Will the current strategies of COVID-19 Prevention work against Omicron?


Will the current strategies of COVID-19
Prevention work against Omicron?
Prof. Mulazim Hussain Bukhari,
Azad Jammu Kashmir Medical College, Muzaffarabad

Nearly after the two years of the current pandemic, a new variant Omicron is raising the concern in the world and also in Pakistan, about 32 suspected cases have been reported in Baluchistan while the first case was confirmed in Karachi by gene sequencing techniques.1

Prof. Mulazim Hussain Bukhari

What is new Variant of concern Omicron?

As of November 24, 2021, WHO has stated that a new Variant of Concern (VOC) with 50 mutations and about 30 major mutations in spike Protein only. It is the 13th variant of corona virus spreading the COVID-19 after Delta, that is more than twice as contagious as earlier variants, which was emerged in the summer of 2021, up to now, scientists do no longer recognize whether or not Omicron is greater or less contagious than Delta, however there’s sufficient cause for situation.

Where was its site of Origin?

WHO named the Omicron or B.1.1.529, which was first detected in HIV patients in Botswana, South Africa? It was originally reported in a specimen collected on 9th November 2021from South Africa.

What is the genetic Profiling of the Omicron?

The genetic profile of “Omicron” has raised a great deal of concern. But as a scientist, believe it won’t cause any problems in the future if it’s more deadly, it won’t spread, and if it spreads rapidly, it essentially means it’s not that deadly. There is a lot of concern about more than 50 mutations in the new SARS-COV-2 variant. Let’s see if it can be more contagious, deadly, and will escape our existing immunity due to previous infection or vaccines.1-2

Why is there more Public concern about Omicron?

The WHO has kept it in the list of VOC like previous, alpha (B1.1.7), beta, (B.1.351), gamma (P.1)) and delta (B.1.617.2) variant appeared during this pandemic. The Omicron is causing detrimental changes in epidemiology, with rapid spread, there is increase in its virulence of change in clinical presentation, involving the children less than 5 years and young people there decrease in effectiveness of current COVID-19 vaccine.

There are similar mutations seen on delta as has been detected on the spike proteins of the Omicron, which will increase transmission. One change P681H is at furin cleavage site (delta P681R) where enzymes TMPR SS2 will do its cleavage after attaching its S1 part of SP and will enable rapid fusion of S2 fusion site to ACE2. On behalf of this the binding affinity may be better and electromagnetic forces may be high. It takes one or more days for transmission and during that your immune system may ramp up. But the reported incubation period is prolonged, about up to 8 days, it means it is not a rapidly killing virus, better affinity does not mean, it is more lethal virus.

Omicron and its spread in the world

After its evolution from Botswana, SA, it has been detected in 75 countries up till now but spreading to other countries of the world. If we look on the world meter of COVID-19, the numbers of cases are increasing. The mutations like N679K, N501Y, N679K, D614G, may enhance its ACE2 binding affinity, with more infectivity, viral load and shedding of virus but still the cases are not advancing, we believe it will not cause any detrimental change in epidemiology. However, it is not possible its wide spread and hope it will not compete other variants like delta in particular. Similar its ability to cause breakthrough and repeat infections, and the severity of disease caused this new variant.1-3

PCR detection of these variants

The currently available PCRs kits are still working nicely to detect this new VOC. Many laboratories have indicated that for one widely used PCR test, one of the three target genes is not detected. It means there is S gene dropout or S gene target failure. This test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this VOC has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage over previous mother virus. The use of corticosteroids, IL6, monoclonal antibodies, hopefully will still be effective for managing patients with severe COVID-19.

What are main unanswered questions about the Omicron 1-5

The most important questions about the new strain are whether it is more contagious than the Delta variant, whether it is more likely to cause severe illness, and whether it will affect the effectiveness of available vaccines or treatments. There is still small data to say anything in future about this question, but on the basis of current information, still there is no increased in cases of hospitalization and ventilators or in ICUs. The Omicron may become more efficient or it could be the said, the less efficient than the parent. The efficiency is not absolute thing that it can bind better, it may be more efficient in binding but less lethal. On the available data from South Africa, its symptoms are entirely different from its other relative variants. There is some encouraging news, and some mysteries still associated with Omicron symptoms.5 Most of the Hospitalized patients do not need oxygen. The patients are being treated at primary care level with mild to moderate symptoms and very few patients are seeking admission tertiary care level.

