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

COVID19- The scientific side

This post is all about the data-based findings of well known medical journals explained in lucid words. The objective behind writing this is to enlighten the common man regarding the insights of the virus. 

Pioneering study in Cell Bioscience, published in March 16,2020 - This is a high quality study which made a major difference in medical policy setting. The study has set the stage for control & management of COVID19.

The Cell and Bioscience Journal- Biomedcentral

The highlights are:

• An attack rate of 83% within the family is alarmingly high, indicating the high transmissibility of SARS-CoV-2 (also called COVID19). 
• The clinical manifestations of COVID-19 with more systematic symptoms are seen in older patients. 
• Transmission of SARS-CoV-2 from asymptomatic carriers to others.
• The presentation of diarrhea shows the possibility for gastrointestinal involvement in SARS-CoV-2 infection and fecal–oral transmission.
• It is transmissible in tertiary and quaternary spreading in humans.
• The epidemic doubling time of COVID19 is about 6.4 days.
• Patients with mild and unspecific symptoms are also difficult to identify and quarantine because the absence of fever in COVID19 is more frequent (12%) than SARS and MERS. So, surveillance method by fever detection cannot be the only determining factor for a person to be COVID +ve.

Now the big question arises.

How it should be treated and what treatment options should be made available?

COVID19 is a self-limiting disease in 80% of patients. Severe pneumonia occurred in only 15% of population.
As of now, potential drugs which are proven to cure COVID19 are not available but an Ebola drug named Remdesivir may be promising. Severity of disease, viral replication, and lung damage were reduced in case of MERS which paves a way for the testing of the drug in COVID19.

Other antiviral agents which calls for further clinical investigation include ribavirin, lopinavir, ritonavir, interferons, chloroquine and Arbidol. However, the side effects of these drugs cannot be ignored. Type 1 interferons are beneficial at an early stage of infection but administratoj at a later stage carries a risk of worsening the cytokine storm (an overproduction of immune cells in the lungs) and increase inflamation.
In case of steroids, the window in which steroids might be beneficial to COVID19 patients is very narrow. Steroids can only be used when Covid19 has already been eliminated by immune response. Otherwise, Covid19 replication will be boosted leading to an increased risk of nosocomial transmission and secondary infection (for example, fungal infection in some Wuhan patients). 

Are inactivated vaccines a viable option?
Inactivated vaccines are vaccines consisting of virus particles, bacteria or other pathogens that have been grown in culture and then lose disease producing capacity.

The chance that COVID19 will become endemic in some areas (a disease which is maintained at a baseline level in an area without external inputs) or even pandemic has increased in view of its high transmissibility, asymptomatic, high number of patients with mild symptoms. This calls for the development of vaccines. 

Inactivated vaccines are one major type of conventional vaccines that can be easily produced and quickly developed but there are concerns of antibody-dependent enhancement of viral infection and safety issues.

More updates will be posted until next development.

Till then, #Stayathome, #Staysafe and help the world #Flattenthecovidcurve

In Layman's terms- 'Flatten the curve and raise the line'

Nowadays, whenever the term 'coronavirus' is typed in a search engine box, 'Flatten the curve' is generated. 

Do you agree?

The only solution to prevent the spread of the notorious COVID19 is appearing in bold and capital urging each one of us to participate actively to accelerate the fight against the virus. Not only search engines, even social media like Twitter, Facebook are full with graphical representations explaining the following facts,

1. What is meant by flattening the curve? 

2. How to flatten the curve?

3. Raise the line of hospital capacity and what are the measures to be taken.

What is meant by 'Flatten the curve'?

Known as the best currently available strategy to curb the spread of COVID19 infection. It depicts the containment needs of the virus.

The pandemic curve is used to visualize when and at what pace the new infected cases are recorded in the world. 

Understanding the curve -

X-axis : The height of the curve represents the potential infected cases (will vary country-wise)

Y-axis : The time duration.

