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Genomic technologies for tracking COVID-19

Timeline to show rate of progress to develop genomic technology for the COVID-19 pandemic
© COG-Train

As the SARS-CoV-2 virus spread around the world, and more suspected cases of COVID-19 were emerging, there was a significant need for a diagnostic test with high accuracy.

Genomic technologies like sequencing and polymerase chain reaction (PCR) are used to study and identify an organism’s “genetic signature”. You will learn more about these in the next activity. Sequencing was used to determine the genome of SARS-CoV-2. Once this genome sequence was available, a test could be developed to look for the presence of SARS-CoV-2 in a given sample. The PCR test uses a specific probe (primer) that will only give a positive result in the presence of the SARS-CoV-2 genome.

Figure 1 depicts the timeline of the early outbreak response to the new respiratory infection that emerged in 2019. The pathogen was identified as a virus within a week, tests were developed and deployed that would have been simply impossible without the power of genomic technologies. Once the first sequences of the new virus nCoV (later classified as SARS-CoV-2) became publicly available in early January 2020, it was possible to quickly design the primers for the first PCR tests.

Timeline of PCR testing. 31 December 2019: the first recorded cases of an unknown pneumonia are reported in Wuhan, China. 7 January 2020: China identifies the source of the pneumonia is a novel coronavirus. 12 January 2020: the novel coronavirus SARS-CoV-2 sequence is disseminated to WHO to share around the world. Mid January 2020: Primer design of the RNA virus for PCR testing and first PCR tests for detection of new cases of Covid-19 virus. 21 January 2020: First detected case in North America (USA). 24 January 2020: First detected case in Europe (France). 30 January 2020: WHO declares a public health emergency of international concern. 14 February 2020: First detected case in Africa (Egypt). 24 February 2020: First detected case in South America (Brazil).

Figure 1 – Timeline of SARS-CoV-2 PCR test development

With accurate diagnostic tests, scientists were able to define the reproduction number (R) of SARS-CoV-2. The R number is the average number of additional individuals infected (secondary infections) produced by a single infected individual. An R value of “1” indicates that one infected individual will infect one other person. At an R value of “2”, one infected individual will infect two more individuals. Values lower than “1” indicate that infections are slowing – an R value of “0.5” indicates that for every two infected individuals only one additional infection occurs.

The infection growth rate shows how quickly numbers are changing by the day. It is an approximate percentage change in the number of newly infected individuals. If the growth rate is bigger than 0, the outbreak or epidemic is growing, and if the growth rate is less than 0, the epidemic is shrinking.

Both R values and growth rates are useful for the definition of outbreak, epidemic and pandemic. Comment below your thoughts on what the definitions for COVID-19 may have been like without genomic technology, or if the technology took longer to develop.

© COG-Train
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The Power of Genomics to Understand the COVID-19 Pandemic

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