Evolution of SARS CoV-2 Omicron subvariants BF.7 and XBB.1.5: Time to follow Africa and abort all COVID restrictions

How do we change our approach to COVID with the changing face of disease?

INTRODUCTION

The emergence of SARS-CoV-2 triggered a global health emergency, causing > 7 million deaths thus far. Limited early knowledge spurred swift research, treatment, and vaccine developments. Implementation of public health measures such as, lockdowns and social distancing, disrupted economies and strained healthcare. Viral mutations highlighted the need for flexible strategies and strong public health infrastructure, with global collaboration crucial for pandemic control.

AREAS COVERED

(i) Revisiting diagnostic strategies, (ii) adapting to the evolving challenge of the virus, (iii) vaccines against new variants, (iv) vaccine hesitancy in the light of the evolving disease, (v) treatment strategies, (vi) hospital preparedness for changing clinical needs, (vii) global cooperation and data sharing, (viii) economic implications, and (ix) education and awareness- keeping communities informed.

EXPERT OPINION

The COVID-19 crisis forced unprecedented adaptation, emphasizing public health readiness, global unity, and scientific advancement. Key lessons highlight the importance of adaptability and resilience against uncertainties. As the pandemic evolves into a 'new normal,' ongoing vigilance, improved understanding, and available vaccines and treatments equip us for future challenges. Priorities now include proactive pandemic strategies, early warnings, supported healthcare, public education, and addressing societal disparities for better health resilience and sustainability.

Evaluating mAbs binding abilities to Omicron subvariant RBDs: implications for selecting effective mAb therapies

The ongoing evolution of the Omicron lineage of SARS-CoV-2 has led to the emergence of subvariants that pose challenges to antibody neutralization. Understanding the binding dynamics between the receptor-binding domains (RBD) of these subvariants spike and monoclonal antibodies (mAbs) is pivotal for elucidating the mechanisms of immune escape and for advancing the development of therapeutic antibodies. This study focused on the RBD regions of Omicron subvariants BA.2, BA.5, BF.7, and XBB.1.5, employing molecular dynamics simulations to unravel their binding mechanisms with a panel of six mAbs, and subsequently analyzing the origins of immune escape from energetic and structural perspectives. Our results indicated that the antibody LY-COV1404 maintained binding affinities across all studied systems, suggesting the resilience of certain antibodies against variant-induced immune escape, as seen with the mAb 1D1-Fab. The newly identified mAb 002-S21F2 showed a similar efficacy profile to LY-COV1404, though with a slightly reduced binding to BF.7. In parallel, mAb REGN-10933 emerged as a potential therapeutic candidate against BF.7 and XBB.1.5, reflecting the importance of identifying variant-specific antibody interactions, akin to the binding optimization observed in BA.4/5 and XBB.1.5. And key residues that facilitate RBD-mAb binding were identified (T345, L441, K444, V445, and T500), alongside residues that hinder protein-protein interactions (D420, L455, K440, and S446). Particularly noteworthy was the inhibited binding of V445 and R509 with mAbs in the presence of mAb 002-S21F2, suggesting a mechanism for immune escape, especially through the reduction of V445 hydrophobicity. These findings enhance our comprehension of the binding interactions between mAbs and RBDs, contributing to the understanding of immune escape mechanisms. They also lay the groundwork for the design and optimization of antiviral drugs and have significant implications for the development of treatments against current and future coronaviruses.

A mini review of reinfection with the SARS-CoV-2 Omicron variant

Background

COVID-19 has caused severe morbidity and mortality worldwide. After the end of the dynamic zero-COVID policy in China in December, 2022, concerns regarding reinfection were raised while little was known due to the lack of surveillance data in this country.

Aims

This study reviews the probability, risk factors, and severity of severe acute respiratory syndrome coronavirus 2 Omicron variant reinfection, as well as the interval between infections, risk of onward transmission by reinfected cases, and the role of booster vaccination against reinfection.

Sources

References for this review were identified through searches of PubMed and Web of Science up to September 24, 2023.

Results

The rate of reinfection ranges from 3.1% to 13.0%. Factors associated with a higher risk of reinfection include being female, having comorbidities, and being unvaccinated. Reinfection with the BA.4 or BA.5 variant occurs approximately 180 days after the initial infection. Reinfections are less clinically severe than primary infections, and there is evidence of lower transmissibility. The debate surrounding the effectiveness and feasibility of booster vaccinations in preventing reinfection continues.

Conclusions

The reinfection rate during the Omicron epidemic is significantly higher than in previous epidemic periods. However, the symptoms and infectivity of reinfection were weaker than those of the prior infection. Medical staff and individuals at high risk of reinfection should be vigilant. The efficacy of booster vaccinations in reducing reinfection is currently under debate.

