Diagnostic Virology and Molecular Methods (PCR, NAAT, Antigen/Antibody Kinetics, Sequencing) MCQs

Microbiology · 33 free questions with answers & explanations.

1. A patient is tested for SARS-CoV-2 infection using RT-PCR on a nasopharyngeal swab. The E gene Ct value is 12, N gene Ct value is 14. Rapid antigen test (RAT) is also positive. The patient is asymptomatic. In this context, the LOW Ct value (Ct <20) indicates:
2. Whole genome sequencing (WGS) of SARS-CoV-2 is performed for surveillance of variants of concern (VOCs). Oxford Nanopore Technology (ONT) is preferred for field deployment compared to Illumina. The key advantage of ONT for outbreak genomic surveillance is:
3. A patient returns from a tropical forest area with fever, myalgia, and jaundice. Serology shows: HBsAg negative, anti-HBc IgM negative, anti-HAV IgM positive. The antibody profile indicates:
4. A molecular lab introduces droplet digital PCR (ddPCR) for hepatitis C RNA quantification. What key advantage does ddPCR have over standard real-time RT-PCR?
5. A patient is diagnosed with SARS-CoV-2 infection by RT-PCR of a nasopharyngeal swab with Ct value of 12. A second patient with mild symptoms has a Ct value of 34. What is the clinical significance of the Ct (cycle threshold) value?
6. A patient presenting 3 days after unprotected sexual intercourse is tested for HIV using a 4th-generation HIV antigen/antibody combination assay (Ag/Ab combo). The result is non-reactive. Which statement best describes this scenario?
7. A 35-year-old man with known HIV is tested for hepatitis C co-infection. Anti-HCV ELISA is negative. However, HCV RNA by PCR (NAAT) is positive at 850,000 IU/mL. What explains this discordant result?
8. In whole-genome sequencing (WGS) of a Clostridioides difficile outbreak investigation, 3 patients on the same ward have isolates with SNP (single nucleotide polymorphism) differences of ≤2. A fourth patient on a different ward has a contemporaneous isolate with ≥30 SNP differences from the cluster. What conclusion is appropriate?
9. In the serological diagnosis of hepatitis A, which marker is FIRST to appear and best indicates acute HAV infection?
10. Next-generation sequencing (NGS)/Whole genome sequencing (WGS) is increasingly used in clinical microbiology. Which of the following is the best application for WGS in routine outbreak investigation?
11. In the diagnosis of HIV infection in infants born to HIV-positive mothers, which test is recommended in the first 6 weeks of life, and why is serology (ELISA) unreliable at this age?
12. Next-generation sequencing (NGS)-based metagenomic sequencing (mNGS) of CSF is performed in a patient with encephalitis of unknown aetiology. The test returns with detection of Talaromyces (Penicillium) marneffei sequences. The patient is from Northeast India. Which clinical sign would strongly support this diagnosis?
13. In real-time PCR for respiratory virus detection, what does the Ct (cycle threshold) value represent, and how does it correlate with viral load?
14. A hepatitis C patient's RNA is detectable by RT-PCR (HCV RNA 1.2×10^5 IU/mL). Genotype testing is performed by sequencing the NS5B and Core-E1 region. Why is genotyping clinically important in HCV management?
15. In a patient with suspected CMV retinitis (HIV-positive, CD4 18 cells/µL), plasma CMV DNA quantification by quantitative real-time PCR shows 48,000 IU/mL. What is the significance of viral load monitoring during treatment?
16. A patient presents with acute febrile illness 5 days post-return from a dengue-endemic region. NS1 ELISA is negative. IgM ELISA is also negative. However, RT-PCR for dengue RNA is strongly positive. How do you reconcile these results?
17. During HIV infection, a patient has a positive 4th-generation antigen/antibody combo ELISA but negative HIV-1/HIV-2 differentiation assay. HIV RNA PCR returns 85,000 copies/mL. How should this result be interpreted?
18. A respiratory sample collected from a ventilated patient with suspected influenza is tested by two methods: immunofluorescence (DFA) returns negative, while RT-PCR for influenza A/B returns positive for influenza A (H1N1)pdm09. What does this discordance most likely reflect?
19. A 28-year-old blood donor tests negative for anti-HCV antibody but the blood bank's HCV RNA NAT is positive. The most accurate interpretation is:
20. In interpreting a hepatitis B serology panel: HBsAg negative, anti-HBs positive (>10 mIU/mL), anti-HBc IgG positive, HBeAg negative, anti-HBe positive. Which clinical scenario does this represent?
21. Quantitative RT-PCR for dengue serotyping is most useful in which phase of the illness relative to symptom onset?
22. In HIV-1 diagnostic testing, a reactive 4th-generation HIV Ag/Ab combination test should be followed by which confirmatory algorithm per current guidelines?
23. Next-generation sequencing (whole-genome sequencing) of influenza viruses from outbreak clusters compared with Sanger sequencing offers the primary advantage of:
24. A 28-year-old woman presents with acute hepatitis. Serological profile: HBsAg positive, Anti-HBs negative, IgM Anti-HBc positive, HBeAg positive, Anti-HBe negative, HBV DNA 10^8 IU/mL. What does this serological profile indicate?
25. A neonate born to an HIV-positive mother is tested at 6 weeks of age. The HIV antibody ELISA is reactive. What is the recommended diagnostic approach to confirm or exclude HIV infection in this infant?
26. During a dengue outbreak, a patient presents on day 3 of fever with myalgia and retro-orbital pain. Which laboratory combination offers the highest diagnostic sensitivity at this stage?
27. A real-time RT-PCR assay is used to detect SARS-CoV-2 in nasopharyngeal swabs. The assay targets the E gene and ORF1ab gene. A sample gives a Ct value of 38 for E gene and is negative for ORF1ab. What does this result most likely represent?
28. Sanger sequencing of the HIV-1 reverse transcriptase gene from a treatment-naive patient reveals an M184V mutation. Which antiretroviral drug is this mutation most commonly associated with, and what is its clinical implication?
29. A patient presents on day 5 of illness with fever, myalgia, and thrombocytopenia. NS1 antigen ELISA is positive but IgM is negative and IgG is negative. What is the most likely interpretation?
30. In real-time PCR, the cycle threshold (Ct) value of a respiratory sample for SARS-CoV-2 is 38. The laboratory's validated cut-off for positivity is Ct ≤40. The clinical team asks about infectivity. The most accurate statement is:
31. A 3-year-old child with suspected viral encephalitis has CSF PCR positive for HSV-2. The MOST appropriate antiviral agent and dose is:
32. Next-generation sequencing (metagenomic NGS) of CSF is sent for a patient with encephalitis whose standard tests are negative. A novel bunyavirus is identified. Which feature of NGS makes it superior to conventional PCR for this scenario?
33. A laboratory receives a serum sample labelled 'day 1 of jaundice' from a patient with suspected hepatitis A. The MOST sensitive test to confirm acute HAV infection is: