Laboratory Testing Methods for SARS-CoV-2 – Key Vocabulary

Vocabulary flashcards covering essential terms, technologies, proteins and concepts discussed in the lecture on laboratory testing methods for SARS-CoV-2.

SARS-CoV-2

The novel coronavirus responsible for COVID-19; a positive-sense single-stranded RNA virus first reported in Wuhan, China in 2019.

COVID-19

The respiratory illness caused by infection with SARS-CoV-2, ranging from mild flu-like symptoms to severe respiratory failure.

RT-PCR (Real-Time Reverse Transcriptase-Polymerase Chain Reaction)

Gold-standard molecular test that converts viral RNA to cDNA and amplifies it in real time for qualitative or quantitative detection.

Limit of Detection (LOD)

Smallest quantity of viral nucleic acid a test can reliably detect; SARS-CoV-2 RT-PCR LOD is <10 copies/reaction.

Sensitivity

Ability of a test to correctly identify true positives; RT-PCR for SARS-CoV-2 shows ≈95 % sensitivity.

Specificity

Ability of a test to correctly identify true negatives and avoid cross-reactivity with non-target organisms.

False Positive

Test result indicating infection when the pathogen is absent, often due to cross-reactivity or laboratory contamination.

False Negative

Test result indicating no infection when the pathogen is present, possibly caused by viral mutations or poor sampling.

Multiplex PCR

RT-PCR format using multiple primer/probe sets to amplify several viral gene targets simultaneously for higher robustness.

RdRp Gene

RNA-dependent RNA polymerase gene of coronaviruses, commonly targeted in diagnostic assays for confirmation.

E Gene

Envelope protein gene of SARS-CoV-2, often targeted for initial high-sensitivity screening in RT-PCR tests.

N Gene

Nucleocapsid protein gene; frequently used as a diagnostic RT-PCR or antigen target.

Nasopharyngeal Swab

High-priority respiratory specimen collected from the upper airway for SARS-CoV-2 detection.

ELISA (Enzyme-Linked Immunosorbent Assay)

Plate-based EIA that detects or quantifies antibodies (IgM, IgG, IgA) or antigens using enzyme-linked secondary antibodies.

EIA (Enzyme Immunoassay)

General category of assays, including ELISA, that use enzyme-labeled reagents to detect antigen–antibody interactions.

IgM

First antibody isotype produced after infection; appears 3–7 days post-symptom onset and indicates recent exposure.

IgG

Most abundant antibody isotype; appears 7–25 days after infection and can persist, suggesting past exposure or immunity.

IgA

Antibody isotype important for mucosal immunity; measured to assess response in respiratory infections.

Spike (S) Glycoprotein

Surface protein giving coronaviruses their corona shape; mediates host cell attachment and entry, key vaccine/antibody target.

Nucleocapsid (N) Protein

Internal protein binding viral RNA; involved in genome packaging and a major antigen for serological assays.

Envelope (E) Protein

Small structural protein involved in virion assembly and morphogenesis of SARS-CoV-2.

Membrane (M) Protein

Structural protein that shapes the viral envelope and participates in virion assembly.

ORF (Open Reading Frame)

Segment of viral RNA that encodes a protein; SARS-CoV-2 genome contains 14 ORFs.

ORF1a/ORF1b

Large genomic regions encoding replicase polyproteins essential for viral transcription and replication.

GISAID

Global Initiative on Sharing All Influenza Data; platform where SARS-CoV-2 genomic sequences are shared.

Point-of-Care Testing

Diagnostic testing performed near the patient, delivering rapid results without centralized laboratories.

LFIA (Lateral Flow Immunoassay)

Portable strip test that visually detects SARS-CoV-2 antigens or antibodies in minutes using capillary action.

Convalescent Plasma

Plasma collected from recovered COVID-19 patients containing neutralizing antibodies, used experimentally to treat severe cases.

SVN (Serum Virus Neutralization) Assay

Laboratory test measuring a patient’s antibodies’ ability to neutralize live SARS-CoV-2 infection in cell culture.

Neutralizing Antibody Titer

Highest serum dilution that prevents virus-induced cytopathic effect, indicating functional immunity.

Isothermal Amplification

Nucleic acid amplification performed at a constant temperature, eliminating thermal cycling and enabling rapid detection.

RT-LAMP (Reverse Transcriptase Loop-Mediated Isothermal Amplification)

Isothermal technique using six primers to amplify viral RNA in <30 min with high sensitivity and specificity.

RPA (Recombinase Polymerase Amplification)

Rapid isothermal amplification method employing recombinase and polymerase to amplify target sequences at low temperatures.

HDA (Helicase-Dependent Amplification)

Isothermal technique that uses helicase to unwind DNA strands for amplification without thermal cycling.

SDA (Strand Displacement Amplification)

Isothermal DNA amplification method relying on polymerase-mediated strand displacement.

NASBA

Nucleic Acid Sequence-Based Amplification; isothermal method designed for RNA target amplification.

CRISPR/Cas13a

RNA-guided nuclease system harnessed for specific SARS-CoV-2 RNA detection via collateral cleavage of reporter molecules.

SHERLOCK

Diagnostic platform combining isothermal amplification with CRISPR/Cas13a for highly sensitive, rapid nucleic-acid detection.

NGS (Next-Generation Sequencing)

High-throughput sequencing technology that reads the full ~30 kb SARS-CoV-2 genome for surveillance and mutation tracking.

Biosafety Level 2 (BSL-2)

Laboratory containment level suitable for routine SARS-CoV-2 diagnostic work with precautions like unidirectional airflow.

Biosafety Level 3 (BSL-3)

High-containment laboratory required for culturing live SARS-CoV-2 and performing virus neutralization assays.

ACE2 (Angiotensin-Converting Enzyme 2)

Host cell receptor in lung epithelium that the SARS-CoV-2 spike protein binds for cell entry.

Limitations of Antibody Tests

Include variable timing of seroconversion, potential cross-reactivity, unknown duration of immunity, and risk of false results.

Mutation Impact on Diagnostics

Genomic changes in viral targets can reduce primer/probe binding, leading to decreased test sensitivity or false negatives.

Primer Cross-Reactivity

Undesired binding of PCR primers to non-target organisms, causing inaccurate (false-positive) amplification results.

Conserved Viral Region

Genomic segment with low mutation rate, preferred for designing robust diagnostic primers and probes.