receptor and the TMPRSS2 internalization protease in epithelial cells of the glands and oral mucosae, which translated into a higher salivary viral burden [17] . Moreover, recent evidence provided by Savela et al. suggests that high-sensitivity saliva-based tests can detect the presence of SARS-CoV-2 earlier in the infection when compared to self-collected anterior-nares nasal swabs [18] .

SARS-CoV-2 can also be detected in lower respiratory specimens, although reports from different investigators are contradictory regarding diagnostic sensitivity, perhaps influenced by stage of disease or other patient characteristics. Possible lower tract specimens include sputum, tracheal aspirates and bronchoalveolar lavage (BAL). Tracheal aspirates are much simpler to obtain in intubated patients; however, unlike BAL fluid, the viscosity of the specimens vary. However, BAL has the disadvantage of requiring an invasive procedure. Some studies have suggested that lower respiratory tract specimens may be persistently positive longer than upper tract specimens. In a case reported from Thailand, a patient whose NP and oropharyngeal swab specimens had twice tested negative was diagnosed by RT-PCR detection of SARS-CoV-2 in a bronchoalveolar lavage (BAL) specimen collected on hospital day 8 [19] . One potential explanation for this is that lower respiratory tract epithelial cells and pneumocytes have a higher density of ACE2 receptors that serve as the target for SARS-CoV-2 compared to upper tract epithelial cells [20, 21] .

Understanding SARS-CoV-2 viral dynamics in the respiratory system may help to better guide specimen collection. However, studies addressing SARS-CoV-2 tissue distribution and dynamics are still scarce. Viral loads are known to differ amongst sample types, being higher in respiratory samples at early stages of the disease. For example, a meta-analysis comparing 3442 respiratory samples, including 1299 nasopharyngeal swabs, 1083 oropharyngeal swabs and 1060 sputum samples, indicated that sputum (71% positive samples) was far more sensitive than oropharyngeal swabs (54%) or nasopharyngeal swabs (43%), although when stratified by time since onset of symptoms, sensitivity was diminished for all three specimens types the later in the disease course the specimens were collected [22] . Interestingly, Hou et al. utilized reverse genetics to show a variable infectious gradient throughout the respiratory tract that parallels tissue expression of the ACE-2 receptor [23] . In addition, they assessed viral tropism and distribution in lungs from deceased COVID-19 patients, demonstrating a higher gradient of virus in the upper respiratory tract vs. the lower tract, and suggested that infection of type 2 pneumocytes in the alveolar region is seeded by aspiration of the virus in upper airway secretions [23] . A separate meta-analysis comparing different methodologies identified that pooled nasal and throat swabs gave the highest sensitivity of 97%, followed by nasal swabs (86%) and saliva (85%) and finally throat swabs alone (68%). Moreover, in a different meta-analysis by Weiss et al., it was found that SARS-CoV-2 PCRs remained positive longer in the lower respiratory tract (LRT) compared to the upper respiratory tract (URT), both in mild disease (5.7 days) and moderate-severe disease (5.9 days). In patients with mild disease, the viral load peaked on day 4 of illness with a maximum viral load of 6.61 × 108 viral copies/mL in the URT, as compared to the LRT, which peaked on day 6 at 2.69 × 108 copies/mL. In patients with moderate to severe disease, the URT viral load peaked at 4.60 × 109 copies/mL on day 8 as compared to the LRT with a peak of 3.45 × 108 copies/mL on day 11.

Once the site of sample collection has been determined, the next consideration is the collection device and transport conditions. Traditionally, samples collected for viral testing are transported in viral transport media (VTM), which contains a mix of Hanks balance salt solution, antibiotics, antifungals, and a PH indicator. At the onset of the pandemic, these were in short supply. Many centers tested using saline or phosphate buffered saline (PBS) as transport media and found these performed as well as VTM [24, 25] . It is recommended that samples be stored at 2-80 • C and tested within 72 h, otherwise they should be frozen until they can be tested [10] in order to preserve nucleic acid stability and integrity.

