Topic: Omicron COVID-19 Virus update from South Africa

Speakers: Prof Salim Abdool Karim South African Public Health Medicine Specialist,  Epidemiologist and Infectious Diseases Specialist, Dr Angelique Coetzee National Chairperson South African Medical Association & Dr Akhtar Hussain Chairperson Employed Doctors Advocacy Forum, South African Medical Association

4th December, 2021, Saturday, 9.30am-11am

• The whole world has been through the first, second and third waves. Right now, it is going through the fourth wave. It varies country by country.
• Variants have changed the covid-19 endgame. Vaccines with 95% efficacy were an exciting breakthrough but it’s not so simple and we now know that the endgame is going to be heavily influenced by the variants. There is a concern that variants are going to lead to significant waves.
• The ancestral strain was there for only a very short period. By the time it appeared in Europe, it had developed the D614G mutation, this was the dominant strain when there were no variants.
• In South Africa, D614G strain was originally in the first wave. On 14^th Dec, alpha variant from the UK, 18^th December beta strain from South Africa, and 12^th January the gamma strain from Brazil and 25^th March, the delta variant was identified. On 25^th November, the omicron was identified.
• The first wave in Brazil and South Africa was quite severe compared to that in India.
• The second wave was quite severe due to the delta variant in India; the gamma variant caused the serious second wave in Brazil and the beta variant led to the second wave and in South Africa delta variant caused the third wave. The delta variant rapidly replaced the beta variant in South Africa. 
• Delta became the dominant strain because of the increased transmissibility. The delta variant is more infectious because the viral load in nose and back of throat is ~1000 times higher, patients are positive for longer period and become infectious earlier than with other variants. Also, infections occurred in more vaccinated people than expected and there is a high risk of re-infection in people with past infection.
• South Africa is in the fourth wave and the numbers are rising rapidly. It started with  minimum number of 200-300 -500 and within a week it jumped to 8000 to 10,000. Till yesterday (3^rd Dec), there were 16,555 cases with 24.3% positivity rate. On 2^nd Dec, there were 11k new cases in 24 hours. Death rate not so high. On 3^rd, it was 25. 
• Omicron has replaced the delta variant and has become the dominant strain in South Africa. Currently around 74% of sequences are omicron.
• It is not clear whether Omicron is really faster than delta, but early evidence suggests so. But we do not know how much more transmissible than delta. Doubling time is faster for omicron at this point of time, but it’s still early days. 
• The mutation profile of omicron (B.1.1.529) is quite different from other circulating VOCs/VOIs. It has more than 50 mutations with more than 30 mutations just in the spike protein (shares mutations with other four VOCs). Of particular concern are mutations at positions 417, 484, 681, which are known and have been well-characterised with known phenotypic impact affecting transmissibility, immune evasion. But many other mutations are not well-characterised and their impact is not clear.
• We don’t know how this virus will behave as we don’t know what these mutations will do. But what we know is that overlapping mutations with alpha, beta, gamma and delta are associated with increased transmissibility, improved binding affinity; they enable the virus to partially escape antibodies and impact PCR test by S-gene target failure.
• Some mutations are not present in other VOCs, but we know that some of them help the virus to become more infectious, and make it harder for antibodies to attach and/or kill the virus. The remaining mutations are largely unknown.
• The rate at which omicron is increasing is higher. In Gauteng province, there were less than 200 cases 10 days ago. And yesterday, there were 11,500 cases showing the fast speed at which cases are increasing in Gauteng province. It may be a harbinger of things to come suggesting increased transmissibility and may be expected to replace the other variants.
• Only one PCR test (Thermo-Fisher kit) has shown that one of the three gene targets is not detected (called the S gene target failure), this is not a problem but is a potential advantage in monitoring spread. Other diagnostic tests are detecting omicron. Variant can be presumptively by qPCR assay (before whole genome sequencing).
• There are too few cases to say that the clinical presentation of omicron is worse than its predecessors. 
• Anecdotal information suggests similar presenting illness and mainly in younger people. It is still a mild disease. Symptoms include myalgia, headache, fatigue; unvaccinated people have slightly more severe symptoms. Most of the patients hospitalised with omicron were unvaccinated. But there are no red flags at this time. No deaths reported yet. We can expect to see severe cases in about 2-3 weeks. We do not know yet how long the persons with omicron variant remain infectious. Everyone should get tested if symptoms develop.
• More children are affected so we might see a rapid spread in schools. There is also an increase in hospitalization, but not to the extent as in the previous waves. Fewer ICU hospitalizations due to mild symptoms.
• At this point of time, there is no reason or evidence to suggest a change in current treatment: symptomatic treatment for mild covid-19, hospitalization for oxygen, proning, dexamethasone, tocilizumab and other treatment remain. Effectiveness of monoclonal antibodies has to be assessed; the new oral treatment (paxclovid) may be a potentially important future strategy.
• Preliminary evidence suggests an increased risk of immune escape from antibodies, likely to lead to increased reinfection cases in those with past infection, neutralization of J&J and Pfizer antibodies being assessed. Based on past VOCs, effectiveness for hospitalization and severe disease is likely to remain strong as this depends more on T-cell immunity and less on antibodies.
• We know that these mutations are likely to increase the risk of immune escape and may affect clinical efficacy of Covid-19 vaccines like past variants. But this has been seen with other variants earlier.
• We will probably see more re-infections and breakthrough infections, but vaccinated persons are less likely to have severe infection. 
• Vaccines remain effective over time for all variants for severe Covid-19 and hospitalization. While we may see more mild infections from omicron due to antibody escape, there is less likely to be less impact on severe disease as it depends more on T cells.
• There is no need for panic or over reaction. We have dealt with variants before, including variants with immune escape.
• All current public health measures are expected to work against omicron; masks, social distancing, improved ventilation of indoor spaces, avoiding crowded spaces and hand hygiene remain effective.
• Closing borders has almost no benefits as the virus may already be present in many countries and secondly, the existing five steps to reduce travel transmission risk will work just as well for this new variant (vaccinated, symptom screening at boarding, negative PCR at boarding, masking during the flight and Covid-19 test on arrival).

Participants

Member National Medical Associations

Dr Yeh Woei Chong, Singapore, Chair CMAAO 

Dr Ravi Naidu, Malaysia, Immediate Past President CMAAO

Dr Alvin Yee-Shing Chan, Hong Kong, Treasurer, CMAAO

Dr Heidi Stensmyren, President World Medical Association

Dr Marthanda Pillai, India Member World Medical Council, Advisor CMAAO

Dr Angelique Coetzee, South Africa

Dr Akhtar Hussain, South Africa

Dr Salma Kundi, Pakistan

Dr Md Jamaluddin Chowdhury, Bangladesh 

Dr Qaiser Sajjad, Pakistan 

Dr Kar Chai Koh, Malaysia

Invitees

Dr Salim Abdool Karim, South Africa

Dr Shashank Joshi, India

Dr Monica Vasudev, USA

Dr Russell D’Souza, Australia UNESCO Chair in Bioethics

Dr Suneela Garg, India

Dr Meenakshi Baranwal, India

Dr S Sharma, Editor IJCP Group

Moderator

Mr Saurabh Aggarwal