Predicting Coronavirus 19nCoV (now SARS CoV-2).
Kris Vette was Border Controller for New Zealand’s H1N1 (Swine Flu) Pandemic response in 2009. Previously he managed General Medicine and Infectious Diseases at St Georges Hospital in London during the 2003 SARS outbreak. He is a Clinical Best Practice development expert and now runs an Emerging Technology and Genomic Medicine Consultancy.
The new coronavirus, 19nCoV (now named SARS CoV-2), which causes the disease COVID-19, was notified to the World Health Organisation (WHO) by China on 31 December 2019 as a “pneumonia of unknown cause”. It appears that it will be a significant global event with serious effects. This article gives an overview of what we know, what we should do and what outcomes are most likely.
New viruses threaten the global population every 10 to 50 years. In truth, viruses and bacteria surround us, in the millions every day. Our immune systems are in a continual ‘to and fro’ battle with them, sampling their genetic code and using that information to build up our own immune systems.
Every so often a new or ‘novel’ virus will evolve to breakthrough our individual defences or even our species level immunity, having evolved either from within the human-host population of viruses or jumped across from another species. When a virus infects us it injects itself into our cells. It then uses its own RNA to take over and replicate itself many hundreds of times within our freshly corrupted cells. This has been going on since the origin of life on Earth. But new viruses pose problems to society as we haven’t been exposed to them before. We can’t predict how fast they will spread or how deadly they will be.
Our own immune systems are pretty good at ‘sampling’ new microorganisms and learning their signature. Part of that ‘signature’ are the protein markers they have on their surfaces. Once the surface markers are identified, then our own White Blood Cells (T-Cells and B-Cells in particular) build up and can target them. The Killer T-Cells mount an attack. Over time our body builds up defences against the invaders and our cells ‘remember’ that particular virus.
When a ‘novel’ (new) virus emerges, it causes concern and sometimes extreme stress among us. Often we do things like ‘panic buying’ because we tend to predict worst case scenarios. We haven’t had experience with that particular virus so the unknowns create fear.
Over time viruses burn themselves out, merge into the normal viral population or hide away only to rise up again a few years later (like the Ebola virus). But novel viruses can take a deadly toll while playing out their natural course.
Any epidemic or pandemic has a start, a rise, a peak and a fall. How long that takes relates to two things;
1. Transmissibility Rate [Basic Reproduction Number], known as ‘Ro’ (pronounced ‘R naught’) — that is how many other people get infected for every one person that has it. If Ro = 2, that means two people will get infected for every one person that already has the virus.
2. Mortality Rate — how many people die, out of everyone that has been infected.
These measures are hard to predict at the beginning of an outbreak but can be modeled as more data comes in. They also change as infection control measures and medical intervention become more effective.
For this COVID-19 outbreak, caused by the virus SARS CoV-2, we can look at these two measures and also take a guess at the global peak (from a mix of predictions by WHO, Nature Medicine, Lancet published studies, London School of Hygiene and Tropical Medicine and JAMA, references available).
COVID-19
Transmissibility (Ro): 2.4 people will get infected from every one that is infected. Note the actual figure could end up being lower depending on effectiveness of the control measures put in and the final numbers infected. Transmissibility (for COVID-19) of 2.4 is significant. Note the Spanish Flu was 1.8.
Mortality Rate: Estimated to be 1% to 2% (of those infected) — this varies according to age and illness or immune system strength. The mortality rate is likely to be higher if you are older or sicker (just like the seasonal flu). For the over 80 year old group it is possibly around 9–10%. So 90% of people over 80 that get infected will recover.
Global Peak: Very hard to predict as it is partially related to the season and hemisphere. Hotter climates can fair better as viruses are partially inhibited in warm weather. We don’t know enough about the SARS CoV-2 virus yet to know if it can be slowed by warmer weather. Some pandemics come in waves that relate to containment or viral mutation. The 1919 Spanish Flu had at least two significant waves. Lower and slower peaks are what we need.
