Transmission path of COVID19 decoded by genomic technology

Before jumping directly into the transmission pathway of the notorious COVID19, let us know what is genomic epidemiology. This deals with the study of genetic sequences of pathogens to understand their path of transmission.

Process of spreading-

COVID19 is indeed a notorious one which mutates at an average of 2 mutations per month. When someone is exposed, they will incubate the virus  for 5-7 days approx. before becoming symptomatic.  So, we have 7 days from one infection to the next (shown below)

As the transmission happens, the virus will mutate twice in a month (shown below)

With the advancement in technology, it is feasible to sequence the genome of the novel coronavirus. This works by taking a swab from nose and extracting the RNA from the sample to determine the letters of this RNA genome. Each person's coronavirus infection will yield a sequence of 30,000 letters, 'A', 'G', 'C', or 'T'.

Considering the genomes, 'ATTT', 'ATCT' and 'GTCT' , it can be concluded that the infection with genome 'ATTT' lead to the infection with genome 'ATCT' which in turn gave rise to the infection with genome 'GTCT'.

An explanation of the transmission-

Let us consider that the first COVID positive case in US as WA1 (a traveller who has arrived from Wuhan in the US in mid-January)
Also from the Seattle Flu Study, a first positive was found from a sample from Snohomish County (Washington). Let us take this case as WA2.

Interesting features of WA2 case-

The second case in the US who had sought treatment for flu-like symptoms and was sent home on account of a mild disease.
The case was under diagnosis and was later confirmed to be positive.

Surprisingly, the WA2 genome was identical to the WA1 genome except the fact that it has three additional mutations.

Now comes the valid question of 'community transmission'...

Bingo!

WA2 genome is a direct descendant of WA1 genome.
The virus had circulated locally for 5 weeks.(i.e. WA1 arrival in Jan 15 and a second positive case, WA2 being diagnosed in Feb 28).

The Seattle Flu study has screened viruses from all over the Seattle area but the positive case was found in the Snohomish County with cases less than 15 miles apart. This is suggestive of 'continued transmission'.
The above scenario is explained well in the following flowchart-

There is the possibility of WA1 case infecting someone else to the virus in between Jan 15 and Jan 19. It would be difficult detecting the second case as it had mild symptoms or was asymptomatic thereby leading to community transmission.

An inference can be drawn that a person who tests positive may not necessarily have a travel history to and from China or may have come to direct contact with a positive case. This person may not be even taken for testing leading to an error and an outbreak in the Snohomish County before even it was detected.

Interventions to be followed individually-

1. Practice social distancing.
2. Work from home.
3. Avoid touching mouth, eyes and nose with unwashed hands.
4. Cover when you sneeze with your elbow or tissue.
5. Disinfect frequently touched surfaces like door knobs.

Last but not the least,
Do not panic. It gives unwanted stress and anxiety.


For more posts on Covid19, visit the following links-

• From where do new viruses originate?
• In layman's terms- Flatten the curve and raise the line
• COVID19- The scientific side