Detection of the presence of viral RNA using NAAT has become the mainstay of SARS-CoV-2 diagnosis with real-time polymerase chain reaction (RT-PCR) being the most common NAAT method currently employed [10] . RT-PCR involves several steps, the first being extraction of viral RNA from the collected specimens using silica or magnetic particlebased methods. Next, there is reverse transcription of the viral RNA to a single-stranded DNA copy (cDNA) using a reverse transcriptase enzyme. Finally, there is the amplification step where the extracted viral RNA is mixed with reagents containing the primers, probes and master mix and detection is obtained through a coupled fluorescent marker [26] . The first RT-qPCR for SARS-CoV-2 detection was developed by China's Center for Disease Control and Prevention and was designed to detect the N and the ORF1ab genes [27] . Next, the Charite Institute developed a protocol incorporating primers targeting genes of the E, N, and RdRp [27] . In the U.S., the first RT-PCR protocol was developed by the CDC and targeted N1 and N2 [27] . Internationally, there are many different primers and probe sets available from the World Health Organization [28] . Vogels et al. compared seven primer sets and found they all had similar performance characteristics [29] . It is important to mention that, as specified by Corman et al., the performance varies for different targets across the viral genome, potentially affecting sensitivity and specificity [30] .

In the U.S., multiple commercial assays are now marketed [31] and several assays are available as part of a test system that utilizes a single, self-contained, high-throughput instrument to perform all the PCR or other NAAT steps (Table 1 ). To address the urgent need for diagnostic test capacity, these tests were reviewed by the US Food and Drug Administration (FDA) through an emergency use authorization pathway. The early EUA process required companies to submit analytic sensitivity, limit of detection, along with cross-reactivity studies [32] . Initial studies submitted to the FDA were performed using contrived samples, not patient samples, and therefore clinical correlation was not performed. Consequently, determination of sensitivity and specificity against a clinical gold standard is not generally available for these assays [31] . Table 1 . Comparative list of nucleic acid amplification tests for the detection of SARS CoV-2, by manufacturer, origin of specimen, target gene, sensitivity, specificity, limit of detection and the time to produce one successful run. Assay selection relies on several factors, including availability of reagents, cost, throughput and performance characteristics [32] . Various publications have appeared over the past year, comparing the performance characteristics of the different commercial assays. One publication from Moran et al. tested 103 specimens on the Roche cobas SARS-CoV-2 test and Cepheid Xpert Xpress SARS-CoV-2 assay and found that 42 tested positive and 60 tested negative with both systems for agreement of 99% [60] . Rhoads et al. tested 96 samples using the CDC EUA as the gold standard and found the positive predictive value of the Diasorin Simplexa COVID-19 Direct assay to be 96% with four false negative samples [53] . A multicenter study of the Cepheid Xpert Xpress SARS-CoV-2 test, a rapid PCR instrument widely available in many clinical labs, demonstrated an LOD of 0.01 PFU/mL. When residual clinical samples were compared to various other PCR assays, it demonstrated a 99.5% positive agreement and 95.8% negative agreement [33] . Fung et al. compared the analytic limit of detection across seven molecular platforms using a pool of positive patient samples quantified via digital droplet PCR. Limits of detection ranged from ≤10 to 74 copies/mL for commercial high-throughput laboratory analyzers (Roche cobas SARS-CoV-2 Test, Abbott RealTime SARS-C0V-2 assay and Hologic Panther Fusion SARS-CoV-2 assay) and 167 to 511 copies/mL for sample-to-answer (DiaSorin Simplexa COVID-19 Direct assay, GenMark ePlex SARS-CoV-2 Test) and point-of-care instruments (Abbott ID NOW COVID-19 test) [34] . Overall, most commercial RT-PCR assays show excellent analytic sensitivity [38, [61] [62] [63] [64] [65] [66] [67] [68] . Differences in results may be due to a number of factors, including whether there is a full extraction step prior to amplification [69] , whether the patient has a low viral load close to the limit of detection of the assay [69] , volume of sample tested and assay design, such as targets chosen [32] . Finally, the quality of the sample received likely has a significant impact on the likelihood of a reliable result [32, 70] .

