Tagged: SARS-CoV-2

Rate of Infection R0, why this so important when it comes to COVID-19?

R0 describes how many cases of a disease an infected person will go on to cause – in this imagined scenario R0=2.

FOR THE first SARS pandemic in 2003, scientists estimated the original R0 to be around 2.75. A month or two later, the effective R0 dropped below 1, thanks to the tremendous effort that went into intervention strategies, including isolation and quarantine activities.

Scientists use R0 – the reproduction number – to describe the intensity of an infectious disease outbreak. R0 estimates have been an important part of characterizing pandemics or large publicized outbreaks, including the 2003 SARS pandemic, the 2009 H1N1 influenza pandemic and the 2014 Ebola epidemic in West Africa. ‘It’s something epidemiologists are racing to nail down about SARS-CoV-2, the virus that causes COVID-19.’

Since SARS-CoV-2, the virus that causes COVID-19 is a sister clade of SARS, it is extremely useful to simply refer to the bug as SARS2. In fact much of what was learnt during the first epidemic should be applied to the latest outbreak. For example, SARS was transmissible via respiratory and bodily fluid. Until evidence is provided to the contrary, one must assume this to also be the case with SARS2.

In the 1950s, epidemiologist George MacDonald suggested using R0 to describe the transmission potential of malaria. He proposed that, if R0 is less than 1, the disease will die out in a population, because on average an infectious person will transmit to fewer than one other susceptible person. On the other hand, if R0 is greater than 1, the disease will spread.

When public health agencies are figuring out how to deal with an outbreak, they are trying to bring R0 down to less than 1. This is tough for diseases that have a high R0.

When SARS2 arrived, it was assumed the R0 was similar to the previous epidemics. Initially SARS2, the novel coronovirus, was spreading within a range of 2.2 to 2.7 then it shot up to 4.7 – 6.6

This places it in the realm of Smallpox which has an R0 of 5–7.

You  can read more on How Scientists Quantify the Intensity of an Outbreak Like COVID-19

Coronavirus: Simple statistical predictions for South Africa

Coronavirus: Simple statistical predictions for South Africa

Covid-19 Facts: Surviving the Covid-19 ‘Immunity’ Disaster

1. What is SARS-CoV-2 and Covid-19?

“Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)” is the name of the new virus according to the International Committee on Taxonomy of Viruses (ICTV). “COVID-19” is the name of the new disease caused by SARS-CoV-2 following guidelines previously developed with the World Organisation for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO).

This means it is related to the coronovirus responsible for the 2003 SARS epidemic. ‘Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2.’

2. What are the Symptoms?

The most common symptoms of COVID-19, according to the WHO: fever (in 88% of cases), dry cough (68%), fatigue (38%) and sputum/phlegm production (33%). Shortness of breath occurred in nearly 20% of cases, and about 13% had a sore throat or headache, the WHO said in a report drawing on more than 70,000 cases in China.

3. How Infectious is SARS-CoV-2?

Covid-19 is more infectious and contagious than previously assumed. R0 value is likely to be between 4.7 and 6.6., and not 2.2 to 2.7 as previously reported. This places it in the realm of Smallpox which has an R0 of 5–7.

It can survive for up to 3 days+ on surfaces and remain airborne for hours.

It is most infectious during incubation, and first week of symptoms and less infectious during post-symptomatic recovery period. Incubation period averages 5.1 days.

It follows that since SARS-CoV-2 is related to the SARS 2003 virus, the same protocols should apply, ‘avoid direct contact with respiratory secretions or body fluids.’

Note: It is well worth reading up on predecessor SARS 1

Can We Learn Anything from the SARS Outbreak to Fight COVID-19?

The problem is that since the coronovirus is a new pathogen, we do not possess natural immunity. South Africans will eventually gain ‘herd immunity’ which is ‘the resistance to the spread of a contagious disease within a population that results if a sufficiently high proportion of individuals are immune to the disease, especially through vaccination’.

4. How many South Africans are likely to catch COVID-19?

If one uses Boris Johnson and Angela Merkel’s estimates that 40%-60% of the population will invariably be infected: South Africa with a population of 56+ million must plan for some 22 400 000 to 33 600 000 cases of which 1 904 000 will be critical according to WHO average mortality rate of 3.4. This makes it a major problem for the public health system. See Coronavirus: Simple statistical predictions for South Africa

Luckily we have a relatively young population. Age of a population is a factor in mortality rate.

5. How many hospital beds does South Africa have?

There are currently some 80 000 beds in the public health system, and 5000 beds in the private health care system according to MOH Dr Zweli Mkhize today. This means a potential shortfall of 1 819 000 beds. Nationally, there is only 1 hospital, 187 hospital beds and 42 surgical beds per 100 000 population.

6. Which groups are most at risk from SARS-CoV-2?

Most reports suggest that the elderly, infirm and those already possessing co-morbidity, i.e underlying disease such as HIV, Diabetes, Cardiovascular disease are particularly at risk from falling critically ill from the disease.

COVID-19 update: What you need to know now that it’s officially a pandemic

7. Why should I be concerned about SARS-CoV-2 & COVID-19?

Patients with SARS-CoV-2 infection are presenting with a wide range of symptoms. Most patients seem to have mild disease, and about 20% appear to progress to severe disease, including pneumonia, respiratory failure, and, in some cases, even death, according to the Lancet.