One model for the current outbreak predicts a peak around late March or April 2020 with a decline of two to three months after the peak (modelling by London School of Hygiene and Tropical Medicine) — but that estimate could end up being out by a month or even more. It is also likely to have a few peaks as it hits different countries and continents.
Is this the same as Seasonal Flu?
No, this virus (SARS CoV-2) is a new virus for humans so it is harder to predict the actual course. It is more transmissible and has higher mortality than seasonal flu. Additionally we don’t yet have any mass-produced vaccines that work. Its eventual outcome in terms of total numbers affected is likely to be a lot higher than even a bad flu season (and remember the flu is nasty).
How does this compare with other major outbreaks in history?
Influenza Pandemics have been noted in writing since Greek times but the first widely accepted report in medical literature comes in the year 1580.
Remember ‘Transmissibility’ is a measure of how easily the virus spreads. The higher the number the more spread through the population it will have.
The current COVID-19 has a Transmissibility (Ro) of 2.4.
The 1919 Spanish Flu Pandemic of 1919 Transmissibility (Ro) was 1.8.
The Spanish Flu was by far the worst pandemic in recent history and actually originated in the United States, on a Maryland Farm. It was transported to Europe by troops heading to the First World War. It’s Mortality Rate was around 3% and cruelly hit the world at the end of the First World War. It killed a vast number of people, incredibly calculated to be 50 million people or possibly more. While we do have rapid air travel today, which acts as a rapid vector of spread we do also have other mitigating factors. Our infection control measures, medical treatment and understanding of infectious disease transmission are better now. We would expect a far better outcome now than in 1919.
The 1957 Asian Flu Pandemic Transmissibility (Ro) was 1.65.
The 1968 Hong Kong Flu Pandemic Transmissibility (Ro) was 1.8.
The 2009 Swine Flu Pandemic (Ro) was 1.46.
Normal ‘Seasonal Flu’ Transmissibility (Ro) is on average about 1.3.
Measles by comparison is highly infectious, with Transmissibility (Ro) at 12–18.
Will it stress health systems?
Yes, definitely in developing countries and even in developed countries. Health systems typically run at capacity during the winter months. That means that hospitals and Intensive Care Units (ICU’s) don’t usually have many spare beds in the winter season. They usually have plans for opening up other wards if a Flu season becomes bad but things become more difficult if needing to create more ICU or High Dependency beds for very sick and infected patients requiring isolated 1:1 or 1:2 nursing care. So we need to slow the ‘spread’ through the community, giving healthcare systems and hospitals lower peak loads of sick patients.
So far 15–20% of COVID-19 cases have become severely ill. The rest suffer either no symptoms or mild to moderate symptoms that usually can be managed at home. In the last day we have heard there are two strains with one potentially being more virulent. However typically viruses evolve to become less dangerous over time.
Health systems that have coped well so far (like China, Taiwan and Singapore) have been responsive, had rapid capacity capability, had good emergency plans and training in place and had System-Wide health IT platforms. For example, Taiwan were able track all their patient’s health records and link their travel records to those who got sick. They had good interoperability between databases and could quickly put infection control plans in place to track and isolate infectious patients.
What should nations do?
The main aim for countries is to first contain any outbreaks and then slow the spread through the community. The goal is to slow and dampen the peak load on the health system.
All Ministries of Health or governments should have pre-existing plans in place. These will involve:
Regular, clear and honest communications to the population.
Whole of government, integrated communications and emergency management systems.
Systems linking inbound travellers to individual health records (possible with linked or integrated healthcare databases or a blockchain platform).
Contact tracing systems linked to infected patients.
Restricting access to Aged Care Homes and hospitals.
Revised Triage hospital protocols.
In particular ICU/Critical Care and High Dependency Unit bed capacity will need significant expansion. Patients ill with COVID-19 typically have respiratory problems.
Publicised Healthcare phone lines and mobile/remote treatment teams and systems to treat patients at home.
Isolation facilities for those requiring isolation unable to self-isolate.