One potential advantage of RT-PCR-based tests is the ability to generate a cycle threshold (Ct) value. Ct values have been suggested as a surrogate for viral load [71, 72] . The Ct value refers to the number of PCR cycles needed to amplify the target sequence to a detectable level [26] . A specimen containing more virus (higher viral load) will need fewer PCR cycles to produce a positive signal; thus, a lower Ct value implies a higher viral load in the original sample. In assays with more than one target, more than one Ct value may be generated. However, caution must be used in the interpretation of Ct values generated by assays intended to produce a qualitative result (e.g., detected or positive vs. not detected or negative) and that have not been designed to produce quantitative results or and have not been standardized against control samples of a known concentration. In some NAAT assays, the relationship between the Ct vale and the concentration of target RNA in the sample may not be linear [72] . Another caveat is that a Ct value generated in one assay platform cannot be correlated directly with a value generated using a different assay due to heterogeneity among the targets and amplification protocols used by different assays and test platforms. Additionally, variability in collection techniques as well as the intrinsic heterogeneity of specimens that contain respiratory secretions contribute to the difficulty of standardizing the viral loads in these samples [72] . Further complicating interpretation of their significance is the finding that Ct values overlap in specimens from symptomatic and asymptomatic patients [73, 74] and may not always indicate disease severity.

Disadvantages of PCR testing include the need for specialized and costly reagents, expensive laboratory instrumentation, and highly skilled laboratory personnel. Processing large numbers of specimens is time-consuming and even with automation of many processing steps can take a prolonged period of time to generate results [75, 76] . One major limitation of RT-PCR methods is that the tests are overly sensitive and do not distinguish between active infection and non-viable virus [76] . It has been demonstrated that in individuals with COVID-19, viral shedding approximately begins 2-3 days before symptoms appear [77] . The average duration of viral shedding is 20 days [78] ; however, viral shedding by immunocompromised hosts may be prolonged for 3-5 months or more [79, 80] . In some cases, the shed virus may still be viable. Shedding of replication-competent SARS-CoV-2 has been shown in cell cultures inoculated with respiratory samples from two patients with prolonged, severe COVID-19 [81] .

Transcription-mediated amplification is an alternate type of NAAT testing that forms the basis for the APTIMA assay performed on the high-throughput Panther platform. After hybridizing the viral RNA to a T7 promoter primer, it is reverse-transcribed into a complementary cDNA. The target RNA strand is subsequently degraded by RNAse H, leaving a single-stranded cDNA that includes the T7 promoter. An additional primer is used to generate a double-stranded DNA. T7 RNA polymerase then transcribes the ds-DNA into RNA amplicons, which can then restart the process, allowing this exponential amplification [82] . Its performance characteristics suggest the assay is highly sensitive [83] .

Other NAAT methods that have been considered for SARS-CoV-2 test manufacturing include reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), nicking endonuclease amplification reaction (NEAR), and Recombinase Polymerase Amplification (RPA) [84] . The increasing need for efficient and rapid testing has also opened the door to alternate approaches such as the quantitative Selective Temperature Amplification Reaction (qSTAR) technology, a qualitative non-isothermal nucleic acid amplification technique based on a two-step cycling protocol that capitalizes on the activity of polymerase and a nicking enzyme and shuttling between temperatures [85] . For RNA STAR, complete incorporation of an extraction buffer allows the sample to be loaded directly, removing the extraction step and significantly shortening the hands-on time by combining lysis and amplification into a single step [85] .

