[Publication date of latest article cited: July 21, 2022]
Like many viruses, coronaviruses can take several forms: whole, viable viruses, called virions, or incomplete virus particles. The virions can enter cells and get them to replicate more viruses while destroying the cells. But the virus particles cannot do that. Scientists and clinicians tested for these viruses most commonly with samples from nasopharyngeal swabs (which have a moderate positive rate) and less often with bronchoalveolar lavage fluid, rectal swabs, and sputum (higher positve rates), and oropharyngeal swab, feces, blood samples, and urine (lower rates). They used polymerase chain reaction (PCR) tests to search for the viruses’ genomes, which are made of ribonucleic acid (RNA) (Abasiyanik et al.; Böger et al.; Bwire et al.). The different PCR methods include:
- real-time polymerase chain reactions (RT-PCR)
- reverse transcriptase polymerase chain reaction (also called RT-PCR)
- quantitative PCR (called qPCR).
The advantage of using this high tech equipment is that it can rapidly find and identify tiny amounts of viral RNA. But it identifies the RNA inside infectious whole virions, antibody-neutralized non-infective viruses, or non-infective particles with genetic material. These tests cannot distinguish between the infectious and non-infectious virus parts (Fontana et al.; Joynt; Katz; Liotti et al.; Morrow et al.; Sethuraman et al.). The PCR cycle threshold value (Ct) indirectly indicates the viral load: high Ct value shows low viral RNA quantity, and vice versa (National Centre for Infectious Diseases). Testing asymptomatic cases at a wrong time often results in false negatives (Zhang Z, Bi Q, et al.). So the most of the following studies indicate that SARS-CoV-2 viruses are probably transmitted by saliva, mucous, blood, feces, urine, air, and surfaces. They cannot prove it completely, but well enough to take action to prevent transmission.
Sometimes scientists used more definitive tests of culturing whole virions in cells. This is more difficult and time-consuming, but they prove that the viruses could transmit to and infect cells. (Arons et al; Kujawski et al.; Santarpia, Herrera, et al.; Santarpia, Rivera, et al.; van Doremalen et al.; Wölfel et al.; Zhu N, Zhang D, et al.). In many of the studies cited in these web pages, scientists did more thorough studies to find if transmissible whole virions are in each body fluid or location (Adenaiye et al.; Brosseau; Fontana et al.).
Scientists also looked at SARS-CoV-2 with electron microscopy. Samples from infected people’s airways were fixed, embedded in resin, sliced, and observed, showing the spherical 60 – 140 nm diameter virions both inside and outside human cells (Nazaroff; Zhu N, Zhang D, et al.). These electron-based imaging techniques included cryo-electron tomography, X-ray crystallography, and single-particle cryo-electron microscopy (Saville et al.), and transmission electron microscopy (TEM) (Santarpia, Herrera, et al.).
Others tested for antibodies to SARS-CoV-2 using Enzyme-Linked Immunosorbent Assay (ELISA). The advantage of these is finding infection histories both during and after active infection. Their disadvantages are inabilities to detect during presymptomatic and early symptomatic periods, and variability after symptoms (Sethuraman et al.) Some discussed using positive antibody test results as certification for allowing previously-infected people to resume more normal activities, called “immunity passports.” The advantages of this are allowing those individuals more freedom to work and improve the economy (Brown et al.). Disadvantages are: inaccuracies and variability of tests; and creation of incentives to develop over-sensitive tests with false positives. Some people might try to get infected, which might cause them to get seriously ill or spread infection to others (Hall et al.; Persad et al.; World Health Organization “Immunity…”).
Scientists and clinicians also sometimes used antigen tests for patients and in surveys, because they cost less time and money than PCR, and can be almost as accurate. For example, one point-of-care antigen test had a specificity of 99.9%, and sensitivity ranging from 77.3% to 100% (Muhi et al.). Another rapid antigen detection (RAD) test had low sensitivity, but high concordance with viral culture tests (87%-95%), showing it could less-expensively estimate SARS-CoV-2 viability (Uwamino et al.).
In addition to those techniques testing infection, scientists tested for ways SARS-CoV-2 could potentially bind to cells using Enzyme-Linked Immunosorbent Assays (ELISA), Western blotting, immunohistochemistry (IHC), and immunocytochemistry (ICC) (Liu Y, Wu Q, et al.; Santarpia, Herrera, et al.; Zhu F, Zhong Y, et al.).
Infected people’s transmission’s modes of SARS-CoV-2 have not been completely proven; for each infected case that probably was infected via one mode, that person might have been exposed to another mode (Klompas et al.; Lee E, Wada et al; WHO “Transmission of SARS-CoV-2”). But large numbers of studies have found these transmission modes, and how to prevent them, that people can use the recommendations to protect themselves.