The line cutting across the middle shows the healthcare system capacity (will vary country-wise).

A rapid spread of COVID-19 will lead to a spike of the new cases hence an exponential growth of the curve will be observed.

Healthcare system capacity - The faster the infection curve rises, the faster the healthcare system will be overloaded beyond its capacity to treat people thereby raising a serious concern. ICU beds are limited everywhere hence an overload of cases will force the patients to go without the facility. Emergency rooms (ERs) in hospitals already operate close to capacity, without coronavirus cases. Adding a sharp spike in the cases will add on to the difficulty in proper patient management.

Flatten the curve means to minimize the surge of the new cases and making it easier and possible for the healthcare to manage and treat patients.

Help the world flatten the curve. 

A flatter curve signifies the following factors :

• Same number is getting infected but for a longer duration. 
• Slower infection rate and less stress on the healthcare system.

What are the interventions undertaken worldwide?

As vaccines are yet to come in another 18 months and proven medicines are not available, containment measures becomes a mandate. These include social distancing, self-quarantine, community lockdown, stop attending social gatherings, work from home, online classes for children and stay at home. Avoid partying around, swimming pools, gyms, malls,  and restaurants.

On an individual level, washing hands for 20 seconds with soap and water, sanitizing the external contact points regularly, going on a self-quarantine for 14 days on arriving from abroad and other possible ways of keeping yourself isolated to reduce the speed of transmission have to be followed judiciously.

Now its time to raise the dotted line (save our bravehearts) -

Keep the coronavirus from infecting the healthcare workers who are the true bravehearts.
Remember, they are at the greatest risk of exposure. We do not want our countries to run out of doctors and nurses. They stand right behind us as the line of defense. How do we keep them seeing patients rather than becoming patients?

• Firstly, help them by staying at home.
• An adequate supply of full-body protective gear including goggles, complete head coverings, N95 particle-filtering masks or surgical masks and hazmat-style suits is a must.
• Mobilizing our industrial capacity to meet the needs of our healthcare workers like masks, ventilators, PPEs , CPAP oxygen tent for the patients and many more.

 This is really a critical pandemic which has totally put the world on a strike.

For the sake of humanity, we need to act vigilantly on both flattening the curve and raising the line.

Stay home. Stay safe. 

For other posts on the origin of new virus and how to spend a quality time at home during self-quarantine phase click on the following links:

From where do new viruses originate?
The phase of self-quarantine: How to face the stay home challenge?

COVID19- From where do new viruses originate?

The world is talking of the virus which is new to the human species, hence COVID19 does not need an introduction. It has become so prominent in our lives that post-dialing the numbers of our loved ones, COVID19 stands at the forefront of discussion. I am sure that you will agree to it!

Where do new viruses come from? Do you have an idea of 'Spillover infection'?

The term 'coronavirus' was coined keeping in mind, the crown-like protein spikes on the membranes of the virus. The spikes are selectively sticky but becomes more sticky when they bump onto specific molecules found on the outsides of animal cells.

The crown-shaped spike protein on the virus membrane 

Different animal species have different types of molecules on the outsides of their cells. Because of this, bird infecting coronavirus usually cannot infect humans.
Unfortunately, the natural process of 'Evolution' can help the virus overcome this problem.

When virus genes are being copied during reproduction, mutations can occur either by error or recombination and re-assortment. 

Mutation that changes the shape of the viral spikes renders the virus useless as their spikes do not stick to any host cells. On rare occasions, a mutation may happen to allow a virus to attach to a new host species. If that modified virus is lucky enough to encounter the new host, 'infection' can occur. This is called 'Spillover infection'. The virus has spilled over into a new host.

What happens next?

Inside the new host, if the virus can survive and reproduce long enough, natural selection will promote any new mutations that will help it better spread and reproduce.

Positive mutations will help accumulate over multiple generations, negative ones are discarded until...