Finally, there has been much interest in use of innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR) [48] , Specific High Sensitivity Enzymatic Reporter UnLocking (SHERLOCK) [56] and MassARRAY [86] . The MassARRAY (Agena Bioscience) is a novel multiplex reverse transcription RT-PCR/MALDI-TOF-based system with a scalable high-throughput capacity and an increased sensitivity achieved by coupling of RT-PCR and mass spectrometry along with a multitarget (N1, N2, N3, ORF1ab, orf1) interrogation of the viral genome. However, a possible limitation to the use of platform as an end-point detection method is that it relies on end-product quantification, and thus does not generate Ct values. To date, the MassARRAY has obtained an FDA EUA for SARS-CoV-2 detection in upper respiratory (nasopharyngeal swab, oropharyngeal swab, nasal and mid-turbinate swabs, and nasal and nasopharyngeal aspirate) and lower respiratory (bronchoalveolar lavage) specimens collected and stored in VTM or UTM [87] .

SARS-CoV-2 genetic variability has become a pressing issue, particularly in the context of the worldwide emergence of variants of concern and the potential to affect diagnostic performance. Of note, early in the pandemic, Artesi et al. reported on a recurrent mutation at position 26,340 of SARS-CoV-2 associated with dropout of the E gene on the Roche cobas SARS-CoV-2 Test [88] . More recently, Bal et al. reported a spike deletion H69-V70 identified in several variants, leading to S gene target dropout in the TaqPath qPCR (Thermo Fisher, Waltham, MA, USA) assay [43] . A recent study by Wang et al. using a nucleotide-and gene-based analysis determined that of all currently targeted genes, the N gene is the most prone to mutations, followed by the E gene, as opposed to ORF1ab, which showed a higher diagnostic reliability [89] .

Even though the impact of variants on test performance is currently predicted to be low, laboratories should monitor routinely for target failure. This also highlights the importance of incorporating redundancy by targeting more than one target of the viral genome in order to decrease the likelihood of false negative results.

The need for rapid, accurate diagnosis to facilitate appropriate implementation of respiratory isolation measures and patient management has led to the development of point of care testing (POCT); however, there have been concerns with the performance of these tests in some clinical settings. There are currently six rapid point 

the Roche cobas SARS-CoV-2 Test. The overall agreement was found to be 98.6% (352/357); the positive percent agreement for SARS-CoV-2 was 100% (162/162) and the negative percent agreement was 97.4% (190/195) [36] . Although overall this study demonstrated excellent performance characteristics, the FDA recently issued a warning concerning the risks for false positives [90] . Another common POCT test, the Abbott ID now COVID 19 test, was compared to the Cepheid Xpert Xpress SARS-CoV-2 assay using dry nasal swabs. Overall, results from testing by the ID Now agreed for 17 of 31 positive Xpert Xpress samples, with a positive percent agreement of 54.8%. The ID Now results matched 69 of the 70 negative Xpert Xpress results, with 1 positive detected by ID Now but not by Xpert Xpress, for a negative percent agreement of 98.6% [91] . Multiple studies have found lower positive agreement for the ID NOW in comparison to more sensitive molecular platforms [54, 60, 61, 63] . As there is a need for rapid testing results in many settings, particularly emergency rooms, it has been proposed that multistep testing algorithms be developed [92] ; however, further research is likely required to formalize this guidance. Another point of care NAAT test is the Cue COVID-19 Test for Home and Over the Counter (OTC) Use. It is an isothermal nucleic acid amplification assay which tests anterior nares samples that are self-collected by adults or collected by an adult from children. One study from the Mayo clinic compared results from the Cue POCT to standard of care testing in a central lab using either the Hologic assay or an LDT [93] . They found excellent positive and negative predictive values; however, of note, in this study, the Cue swabs were collected by nurses and the testing was carried out by MLTs, not patients, as the product is designed for [93] .

