SARS-CoV-2 and Microbiological Diagnostic Dynamics in COVID-19 Pandemic

We have been introduced to "Coronavirus Disease 2019 (COVID-19)" disease with high mortality and transmission rate caused by a novel human coronavirus, in December 2019 and the microbiological diagnosis of the infection has been in the center of the focus to control the pandemic. It is necessary to understand the dynamics of the virus which was classified among the severe acute respiratory syndrome (SARS) related coronaviruses and named as SARS coronavirus 2 (SARS-CoV-2), to manage testing in the right strategy and for interpretation of the results. However, much remains unclear about the virus and the immune response. SARS-CoV-2, which is an enveloped, RNA virus has been shown to attach to the host cell receptor angiotensin converting enzyme 2 with spike (S) protein and membrane fusion is provided by transmembrane protease serine 2 (TMPRSS2) of the host cell. The most commonly used and reliable test for diagnosis of COVID-19 is reverse-transcribed polymerase chain reaction (RT-PCR) performed by using nasopharyngeal swabs or other respiratory tract specimens. Viral RNA is usually detected two three days before the onset of symptoms and in the first week from upper respiratory tract samples. If possible, the lower respiratory tract specimens are preferable in the second week, especially if former PCR is negative and pneumonia has developed. The clinical sensitivity of SARS-CoV-2 RNA tests has been reported around 55-75%. Negative RT-PCR test result does not exclude COVID-19 or SARS-CoV-2 infection. It should also be noted that viral RNA positivity is not an evidence of active or infectious virus. SARS-CoV-2 infection can be also detected indirectly by testing the host specific immune response to the virus. There is an increasing interest in the use of SARS-CoV-2 antibody tests both for the diagnosis and public health surveillance. However, the antibody tests should not be used as the sole test for diagnosis and case management. Antibody tests are valuable tools in seroepidemiological studies. Anti-SARS-CoV-2 IgM, IgA and IgG antibodies have been shown to be detectable as early as 5th-14th days after the onset of symptoms and most of them become positive on the 21st day. False positivity has been reported more frequently with IgM and IgA tests due to low specificity. It was shown that clinical sensitivity of the diagnostic approach increases when RNA and total antibody tests were integrated as co-tests, especially after the second week of the disease. Specificity, sensitivity, positive and negative predictive values are needed to be evaluated with large and standard studies targeting populations with different prevalences. It is also necessary to create evidence with larger seroconversion studies. In this review article, the information and data obtained until today about SARS-CoV-2 and its microbiological diagnosis have been discussed.