BOOOOM! A new epidemic is on the news.

There is a long and slow burn before the explosion (Slowly evolving spillovers have been the cause of almost every major outbreaks in history).

Timeline and its origin:

SARS virus - In early 2000s, a coronavirus that used to infect only bats appears to have spilled over into civets. Further mutation happened and the modified virus spilled over into humans known as SARS (Severe Acute Respiratory Syndrome).

MERS virus - A coronavirus (Middle East Respiratory Syndrome virus) from camels also spilled over into humans causing many deaths.

 COVID-19 might just be one more example of 'Normal Evolution'.

The entire world is now connected through international flights, you realize that What happens in Vegas does not actually stays in Vegas.

Comments are most welcome.

The phase of self-quarantine- How to have a productive and quality time at home?

Right now, 'COVID-19' is dictating movement of people across the globe that resulted in travel restrictions.

As a result, there will be a gap in my frequency for blogposts. 

Self-isolation at home is the sole solution.

The current phase well-defined by:

'There are decades where nothing happens and 

 There are weeks when decades happen' - Vladimir Lenin

In his 2015 TED talk, Microsoft magnate, Bill Gates underlined how the next big disaster to strike humanity would be due to microbes and not a nuclear war. The world would be under-prepared for the strike.

This is not negativity or a way to imbibe fear within us. Instead, let us take ample opportunities to spend time on our development and indulge in some productive activities.

Enough of COVID-19!

Now coming straight to the point of my post today.

How am I making a perfect utilization of the quarantine phase?

1. As the first step, for a while, I have stopped reading and watching news related to the pandemic which reduced my  panic hence less stress & anxiety. In addition, no discussion on COVID-19 is taking place in the family too.

2. I am spending an adequate time with my family (which otherwise was not possible in case of working men and women).

3. In the process of learning new recipes from YouTube; preparing the same; pampering the taste buds. Trying my best to get promoted to a 'Better' chef than what I was yesterday.

4. Painting and sketches- Being an ardent lover of painting & sketching, I have made sure to give 30 mins to my art paper. The papers were piled up in some corner, dusty and getting neglected. A rendezvous with my art paper was fixed during the quarantine period time.

Thanks to COVID-19!

Two of my paintings/sketches are given below for the first two days of quarantine:

5. Online courses - I have enrolled myself in two courses on www.udemy.com related to my passion and field of work to enhance my skills & knowledge. One of them is Google Analytics and the other being Time Management.

6. Read books - Do you have any books which are left aside unread? Or some unfinished reads?  Friends, this is the right time to finish the unfinished. Do not let your books lie on shelves, choose one and start reading. 

I am a hungry reader and have shortlisted books for this period.

Recommended books to read, in case you are interested,

• The Fifth Beatle - the Brian Epstein Story
• Atomic Habits by James Clear
• Sapiens by Yuval Noah Harari
• This Beautiful Life by Helen Schulman
• Guru Dutt by Arun Khopkar
• The Free World by David Bezmozgis
• Monsoon Feelings : A history of emotions in the rain 
• The Angel's Beauty Spots by K.R. Meera

7. If you are an avid writer, then pen down your thoughts in a diary. Make a list of things which you want to accomplish in your lifetime known as bucket list.

As a travel blogger, I keep visiting places and share my experience with the world through my blogs. 

8. Also a music lover, playing harmonica was one of my listed dreams. So why not this time? I am also learning how to play a harmonica.

8. Amidst all the mental de-stress procedures, now let us turn our heads towards our physical well being. Workout for at least 30 minutes in the form of zumba, cardio, jogging or free hand exercises. Choose whichever you like to lift up your morale.

9.  Last but not the least, sing, dance and play games.

For the time being, why not focus on being a better person than yesterday.

Why not think that God has given us a chance to self ponder?

Needless to say, stay at home and help the world to 'Flatten the COVID-19 Curve'.