Rapid antigen tests (RATs), which detect the presence of viral proteins, are another form of POCT ( Table 2 ). Most of these types of tests are lateral-flow immunoassays that create a fluorescent band on the test strip if the target viral proteins are present [6] . These tests are usually cheap and rapid. Beck et al. compared 346 paired NPS tested on both the Sofia Quidel and Hologic Panther Aptima assays and found overall lower agreement amongst the positive samples compared to the negatives (PPA 77% vs. NPA 99.6%). However, it is notable that the PPA of the SOFIA test with the APTIMA TMA test was 82.0% for patients tested ≤ 5 days from symptom onset and 54.5% for patients tested > 5 days from symptom onset [94] . Young et al. compared the BD Veritor System for Rapid Detection of SARS-CoV-2 to the Lyra SARS-CoV-2 assay and, in a separate analysis, compared the BD Veritor System for Rapid Detection of SARS-CoV2 antigen test to the Sofia SARS Antigen FIA. Compared to the Lyra PCR assay, the positive predictive agreement was 88% for patients with two or more symptoms consistent with COVID-19 but dropped to 57.1% and to 66.7% for specimens from patients with only one symptom. Overall, the two rapid antigen tests were reported to have similar performance characteristics [95] . A Cochrane review of rapid antigen tests found that test sensitivity ranged from 30% to 80% with a pooled sensitivity of 56% [96] . It has been proposed that despite a lower positive predictive value in comparison to NAAT tests, there are potential uses for antigen tests. One use could be for rapid diagnosis of symptomatic patients. However, negative results would not rule out asymptomatic carriage and would likely still require PCR confirmation, and positive findings in asymptomatic require a second methodology to rule out a false positive result. Another potential use for the test might be to predict which patients are likely to be infectious to others. One group demonstrated that antigen positivity has a 90% PPV of having culturable virus vs. only 70% amongst PCR positive patients [97] . The CDC has proposed an algorithm for how to best use antigen testing [98] . Even though most of the commercially available antigen tests target the viral nucleocapsid protein (N gene), the very few assays that target the spike protein (S gene) may be negligibly affected by current emergent variants. However, to date, there are no studies confirming the potential impact of variants in antigen-based test performance [99] . Table 2 . Comparative list of rapid antigen tests for the detection of SARS CoV-2, by manufacturer, origin of specimen, target gene, sensitivity, specificity, limit of detection, and the time to produce one successful run. 

Serologic testing is an important tool at the population level, since establishing seroprevalence can enhance understanding of the epidemiology of COVID-19 and assist in public health planning. For an individual, serology can help establish potential susceptibility to infection or may be used as an adjunct to PCR testing for diagnosis, particularly when patients present late in the course of illness when the virus may no longer be detectable [107] . For symptomatic individuals, IgM can be detected at a median of 5 days, and IgG at a median of 14 days, after symptom onset [108] . IgG antibodies have been shown to correlate with disease severity, decline at varying rates, and may be detectable for months following infection [109, 110] . However, between 4% and 10% of the individuals with confirmed SARS-CoV-2 infection may have an undetectable or delayed antibody response [111] . The humoral response includes antibodies directed against RBD, S and N proteins, which serve as the primary targets for COVID-19 serologic assays [6] . Some general limitations of serology studies for COVID-19 include: it is unknown how long protection lasts; protection is unlikely to be durable given short-lived immunity to other coronaviruses; some people with mild/asymptomatic infections never develop antibody responses at all; serology cannot be used in acute diagnosis; combination IgM/IgG assays are of questionable value due to concerns of cross-reactivity of IgM and other coronavirus antibodies [6, 82, 107, 112, 113] .

At present, serology is not recommended to assess the response to COVID-19 vaccination. Since vaccines induce antibodies to specific viral protein targets, post-vaccination serologic test results will be negative in persons if the test used does not detect antibodies induced by the vaccine [113] . As for direct viral testing, there is no gold standard for antibody testing. RT-PCR positivity is currently used as a surrogate; however, patients may have negative serologic results with a positive PCR test for any number of reasons including: (1) failure to mount a measurable serologic response in immunocompromised hosts; (2) clearance of infection by T cells or other immune mechanisms; (3) presence of an interfering substance in the patient's serum; (4) false positive PCR result in a patient who did not have an infection with SARS-CoV-2 [114] .