Coronavirus turns deadly when it leads to ‘cytokine storm’; identifying this immune response is key to patient’s survival

Since COVID-19 may also reduce lung function, opportunistic infection from Pneumococcus, Streptococcus and Mycobacterium Tuberculosis within the South African context may also be inferred. This presents a substantial and heretofore under-reported risk.

Unless we think globally and act locally to contain and prevent transmission, new waves of the pandemic are likely to hit the sub-continent.

8. What can I do to prevent transmission?

Social distancing, avoiding large crowds, hand-washing, the Covid “handshake” and sneezing into ones elbow are all behavioural changes suggested by our MOH.

Providing hand-sanitation stations at Taxi ranks, Metro-Rail and public venues is another suggestion, so too providing UV lights and/or latex gloves and hand sanitiser to those who deal with money at checkouts, and also pump jockeys at Petrol Stations.

Disinfection of Public Transport and Taxis should be prioritised!

Predecessor SARS 1 showed sensitivity to UV light, renders inactive.

Traditional burning of Imphepho or African Sage may assist poor households in removing bacteria and viruses from the air, as inferred from Journal of Ethnopharmacology, since havan samagri has the potential to kill 94% of bacteria.

9. Is there a cure?

Treatment is currently symptomatic. Several treatment therapies have been advanced, including the use of chloroquine phosphate to treat fever, antivirals such as protease inhibitors to treat viral reproduction and other therapies. Anecdotal evidence suggests that codeine and ibuprofen exacerbates the fever and should not be taken without doctor supervision. Favipiravir, a Japanese flu drug has also proven effective.

Covid-19: ibuprofen should not be used for managing symptoms, say doctors and scientists

See Could an old malaria drug help fight the new coronavirus?

Warnings issued on lethal dose of Chloroquine 

Nvidia is calling on gaming PC owners to put their systems to work fighting COVID-19 by assisting projects already  ‘simulating potentially druggable protein targets from SARS-CoV-2

Avoid Coronophobia, the fear of Coronoviruses killing you. Rational thinking rather than fear, panic and denial is the key here.

10. Can I test for SARS-CoV-2?

Yes, currently the only tests available are via pathology labs, designated public hospitals such as Tygerberg and the private health system and cost anywhere between R1400 to R900. Local tests have a 48 hour turnaround. This is a significant downside to an otherwise excellent disaster plan. Singapore for instance has rolled out a four-hour turnaround swab-test at entry points, while Senegal is working on a 10-minute PCR test.

Demand better screening, lowering of threshold of surveillance and access to free testing.

11. Is there a Vaccine?

South Africa has no candidate vaccine at this time.

See: How can AI help biotech companies seeking vaccines?

Passive antibody therapy, an Antibody Method from the 1890s is being used to provide stop-gap immunity.

A Phase 1 clinical trial evaluating an investigational vaccine designed to protect against coronavirus disease 2019 (COVID-19) has begun at Kaiser Permanente Washington Health Research Institute (KPWHRI) in Seattle.

Immunisation will take time, we need to be vigilant and patient until then.

Everything You Need to Know About Coronavirus Vaccines

12. Which borders are closed?

A travel ban has been enforced on foreign nationals from high-risk countries such as Italy, Iran, South Korea, Spain, Germany, the United States, the United Kingdom and China. There is currently no word on Japan,  Spain and other places of concern.

13. How will this effect the global economy?

In 2004 Jong-Wha Lee and Warwick J. McKibbin in ‘Estimating the Global Economic Costs of SARS’ published in ‘Learning from SARS: Preparing for the Next Disease Outbreak‘ produced a global model to simulate the economic impact of a long-term SARS epidemic using the period 2002–2081. The so-called ‘G-Cubed (Asia-Pacific) model’ is eerie and prescient in its description. I reproduce it here:

First, fear of SARS infection leads to a substantial decline in consumer demand, especially for travel and retail sales service. The fast speed of contagion makes people avoid social interactions in affected regions. The adverse demand shock becomes more substantial in regions that have much larger service-related activities and higher population densities, such as Hong Kong or Beijing, China. The psychological shock also ripples around the world, not just to the countries of local transmission of SARS, because the world is so closely linked by international travel. Second, the uncertain features of the disease reduce confidence in the future of the affected economies. This effect seems to be potentially very important, particularly as the shock reverberates through China, which has been a key center of foreign investment. The response by the Chinese government to the epidemic was fragmented and nontransparent. The greater exposure to an unknown disease and the less effective government responses to the disease outbreaks must have elevated concerns about China’s institutional quality and future growth potential. Although it is difficult to measure directly the effects of diseases on decision making by foreign investors, the loss of foreign investors’ confidence would have potentially tremendous impacts on foreign investment flows, which would in turn have significant impacts on China’s economic growth. This effect is also transmitted to other countries competing with China for foreign direct investment (FDI). Third, SARS undoubtedly increases the costs of disease prevention, especially in the most affected industries such as the travel and retail sales service industries. This cost may not be substantial, at least in global terms, as long as the disease is transmitted only by close human contact. However, the global cost could become enormous if the disease is found to be transmitted by other channels such as through international cargo.

14. How will this effect the local economy?

Our economy is so intertwined with the rest of the world that the impact is bound to last for a very long time. In the meantime, think about the benefits and opportunities of buying local, sharing with your neighbour, lending a hand and being prepared. Household responsibility dictates that it is up to individual households at the end of the day to provide for oursselves and to figure out how best to move the economy forward.