COVID-19 mortality paradox (United States vs Africa): Mass vaccination vs early treatment

The coronavirus disease 2019 (COVID-19) mortality rate in 55 African countries is almost 4.5 times lower than in the coronavirus disease 2019 (COVID-19) despite Africa having over 4.2 times more people. This mortality paradox is also evident when comparing Nigeria, a heavily populated, poorly vaccinated and weakly mandated country to Israel, a small, highly vaccinated and strictly mandated country. Nigeria has almost 4 times lower COVID mortality than Israel. In this Field of Vision perspective, I explain how this paradox has evolved drawing upon my academic, clinical and social experience. Since April 2020, I've developed and been using the Egyptian immune-modulatory Kelleni's protocol to manage COVID-19 patients including pediatric, geriatric, pregnant, immune-compromised and other individuals suffering from multiple comorbidities. It's unfortunate that severe acute respiratory syndrome coronavirus 2 is still evolving accompanied by more deaths. However in Africa, we've been able to live without anxiety or mandates throughout the pandemic because we trust science and adopted early treatment using safe, and effective repurposed drugs that have saved the majority of COVID-19 patients. This article represents an African and Egyptian tale of honor.

Retrospective study about clinical severity and epidemiological analysis of the COVID-19 Omicron subvariant lineage-infected patients in Hohhot, China

BACKGROUND

Fear of a global public health issue and fresh infection wave in the persistent COVID-19 pandemic has been enflamed by the appearance of the novel variant Omicron BF.7 lineage. Recently, it has been seeing the novel Omicron subtype BF.7 lineage has sprawled exponentially in Hohhot. More than anything, risk stratification is significant to ascertain patients infected with COVID-19 who the most need in-hospital or in-home management. The study intends to understand the clinical severity and epidemiological characteristics of COVID-19 Omicron subvariant BF.7. lineage via gathering and analyzing the cases with Omicron subvariant in Hohhot, Inner Mongolia.

METHODS

Based upon this, we linked variant Omicron BF.7 individual-level information including sex, age, symptom, underlying conditions and vaccination record. Further, we divided the cases into various groups and assessed the severity of patients according to the symptoms of patients with COVID-19. Clinical indicators and data might help to predict disadvantage outcomes and progression among Omicron BF.7 patients.

RESULTS

In this study, in patients with severe symptoms, some indicators from real world data such as white blood cells, AST, ALT and CRE in patients with Omicron BF.7 in severe symptoms were significantly higher than mild and asymptomatic patients, while some indicators were significantly lower.

CONCLUSIONS

Above results suggested that the indicators were associated with ponderance of clinical symptoms. Our survey emphasized the value of timely investigations of clinical data obtained by systemic study to acquire detailed information.

The African Kelleni's roadmap using nitazoxanide and broad-spectrum antimicrobials to abort returning to COVID-19 square one

For over 3.5 years, SARS CoV-2 is continuing to evolve threatening to return all and any improvement the world has made into square one. In this clinically oriented systematic review and perspective, the author explains how the best current medical evidence is strongly supporting the use of the low cost, widely available and very safe nitazoxanide in early management of COVID-19, debates the relevant theoretical studies that negated or doubted this benefit, and suggests an African roadmap to preempt the worst-case scenario if or when a new SARS CoV-2 (sub) variant or even a new respiratory virus causes a new global surge of morbidity and mortality. Kelleni's protocol, including nitazoxanide as an integral component, is continuing to perfectly save lives of patients infected with many viruses, including SARS CoV-2 and the author stresses that respiratory RNA viruses are best managed with early pharmacological treatment. Broad-spectrum antimicrobials as nitazoxanide and azithromycin together with other therapeutics as non-steroidal anti-inflammatory drugs and the antihistaminic loratadine should be considered first to personalize the clinical management of COVID-19 and selected other alarming viral infections.

First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger

The emergence of the Omicron variant in November 2021, has caused panic worldwide due to the rapid evolution and the ability of the virus to escape the immune system. Since, several Omicron sublineages (BA.1 to BA.5) and their descendent recombinant lineages have been circulating worldwide. Furthermore, in December 2022, a new Omicron subvariant XBB.1.5 characterized by an unusual mutation in the spike protein evolved in the United States and rapidly spread to the other continents. Our study reports on the first cases of XBB.1.5 sublineage among indigenous Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) positive cases detected through the influenza sentinel surveillance system in Niger. All influenza suspected cases were tested for both influenza and SARS-COV-2 using the Centre for Disease Control and prevention (CDC) Influenza SARS-COV-2 Multiplex quantitative Reverse-Transcription Polymerase Chain Reaction (qRT-PCR) Assay. SARS-COV-2 positive samples with cycle threshold ≤28 were selected for whole genome sequencing subsequently using the Oxford Nanopore Midnight protocol with rapid barcoding on a MinIon MK1B device. A total of 51 SARS-COV-2 positive samples were confirmed between December 2022 and March 2023. We successfully obtained 19 sequences with a predominance of the XBB.1/XBB.1.5 sublineages (73.7 %). In addition, a recombinant XBD sequence was also first-ever identified in early March 2023. Our findings support the need to strengthen the influenza sentinel surveillance for routine Coronavirus Disease 2019 (COVID-19) surveillance and SARS-COV-2 variants monitoring in Niger.

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.