Serologic testing assays can be broadly divided into three main categories: detection of total antibodies, detection of specific antibody subclasses (IgG, IgM or IgA), and detection of neutralizing antibodies (nAbs) using qualitative or semi-quantitative methods [107] . Detection of IgA is not routinely recommended for clinical assays [113] ; detection of total antibodies may enhance sensitivity [114] . Currently, commercially produced antibody methods include rapid diagnostic tests (RDTs), enzyme-linked immunosorbent assays (ELISA) and chemiluminescence immunoassays (CLIAs) [107] . RDTs are based on antibody detection using a nitrocellulose membrane. The sample is loaded onto a loading pad and then flows via capillary motion when buffer is added. Antibodies in the specimen bind to nanoparticles on the membrane which then are captured by anti-human antibodies. The convenience of these assays makes them popular as POCTs but there has been a wide variability in performance characteristics for these assays across different vendors. For ELISA-based methods, patient specimens are added to a tube or well of a multiassay plate coated with viral antigens. A secondary (anti-human) antibody is linked to an enzyme that will produce a color readout when its substrate is added. Development of color when the substrate is added indicates that a human antibody to the viral antigen bound to the well or tube was present in the patient specimen. Multiwell plate assays or high-throughput platforms allow for large-scale testing but are expensive and must be performed in a laboratory. CLIA is a similar technique to ELISA, but a fluorescent molecule is used as the indicator [107] .

Several available serologic assays were compared directly by the National SARS-CoV-2 serology assay evaluation group, including four commercial and one home-brew serologic assay: the SARS-CoV-2 IgG assay (Abbott), Liaison SARS-CoV-2 S1/S2 IgG assay (Diasorin), Elecsys Anti-SARS-CoV-2 assay (Roche), SARS-CoV-2 total assay (Siemens) and the Oxford Immunoassay. The results for 976 pre-pandemic blood samples and 536 samples from patients with confirmed SARS-CoV-2 infection, collected > 20 days after symptom onset, were evaluated. All five assays demonstrated a sensitivity and specificity of >90%, with a sensitivity of >98% for specimens obtained > 30 days after symptom onset [114] . Similar findings have been obtained in other comparative studies [115] [116] [117] [118] . There are currently over fifty serologic assays with FDA EUA [32] . As a result, comparison of performance can be difficult due to differences in the approach, the sample size, sample collection time and disease prevalence in the population tested by each manufacturer, which vary widely [107] . A summary of some of the currently available serologic tests can be found in Table 3 . Table 3 . Comparative list of serology tests for the detection of SARS CoV-2 by manufacturer, origin of specimen, target antibody, sensitivity, specificity and the time to produce one successful run. The diversity of molecular assays targeting different SARS-CoV-2 genes has enhanced diagnosis capacity and precise identification of SARS-CoV-2 infections. However, the accumulation of nucleotide changes during viral replication has led to the emergence of variant viruses and potentially impacts diagnostic test accuracy for detection of SARS-Cov-2 infection. This highlights the importance of monitoring performance of already released and under-development assays, as well as the need for continued genomic surveillance aimed at detection of variants and their impact on diagnostic target regions. Additionally, the wide circulation of virus variants and concerns regarding the ability of current molecular assays to reliably identify future SARS-CoV-2 emerging variants emphasizes the pressing need for increased and timely whole genome sequencing and surveillance.

In one year, we have learnt a great deal about SARS-CoV-2, a novel coronavirus. As the pandemic continues, the state of knowledge will continue to evolve. This review provides an overview to assist providers in better understanding the testing options for detection of SARS-CoV-2 infections and to assist in the management of patients with COVID-19.

Funding: This research received no external funding.

The authors declare no conflict of interest.

