SARS-CoV-2 Omicron variant prompts system sciences and precision medicine

By Nidhi Saha, BDSFeb 21 2022Reviewed by Aimee Molineux

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

This variant was found to be highly transmissible and infectious, invades natural defense mechanisms of the body, is less responsive to vaccines, and is highly mutable – with 50 new mutations detected, of which 30 were found at the spike protein.

By January 2022, Omicron spread in more than 145 countries, with the transmission rate doubling within 2-3 days. It was declared as 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 predictions by experts regarding this VOC and the management strategies for the coronavirus disease 2019 (COVID-19) infection caused by this variant.

The present review entailed 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 exhibited 15 mutations at the receptor-binding domain (RBD) whereas the Delta variant showed only two mutations. These mutations are said to render higher infectivity, transmissibility and resistance to treatments and vaccines to the Omicron variant – which now accounts for nearly 90% out of the total COVID-19 infections globally.

Findings

In a study where cryo-electron microscopy (Cryo-EM) analysis of human angiotensin-converting enzyme 2 (ACE2) in complex with the spike protein of SARS-CoV-2 Omicron variant was carried out, it was found that the affinity of Omicron 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 the Beta and Delta variants, immune escape was not evident – in population-wide epidemiological studies.

Recent reports suggest that the altered active and blocking sites in the Omicron variant results in the decreased efficacy of COVID-19 vaccines against the virus. Reportedly, an impairment has been found in the Omicron variant’s spike fusogenicity, which causes the decreased formation of syncytes leading to a reduced replication of transfected cells of the lung. However, the involvement of any other organ or organ systems remains unclear.

Scientists state that mutations render the Omicron variant partially resistant to natural immunity, monoclonal antibodies, and vaccine neutralizing antibodies. Evidence suggests altered natural and vaccine-induced immunities in humans against the Omicron variant.

The foremost thing in the management of the infected patients is diagnosis through polymerase chain reaction (PCR) and antigen COVID-19 tests—as these can effectively detect the Omicron variant because of its association with the S-protein. Nonetheless, these methods are time-consuming and expensive. Alternatively, using nanoparticles for isolating RNA or DNA from samples via magnetic field can aid in rapid diagnosis. The nano-enabled SARS-CoV-2 sensors selectively detect virus concentration even at low levels (picomolar level).

Other efficient biomarkers have been investigated for selective detection of SARS-CoV-2, such as, segment selective DNA/RNA, antibodies and CIRSR/Cas. These nanotechnology-supported biosensing systems need validation and confirmatory epidemiologically before use in clinical and point-of-care (POC) testing.

These biosensors are yet to be tested against the Omicron variant, although theoretically they are speculated to be effective as they act against the spike protein. Because of the numerous mutations at the spike protein of the Omicron variant, a well-designed and highly validated diagnostic tool is warranted for detecting and confirming this variant in large populations.

The internet of medical things (IoMT)- supported biosensing approach and artificial intelligence (AI) utilizes the information regarding viral load to understand disease progression and assess treatment efficacy. These can be used in the detection of the Omicron variant and also as a part of telemedicine for analyzing health consequences with reference to medical conditioning/profiling of individuals. Hence, personalized monitoring of the Omicron variant’s infection progression can be done.

To prevent viral infection and transmission, proper hygiene must be maintained, protective devices and masks should be used. In addition, implementation of physical distancing, mass testing, restricted travels, patient-tracking, and home testing campaigns should be strictly followed. Special care should be taken while monitoring high-risk populations. Ready-to-market multidisciplinary approaches to bedside or point-of-care (POC) platforms could help in the appropriate management of the Omicron variant.

More effective diagnostic tools and therapeutic modalities should be developed through personalized/precision medicine. A booster dose following full vaccination has proven 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 for the therapeutics to be investigated; infection-associated side effects to be analyzed, and post-infection recovery of a patient to be monitored – to achieve the novel pharmacological relevant therapeutic involvement in every aspect of nanomedicine.

There exists an urgent need to engineer available vaccines that can be delivered at the target site through nanomedical approaches. Other therapeutic agents can be used along with nanomedicine to manage post-infection consequences—nutraceuticals can be a good choice. Optimization of nutraceuticals and nanomedicine—formulated by an engineered vaccine as precision medicine—can be undertaken. This can further be formulated as personalized medicine according to a patient’s health profile.

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

Discussion and conclusions

According to health experts, a multidisciplinary approach is required to combat this third wave of COVID-19 pandemic, including a further understanding of the infection caused by the predominant Omicron variant. AI can be used to design new therapies or monitor the efficacy of drugs and disease management strategies; for increasing the awareness about vaccination, especially the booster dose programs; in using biomedical/biotechnology-based approaches that are focused in developing better testing systems; for gene sequencing and more effective therapies; and to ensure a better public-private partnership for health wellness and regulatory socioeconomic balance.

There is an urgent need to pay attention to the viral evolution, transmission, disease course and prognosis, while not discounting the epidemiology of the disease and prophylactic vaccinations – to combat COVID-19, as well as any future pandemics.