Testing Virus survival

There are a large number of claims about how the virus that causes covid-19 : the SARS-CoV-2 virus can or cannot survive under certain conditions

For example, can it survive in the sun, on metal, in water etc

Unlike testing for the presence of the virus – which is done with detection of viral RNA, testing for the viability of virus is very much more difficult. Most of the claims – if based on fact at all -are extrapolation from what is known for poliovirus – the standard test virus

To test SARS-CoV-2, it is necessary to culture the virus. consider the question “can the virus survive in swimming pool water?”

To test this we would put a known quantity of virus into standard swimming pool water, and then at some later stage attempt to grow the virus in a cell culture. It can be grown in the Vero-E6 line

https://www.protocols.io/view/culture-of-the-severe-acute-respiratory-syndrome-c-bcduis6w

and it is easy to see which cells have been killed by the virus.

Such sorts of tests need to be undertaken in a highly secure lab – so the virus cannot get out. Australia has only 3 such PC4 (Physical containment labs)

https://apps.who.int/iris/bitstream/handle/10665/311625/WHO-WHE-CPI-2018.40-eng.pdf

China has a few too – one in Wuhan

Developing a Vaccine

It is hoped that a vaccine can be developed for the virus quickly. That may not be so easy

There are some early results suggesting that antibodies to the spike protein of the virus have some promise in protecting cells against infection. Translating this into a vaccine which is safe to administer to millions of healthy people will not be quick

https://www.theverge.com/2020/2/28/21156385/covid-coronavirus-vaccine-treatment-moderna-remdesivir-research

Development of any pharmaceutical needs careful development. Progress occurs through phase 1 (safety) studies, through phase 2 and 3 (efficacy) studies. Research to refine the target population and the optimum dose is required.

Rushing such a thing can lead to problems. It is widely thought that immunization for the “swine flu” in 1976 caused an outbreak of Guillain-Barre´ s syndrome. There were issues with the testing and manufacture in response to the pandemic

https://academic.oup.com/jid/article-pdf/176/Supplement_1/S69/2797707/176-Supplement_1-S69.pdf

That can be contrasted with the careful development of the Gardasil vaccine

http://www.hu.ufsc.br/projeto_hpv/Safety,%20immunogenicity,%20and%20effi%20cacy%20of%20quadrivalent%20human.pdf

which took years of development.

Potentially life saving experimental treatment for desperately unwell patients with no other options is one thing. Giving inadequately tested vaccine to healthy people is another entirely

The diagnostic test

The gold-standard test for Covid-19 is qRT-PCR. This stands for quantitative, reverse transcriptase polymerase chain reaction. In essence this converts viral RNA to DNA and then amplifies the DNA for detection.

There is much written about the shortage of “kits”. These are now available

https://www.biovision.com/coronavirus-sars-cov-2-pcr-detection-kit.html

Unique to a kit is the specific primers to identify the viral gene and the positive control for the disease.

The test subject must first be swabbed and the hope is that if the subject is affected by the disease:

  • He or she will be shedding virus onto the membrane that is swabbed
  • That the swab will pick up the virus
  • That the virus will survive the transport to the lab

Then the RNA needs to be extracted from the swab using a protocol similar to

The cotton tips were stored in 350 µL phosphate buffered gelatin saline (PBGS). For the extraction, the cotton tip was lifted out of the PBGS and placed in a clean microcentrifuge tube. The extraction was conducted using the RNeasy Plus Mini Kit (QIAGEN) following the manufacturer’s instruction for tissue samples.

Habarugira, Gervais, et al. “Mosquito-Independent Transmission of West Nile virus in Farmed Saltwater Crocodiles (Crocodylus porosus).” Viruses 12.2 (2020): 198.

The extracted RNA needs to be processed in a qRT-PCR machine using the kit. Machines are available as 96 or 384 well devices – this is the number of simultaneous tests that can be done.

The test run takes 2-3 hours to do.

There has been some promising development of a new test for the virus known as RT-LAMP https://www.medrxiv.org/content/10.1101/2020.02.19.20025155v1

The new test uses a different enzyme for dna polymerization and does not require thermal cycling. Theoretically, the test could be read by naked eye in the field

Although this is yet to be validated on real virus or virus samples, it is a very positive development. The test could theoretically be done in the matter of hours at the doctor’s surgery