Since 15 November 2021, with the start of 4th wave, all the patients were showing mild symptoms like, blocked or runny nose, headache, scratchy or sore throat with fatigue. Most of the Hospitalized patients do not need oxygen. The patients are being treated at primary care level with mild to moderate symptoms and very few patients are seeking admission tertiary care level. 800 admission 75% were unvaccinated. There were seven deaths and their age was 58-92 years and all were having co morbidities. Only 4 were due to COVID19 while other three died due to some other cause. Among these only 4 were not vaccinated.

It is being suspected that among 50 mutations, there is one insertion at 214 EPE level. This is T cell receptor which means the omicron has taken one gene from human coronavirus during it transcription in any patient with dual infection. As a result it is not resulting in severs immune reaction and IL6 release which was seen with previous COVID19 cases.

The changes in Receptor binding domain which is interacting with ACE2 are interesting and may raise the question about its escape from current available vaccines but still we are not looking such drastic change. All the changes are changing the dynamic of bindings of virus with ACE2 receptors of human; they may make it more efficient? They may make the electromagnetic forces Better? They may make them to be bad? They may make the phenotype be better and better fit or may make them? The 30 changes in SP and 20 others, which are making it VOC, these changes can make the virus unstable as well as the WHO is expecting and these changes may make the virus incompetent

What about the re-infection?

The data from South Africa is showing it is causing re-infection in those who have recovered at least after 90 days, So we can expect that there may be an extended threat of re-infection with Omicron (ie, human beings who have previously had COVID-19 should become re-infected more effortlessly with Omicron). More information on this could end up to be had inside the coming days and weeks.

WHO is working with technical companions to apprehend the capability impact of this variation on the existing countermeasures, which includes current vaccines being used for the control of COVID-19. The use of vaccines remains critical to reducing intense sickness and death, including towards the dominant circulating variation, Delta, cutting-edge vaccines stay effective against excessive disease and death. Hopefully the vaccine will still work against new VOC, Omicron. Therefore no need to ne panic about this variant.

The most important advise for the communities are using the SOPs, Using masks, keeping social distance, washing hands, using sanitizers and using open windows to improve ventilation, avoiding chances of super spread, going crowded spaces and get vaccinated when it’s their turn and get booster dose if prior vaccination of six months. Remain vigilant to see the updates coming from South Asia.

What should Pakistan Do?

The Pakistan must enhance surveillance and increase the testing rates. There must be sequencing of cases coming for testing or with new signs and symptoms. The NCOC must share the information and sharing genome sequences. The government increases the vaccination process and advises the people to get vaccination through Medias and SMS. As advised by the WHO Pakistan should continue to implement the effective public health measures, SOPs to reduce COVID-19 circulation overall, using a risk analysis and science-based approach. More vaccination to ensure that vulnerable groups everywhere, including health workers and older persons, receive their first and second doses, alongside equitable access to treatment and diagnostics.


  1. COVID-19 in Pakistan: Baluchistan reports 32 suspected cases of Omicron. https://www.geo.tv/latest/389087-balochistan-reports-30-suspected-cases-of-omicron-variant. Dated 20.12.2021
  2. Daria S, Bhuiyan MA, Islam MR. Detection of highly muted coronavirus variant Omicron (B.1.1.529) is triggering the alarm for South Asian countries: Associated risk factors and preventive actions. J Med Virol. 2021 Dec 4. doi: 10.1002/jmv.27503. Epub ahead of print. PMID: 34862624. VOC Omicron GR/484A (B.1.1.529) first detected in Botswana/Hong Kong/South Africa. https://www.gisaid.org/hcov19-variants/. Dated 1.12.2021
  3. Bukhari MH. Recently discovered Omicron: fifth wave of Pandemic in Pakistan. What strategies can be adapted to control it spread. JIIMC 2021; 16: 212-214
  4. Volkov O. Predicted Symptomatic Effectiveness of Pfizer-BioNTech BNT162b2 Vaccine Against Omicron Variant of SARS-CoV-2. medRxiv. 2021 Jan
  5. Karim SS, Karim QA. Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. The Lancet. 2021 Dec 11;398(10317):2126-8.