Laboratory diagnosis of covid 19 disease

This presentation is helpful for MBBS/BDS/Paramedical students.
It is also helpful for Junior residents of different branches.

1. Laboratory diagnosis of COVID-19 Dr Adil Raza Associate Professor , Department of Microbiology, JNMC, AMU, Aligarh

2. Coronavirus disease 2019 (COVID-19) is a severe acute respiratory infection caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). The disease primarily spreads via close contact of respiratory droplets generated by infected individuals

3. Sample collection

4. Adequate standard operating procedures (SOPs) should be followed before collecting any specimen, packaging, storage and transport.

5. Samples to be collected Upper respiratory specimens Oropharyngeal swab Nasopharyngeal swab Anterior nasal swab Lower respiratory specimens Sputum BAL Endotracheal aspirate Other specimens Stool Blood Paired serum Lung

6. Viral Transport Media (VTM)

7. Sample collection Nasopharyngeal swab Oropharyngeal swab Anterior nasal swab

8. Normal Anatomy

9. Nasopharyngeal Swab

10. Anterior nasal swab

11. NOTE Calcium alginate and cotton swabs should not be used as these are inhibitory to viruses. Only dacron and polyester swabs should be used Wooden stick should not be used. Temperature should be maintained 2 to 8 C during transport, if sample delivery is assured within 5 days. If is more than 5 days it should be -70 C.

12. Laboratory testing for COVID-19 virus Nucleic acid amplification tests (NAAT) Serological testing Antigen detection Viral sequencing Viral culture

13. Molecular (rRT-PCR) tests have generally targeted a combination of the following genes: Envelope (E) RNA dependent RNA polymerase (RdRp) Nucleocapsid (N) Open reading frame 1ab (ORF 1ab) Nucleic acid amplification test (NAAT): rRT PCR

14. Sampling Nucleic acid isolation RT Real time PCR amplification S w ab RNA cDNA PCR Figure: General work flow

15. Test interpretation (WHO): Screening test (+) and confirmatory test (+): positive for COVID-19 (SARS-CoV-2 detected). Screening test (+) and confirmatory test (-): negative for COVID-19 (SARS-CoV-2 not detected). Screening test (-) and confirmatory test (-): negative for COVID-19 (SARS-CoV-2 not detected). Screening test (-) and confirmatory test (+): retest or refer to a reference laboratory for additional testing.

16. Based on the detection of IgM/IgG antibodies. Antibody test results are especially important for detecting previous infections in people who had few or no symptoms. Cross reactivity to other coronaviruses can be challenging. Not recommended by WHO or CDC for diagnosis. Serological testing

17. Figure: Variations in the Levels of SARS-CoV-2 RNA, IgM and IgG after infection.

18. Antigen detection COVID-19 Antigen test is a lateral flow immunochromatographic assay intended for the qualitative detection of the nucleocapsid protein antigen from SARS-CoV-2 This test is authorized for use at the Point of Care (POC).

19. Antigen detection Negative results should be treated as presumptive, and do not rule out SARS-CoV-2 infection. Additional confirmatory testing with a molecular test for positive results may also be necessary

20. Viral sequencing Can be useful to monitor viral genome mutations that might affect the performance of medical countermeasures, including diagnostic tests.

21. Viral culture Not r e c ommende d as a r outi n e diagn o s t i c procedure. Human airway epithelial cell lines were used for the initial isolation of the virus.

22. Conclusions Early diagnosis is the key for prompt management of COVID-19. Serological and molecular assays together will further strengthen the diagnosis of SARS-CoV-2. Laboratory networking is the need of the hour for real-time diagnosis of COVID-19