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Assays for the Detection of SARS-CoV-2

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

Food and Drug Administration Coronavirus Disease 2019 (COVID-19) EUA Information

Laboratory diagnosis of emerging human coronavirus infections-The state of the art

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test

Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

Xpert Xpress SARS-CoV-2/Flu/RSV: Instructions for Use

Clinical performance of the point-of-care cobas Liat for detection of SARS-CoV-2 in 20 minutes: A multicenter study

Roche Molecular Systems. cobas SARS-CoV-2 & Influenza A/B Nucleic Acid Test for Use on the cobas Liat System: Instructions for Use

Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2

Roche Molecular Systems. cobas®SARS-CoV-2 Qualitative Assay for Use on the cobas®6800/8800 Systems; Roche Molecular Systems: South Branchburg

Roche Molecular Systems. cobas SARS CoV-2 Test: Instructions for Use

Accula SARS-Cov-2 Test: Instructions for Use

): Instructions for Use

Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70

TaqPath COVID-19 Combo Kit and TaqPath COVID-19 Combo Kit Advanced Instructions for Use

Nucleic Acid-Based Diagnostic Tests for the Detection SARS-CoV-2: An Update

Abbott RealTime SARS-CoV-2: Instructions for Use

PerkinElmer SARS-CoV-2 RT-qPCR: Emergency Use Authorization Summary

Ultra-sensitive and high-throughput CRISPR-powered COVID-19 diagnosis

Aptima®SARS-CoV-2 Assay (Panther®System): Instructions for Use; Hologic

Cue COVID-19 Test for Home and Over-the-Counter (OTC) Use; Cue Health

Inc. AQ-TOP COVID-19 Rapid Detection Kit PLUS: Instructions for Use

Pro-AmpRT SARS-CoV-2 Test

Comparison of Abbott ID Now, DiaSorin Simplexa, and CDC FDA Emergency Use Authorization Methods for the Detection of SARS-CoV-2 from Nasopharyngeal and Nasal Swabs from Individuals Diagnosed with COVID-19

Comparison of Abbott ID Now and Abbott m2000 Methods for the Detection of SARS-CoV-2 from Nasopharyngeal and Nasal Swabs from Symptomatic Patients

ID NOW COVID-19: Instructions for Use

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

Sherlock Biosciences. Sherlock CRISPR SARS-CoV-2 kit: Instructions for Use; Sherlock Biosciences

Food and Drug Administration

Evaluation of a Lyophilized CRISPR-Cas12 Assay for a Sensitive, Specific, and Rapid Detection of SARS-CoV-2. Viruses

Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays

Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens

Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2

Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2

Detection of low levels of SARS-CoV-2 RNA from nasopharyngeal swabs using three commercial molecular assays

Comparison of SARS-CoV-2 detection from nasopharyngeal swab samples by the Roche cobas 6800 SARS-CoV-2 test and a laboratory-developed real-time RT-PCR test

Comparison of Two Commercial Platforms and a Laboratory-Developed Test for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Comparison of commercial assays and laboratory developed tests for detection of SARS-CoV-2

A Comparison of Five SARS-CoV-2 Molecular Assays with Clinical Correlations

Estimating the predictive value of negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) results: A prospective study

To Interpret the SARS-CoV-2 Test, Consider the Cycle Threshold Value

Joint Statement on the Use of SARS-CoV-2 PCR Cycle Threshold (Ct) Values for Clinical Decision-Making

Clinical Course and Molecular Viral Shedding among Asymptomatic and Symptomatic Patients with SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea

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

Molecular diagnostic assays for COVID-19: An overview

SARS-CoV-2 diagnostics: Some reflections on current assays

Temporal dynamics in viral shedding and transmissibility of COVID-19

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective cohort study

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

Prolonged SARS-CoV-2 cell culture replication in respiratory samples from patients with severe COVID-19

Assay Techniques and Test Development for COVID-19 Diagnosis

High-Throughput Transcriptionmediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2. Diagnostics

CoV-2 RNA STAR Complete Instructions for Use for Emergency Use Authorization (EUA) Only

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by Mass Spectrometry

MassARRAY®SARS-CoV-2 Panel Instructions for Use Multiplex RT-PCR/MALDI-TOF Test Intended for the Qualitative Detection of Nucleic Acid from SARS-CoV-2

