Tracking the genetic passport of COVID-19

Implications of different strands of Coronavirus

In late July, scientists claimed that there were six strands of the Coronavirus that caused COVID-19, then there was talk of eight. Sudden outbreaks in the US and Europe have caused speculation that deadlier, infectious strains of the virus may be circulating, with some early studies hinting at as many as 30 kinds of the virus. Coronavirus infections surpassed the 400,000 mark in the first six months alone, exemplifying its formidability as a fast mutating virus. Since the original outbreak in Wuhan, the Coronavirus has infected over 47,428,000 claiming over 1,213,000 lives. Over 11,000 cases have been reported locally with 23 fatalities. Could genetic sequencing better prepare health authorities to deal with the pandemic?

Sequencing could also help to identify which strands are more tenacious and which are dying out. In turn health authorities could use such information to learn how to mitigate the spread of COVID-19, and which medical interventions work best. This is where open-source projects such as NextStrain.org comes in. NextStrain uses genetic sequences of viruses collected from patients, contributed by health authorities from around the world, to track the evolution of epidemics in global maps and phylogenetic charts, the family trees for viruses.

According to Professor Benjamin Howden at the Doherty Institute, Australia, quoted in The Sydney Morning Herald, sequencing or tracking the virus’s ‘genetic passport’, in other words tracing from where a specific strand had been ‘imported’, has now revolutionised how health authorities fight pandemics, and will become critically important in countries that have recently eased out of lockdown. For example, in circumstances where clusters emerge with no clear source, looking for connections in the genetic code of the virus could make contact tracing much more efficient in a country like Sri Lanka where many have been repatriated from countries where COVID-19 is wreaking havoc.

According to health authorities the new strain of the virus, which originated in a new cluster in Minuwangoda, is far more virulent compared to the first wave between March and April. With the virus spreading fast, detected in practically all districts, several hundred patients are reported each day, according to Chief Epidemiologist Dr Sudath Samaraweera.

The latest mutation is unique in its ubiquity, leading to conflagrations in Europe, US and, now Asia. Laboratory experiments suggest that the new strain, officially designated D614G, and familiarly known among scientists as ‘G’, because it has lead to the genetic instruction for the amino acid glycine (G) to be altered, is more infectious and has a higher viral load, making people who have contracted this particular strain more likely to spread it. In fact, the new strain is thought to be as much as 10 times more infectious. The ‘G’ strain, which first appeared in January, is found in the dominant variant of the coronavirus, while the ‘L’ strain that originated in Wuhan is gradually disappearing. The ‘G’ strain, associated with outbreaks in Europe and US, is believed to have originated in Germany, according to NextStrain cofounder Trevor Bedford, a computational biologist at the Fred Hutchinson Cancer Research Center in Seattle, quoted in National Geographic. But nothing is definitive when it comes to the Coronavirus, warns Bedford. Researchers are forced to strike a high-stakes balance between disseminating information quickly and assuring their accuracy.

Scripps Research virologist, Hyeryun Choe, quoted in The Washington Post article titled, ‘This Coronavirus mutation has taken over the world. Scientists are trying to understand why’, points out that, fortunately the ‘G’ strain does not make patients any sicker, despite its higher viral load and any vaccine based on the original strain would be just as effective on the new strain.

Researchers claim that different types or variants of COVID-19 maybe distinguished by a unique set of symptoms. Most pronounced symptoms of COVID-19 include fever, shortness of breath, fatigue, muscle aches, headaches and of course a persistent cough. But several symptoms were later included in diagnostics, as they were increasingly reported by COVID-19 positive patients, such as a loss of sense of taste and smell, the medical terms of which are ageusia and anosmia, respectively. A study by the UK’s King’s College London has grouped these into six ‘symptom clusters’, with a spectrum of breathing difficulties.

1. Flu-like with no fever:

Headache, loss of smell, muscle pains, cough, sore throat, chest pain, no fever.

2. Flu-like with fever:

Headache, loss of smell, cough, sore throat, hoarseness, fever, loss of appetite.

3. Gastrointestinal:

Headache, loss of smell, loss of appetite, diarrhoea, sore throat, chest pain, no cough.

4. Severe level one, fatigue:

Headache, loss of smell, cough, fever, hoarseness, chest pain, fatigue.

5. Severe level two, confusion:

Headache, loss of smell, loss of appetite, cough, fever, hoarseness, sore throat, chest pain, fatigue, confusion, muscle pain.

6. Severe level three, abdominal and respiratory: Headache, loss of smell, loss of appetite, cough, fever, hoarseness, sore throat, chest pain, fatigue, confusion, muscle pain, shortness of breath, diarrhoea, abdominal pain.

According to the King’s College research, quoted in the World Economic Forum article titled ‘COVID-19: Could your earliest symptoms predict how ill you’ll get?’, earliest symptoms might help predict how sick someone could become with the progress of the disease. According to the study 16 percent of group 1 patients were admitted to hospital, while almost half of those in group 6 were. Those of groups 4,5 and 6 were older patients with underlying health conditions ranging from diabetes to obesity.

As such, Charles Chiu, professor of medicine and infectious disease at the University of California, San Francisco School of Medicine, in USA Today article, ‘8 strains of the coronavirus are circling the globe. Here’s what clues they’re giving scientists’, says that it is unlikely that the different symptoms are related to people being infected with different strains of the virus.

In more positive news, the Coronavirus mutates at a fairly steady rate, approximately 20 mutations per year, according to Professor Francois Balloux, who heads the genetics institute at University College London, quoted in The Sydney Morning Herald. It is not as prolific as influenza, a virus that mutates at such an alarming rate that it requires an updated vaccine every season to keep up with all its mutations. Moreover, research has found that no one strain of the virus is more deadly than another.

Strains are also unlikely to grow more lethal as they evolve. In fact, Australian Government agency, Commonwealth Scientific and Industrial Research Organisation (CSIRO), dangerous pathogens lab, Professor Seshadri Vasan believes that, since a virus’s main objective is to spread and not kill off its hosts, over time the Coronavirus will become milder, the way past pandemic flu strains have, as they adapted to their new host. But it could become a recurring phenomenon, much like influenza, at least until vaccination programmes stamp it out. On the bright side, a virus that mutates comparatively slow is unlikely to change to evade a vaccine, opines scientists. (SP)