SARS-CoV-2 Omicron variant prompts systems science and precision medicine

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The Omicron variant (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in South Africa in November 2021. The World Health Organization (WHO) has declared Omicron as variant of concern (VOC) two days after being reported by the Network of Genomics Surveillance in South Africa.

This variant has been shown to be highly transmissible and infectious, invades the body’s natural defense mechanisms, is less susceptible to vaccines and is highly mutable – with 50 novel mutations detected, 30 of which were found at the spike protein level.

Study: SARS-CoV-2 Omicron variant: A next phase of the COVID-19 pandemic and a call to arms for systems sciences and precision medicine. Image Credit: Fit Zstudio/Shutterstock


As of January 2022, Omicron has spread to over 145 countries with the transmission rate doubling in 2-3 days. It has been declared a serious concern in Europe and an emergency in the UK.

The study

A recent article, published in MedComm, aimed to describe the emergence of the Omicron variant, its structure, its impact on health and health systems, the challenges that can be expected due to this variant and presented various expert predictions regarding this COV and the strategies for managing coronavirus disease 2019 ( COVID-19) caused by this variant.

The present review involved a comparison between the Delta variant and the Omicron variant where the Delta variant was established as more contagious compared to the Omicron variant; the latter being more infectious and transmissible. The Omicron variant had 15 mutations in the receptor binding domain (RBD) while the Delta variant had only two mutations. These mutations are said to increase the infectivity, transmissibility and resistance to treatments and vaccines of the Omicron variant – which now accounts for nearly 90% of total COVID-19 infections worldwide.

Results

In a study where cryo-electron microscopy (Cryo-EM) analysis of human angiotensin-converting enzyme 2 (ACE2) in complex with the SARS-CoV-2 variant spike protein Omicron was carried out, it was found that the affinity of Omicron the spike protein to human ACE2 is similar to that of the Delta variant. Neutralization assays showed increased antibody evasion in the Omicron variant, whereas for beta and delta variants immune evasion was not evident – in population-wide epidemiological studies.

Recent reports suggest that altered active and blocking sites in the Omicron variant lead to decreased effectiveness of COVID-19 vaccines against the virus. Apparently, an alteration was found in the fusogenicity of the Omicron variant peak, which causes the decrease in syncyte formation leading to reduced replication of transfected lung cells. However, the involvement of any other organ or organ system remains unclear.

The scientists say the mutations make the Omicron variant partially resistant to natural immunity, monoclonal antibodies and vaccine neutralizing antibodies. Evidence suggests impaired natural and vaccine-induced immunities in humans against the Omicron variant.

The main thing in the management of infected patients is Polymerase Chain Reaction (PCR) diagnosis and COVID-19 antigen tests, as these can effectively detect the Omicron variant due to its association with protein S. However, these methods are time consuming and expensive. Alternatively, use nanoparticles to isolate RNA or DNA from samples via magnetic field can help in quick diagnosis. Nano-enabled SARS-CoV-2 sensors selectively detect virus concentration even at low levels (picomolar level).

Other effective biomarkers have been investigated for the selective detection of SARS-CoV-2, such as segment selective DNA/RNA, antibodies, and CIRSR/Cas. These nanotechnology-supported biosensing systems must be validated and epidemiologically confirmed before being used in clinical and point-of-care (POC) trials.

These biosensors have yet to be tested against the Omicron variant, although in theory they are supposed to be effective because they act against the spike protein. Due to the numerous mutations at the spike protein of the Omicron variant, a well-designed and highly validated diagnostic tool is warranted to detect and confirm this variant in large populations.

The biosensing approach supported by the Internet of Medical Things (IoMT) and artificial intelligence (AI) uses viral load information to understand disease progression and assess treatment efficacy. These can be used in the detection of the Omicron variant and also in the context of telemedicine to analyze health consequences with reference to the medical conditioning/profiling of individuals. Therefore, personalized monitoring of the infection progression of the Omicron variant can be performed.

To prevent viral infection and transmission, good hygiene should be maintained, protective devices and masks should be used. In addition, the implementation of physical distancing, mass testing, restricted movement, patient monitoring and home testing campaigns should be strictly followed. Special precautions should be taken when monitoring high-risk populations. Multidisciplinary approaches ready to market bedside or point-of-care (POC) platforms could aid in the proper management of the Omicron variant.

More effective diagnostic tools and therapeutic modalities should be developed through personalized/precision medicine. A booster dose after full vaccination has been shown to be effective against COVID-19 infection. Nanotechnology can be used to optimize treatments through developed therapies and vaccines. As SARS-CoV-2 infection can affect different organs, there is an urgent need to study therapeutics; infection-associated side effects to be analyzed and a patient’s post-infection recovery to be monitored – to obtain the relevant new pharmacological therapeutic implication in all aspects of nanomedicine.

There is an urgent need to design available vaccines that can be delivered to the target site through nanomedical approaches. Other therapeutic agents can be used with nanomedicine to manage post-infection consequences – nutraceuticals can be a good choice. The optimization of nutraceuticals and nanomedicine – formulated by a vaccine designed as precision medicine – can be undertaken. This can further be formulated as personalized medicine based on a patient’s health profile.

Artificial intelligence (AI), big data pools, subtype science and bioinformatics systems are the formidable arsenal leading to more specific therapies and better patient outcomes.

Discussion and conclusions

According to health experts, a multidisciplinary approach is needed to combat this third wave of the COVID-19 pandemic, including a better understanding of the infection caused by the predominant variant of Omicron. AI can be used to design new therapies or monitor the effectiveness of drugs and disease management strategies; to increase awareness of vaccination, especially booster programs; using biomedical/biotechnology approaches focused on developing better test systems; for gene sequencing and more effective therapies; and to ensure a better public-private partnership for health, well-being and socio-economic regulatory balance.

There is an urgent need to pay attention to viral evolution, transmission, disease course and prognosis, without neglecting disease epidemiology and prophylactic vaccinations – to combat COVID-19, as well as any future pandemic.

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