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

Potential for False Results with Roche Molecular Systems, Inc. cobas SARS-CoV-2 & Influenza Test for use on cobas Liat System-Letter to Clinical Laboratory Staff, Point-of-Care Facility Staff, and Health Care Providers

Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution

Clinical Evaluation and Utilization of Multiple Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2

Evaluation of the Cue Health point-of-care COVID-19 (SARS-CoV-2 nucleic acid amplification) test at a community drive through collection center

Comparison of the Quidel Sofia SARS FIA Test to the Hologic Aptima SARS-CoV-2 TMA Test for Diagnosis of COVID-19 in Symptomatic Outpatients

Clinical Evaluation of BD Veritor SARS-CoV-2 Point-of-Care Test Performance Compared to PCR-Based Testing and versus the Sofia 2 SARS Antigen Point-of-Care Test

Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst

Antigen-Based Testing but Not Real-Time Polymerase Chain Reaction Correlates with Severe Acute Respiratory Syndrome Coronavirus 2 Viral Culture

Interim Guidance for Antigen Testing for SARS-CoV-2

Foundation for Innovative New Diagnostics. The Impact of Novel Variants of SARS-CoV2 on Diagnostic Testing

Quidel Corporation. Sofia SARS Antigen FIA: Instructions for Use; Quidel Corporation

Veritor System for Rapid Detection of SARS-CoV-2

Orasure Technologies, Inc. InteliSwab COVID-19 Rapid Test Pro: Instructions for Use

ScoV-2 Ag Detect Rapid Test: Instructions for Use

Celltrion DiaTrust COVID-19 Ag Rapid Test: Instructions for Use

Corp. Status COVID-19/Flu: Instructions for Use; Princeton BioMediTech

AACC Practical Recommendations for Implementing and Interpreting SARS-CoV-2 EUA and LDT Serologic Testing in Clinical Laboratories

Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19)

Magnitude and Kinetics of Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Responses and Their Relationship to Disease Severity

Differences in Antibody Kinetics and Functionality between Severe and Mild Severe Acute Respiratory Syndrome Coronavirus 2 Infections

Humoral Immune Response to SARS-CoV-2 in Iceland

COVID-19 Antibody Tests and Their Limitations

Interim Guidelines for COVID-19 Antibody Testing

The National SARS-CoV-2 Serology Assay Evaluation Group. Performance characteristics of five immunoassays for SARS-CoV-2: A head-to-head benchmark comparison

Comparative evaluation of six immunoassays for the detection of antibodies against SARS-CoV-2

Comparison of six commercially available SARS-CoV-2 antibody assays-Choice of assay depends on intended use

Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity

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

MidaSpotTM COVID-19 Antibody Combo Detection Kit: Instructions for Use

Sienna-Clarity COVIBLOCK COVID-19 IgG/IgM Rapid Test Cassette: Instructions for Use; Clarity Diagnostics, LLC

COVID-19 IgG/IgM Rapid Test Cassette: Instructions for Use

SGTI-flux COVID-19 IgG Test: Instructions for Use

Antibody Combo Detection Kit: Emergency Use Authorization Summary

Kantaro Semi-Quantitative SARS-CoV-2 IgG Antibody Kit: Emergency Use Authorization Summary

Neutralization Antibody Detection Kit: Instructions for Use

IgG Test System: Instructions for Use

COVID-19 ELISA IgG Antibody Test: Emergency Use Authorization Summary

Dimension EXL SARS-CoV-2 IgG Test: Instructions for Use

VITROS Immunodiagnostic Products Anti-SARS-CoV-2 Total Reagent Pack: Instructions for Use

Elecsys Anti-SARS-CoV-2: Instructions for Use

Inc. Access SARS-CoV-2 IgM Test: Instructions for Use

LIAISON SARS-CoV-2 S1/S2 IgG Test: Instructions for Use

BioCheck SARS-CoV-2 IgG Antibody Test Kit-Instructions for Use

Vibrant America Labs Vibrant COVID-19 Ab Kit: Emergency Use Authorization Summary; Vibrant America Clinical Labs