Increased staffing capacity plans.
Systems to carry out remote monitoring of self-isolated individuals.
Publicised population and society wide infection control measures.
Standardised Clinical Pathways according to international best practice.
What should we do as individuals?
Limit social contact. This is called ‘Social Distancing’ and it works well because you need to have skin to skin/eye/nose/mouth contact or be in close proximity to an infected person for 10 -20 mins or contact a contaminated surface to become infected.
Don’t shake hands or socially hug when greeting.
Wash hands with soap and water, regularly or after contact with potentially infected surfaces or people.
Ensure you stay fit, get enough sleep, eat well and get sunshine daily.
If infected, self-isolate. But note that the incubation period (time between first contact and onset of first symptoms) for the COVID-19 virus is about 5–6 days. So always assume you ‘could’ be infected and practice good hygiene.
Can it be caught from someone without symptoms?
This is called the ‘incubation phase’ (when someone has the virus but is not showing symptoms). For COVID-19 it is about 5–6 days. The best guess from the limited studies done on this outbreak is that it is transmissible in the last couple of days of the incubation period.
Who should we protect?
Primarily we should be thinking about those who are more vulnerable at this stage. We should avoid infecting sick or immune compromised people and older people. Their defences are already low and they are susceptible. As a society we all need to think of their needs and develop systematic ways to check in and care for them on a daily basis, using remote means.
What’s the good news?
Countries that have prepared and now have plans in place, based on previous experience from the 2009 Swine Flu global pandemic, will do well. Population wide infection control measures, health system remote assessment, triage and treatment teams, ICU capacity expansion and isolation procedures all work.
Countries that have trained and practiced with emergency planning ‘exercises’ combining healthcare, airport, airline, customs, social services and other government agencies will be ready.
Genomic sequencing of the virus has already been completed (by Australia’s University of Queensland). This means that plans are underway for vaccine development. However, this will take at least 18 months before we may have a widely available vaccine in sufficient quantities. But the genetic sequence of the virus gives us information on what types of existing medications may be effective for treating existing cases, such as antiretrovirals.
Interestingly children so far seem to be relatively unscathed by this virus. It is unclear why they aren’t catching it or, at least, if they are they aren’t displaying symptoms. However it’s good news as schools may not end up being the potential ‘vector’ for spread seen with other epidemics.
Note however that three neonates (babies) have shown mild symptoms, in Italy. But these babies were possibly infected after being born. At the same time, nine babies in China born to mothers already infected with the virus have all tested negative to the virus. So the chances of transmitting it to an unborn baby seem extremely low.
Significantly, handwashing and social distancing are the most effective measures to prevent spread.
In Summary
There is a lot we don’t know yet about COVID-19. It could burn out. But it will get take some time before that could happen.
Transmissibility (Ro) of 2.4 and Mortality of 1% is serious when global numbers are predicted. This will be the most deadly pandemic to hit us since the Spanish Flu. It will likely play out similar to a severe flu season but will hit the globe in a continuous set of waves over a couple of years. This will stress healthcare systems, the workforce and the economy.
We want to avoid COVID-19 flu hitting the population all at once and on top of normal seasonal flu loads. Population infection control is the most critical thing any country can do. The main aim is to slow the rate of ‘spread’ through the communities so that we don’t overload hospitals, ICU beds and communities all at once.
Protecting the population that is older, already sick or immune compromised is important. We need systems for regular contact and checking-in with them.
Having pre-planned systems including standardised procedures for nationwide communication, national clinical protocols, agency interoperability, triage and remote treatment capacity are vital.
Development of rapid capacity expansion for ICU and High Dependency beds is essential.
Limiting social and close contact with others,with regular handwashing is the most effective control measure.
Think ahead and prepare for a difficult twelve months. We could end up with a bad seasonal flu in most countries but it’s looking likely to be worse than that.
Governments and health systems are sharing best practice. They should have effective interoperability working between agencies and systems in place to deal with this emergency.
This won’t be the last time we face a global pandemic.
