Potential threat and possible global spread of the novel SARS-CoV-2 Omicron subvariants including XBB.1.16 during the Indian Premier League 2023: strict implementation of traveller guidelines suggested

Prospective clinical performance of CoVarScan in identifying SARS-CoV-2 Omicron subvariants

The purpose of this work was to evaluate the performance of CoVarScan, a multiplex fragment analysis approach, in identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of the Omicron lineage rapidly and accurately. The ability to identify variants with high fidelity and low turnaround time is important both epidemiologically and clinically for pandemic monitoring and therapeutic monoclonal antibody (mAb) selection. Currently, the gold-standard test for this task is whole-genome sequencing (WGS), which is prohibitively expensive and/or inaccessible due to equipment requirements for many laboratories. Omicron variants have been closely related, so the ability of genotyping tests to differentiate them is an important, outstanding question. CoVarScan uses PCR targeting eight SARS-CoV-2 mutational hot spots. In total, 4,918 SARS-CoV-2-positive cases between 17 December 2021 and 31 January 2024 were included in the analysis. CoVarScan achieved 96.5% concordance with WGS and could detect unique mutational signatures for BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, XBB, and BA.2.86. These are the major variants of concern (VOCs) that have dominated since Omicron originally appeared in December 2021. Lastly, based on panel design, we predict a unique mutational pattern for the newly emergent, highly mutated variant BA.2.87. CoVarScan can rapidly, accurately, and cost-effectively identify all Omicron variants in a scalable manner. Furthermore, CoVarScan does not require design alterations to detect new VOCs. CoVarScan performs as accurately as WGS with higher sensitivity, allowing its use as a tool to quickly identify variants for epidemiological surveillance and clinical decision-making in the selection of effective therapeutic mAbs.IMPORTANCEAlmost 5 years since the start of the pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern continue to emerge, with mutations conferring new properties like increased transmissibility and resistance to therapeutic monoclonal antibodies and vaccines. Conventionally, whole-genome sequencing (WGS) has characterized new SARS-CoV-2 variants, but results come too late for clinical actionability. WGS suffers from high failure rates for samples with low viral RNA and is inaccessible for lower-resource laboratories. As new variants like Omicron appear, it is necessary to develop rapid and accurate testing to distinguish between variants. Fast and accurate identification of sensitive viral lineages would allow tailored use of monoclonal antibodies that may otherwise have been pulled from the market due to rising overall resistance. Rapid results also allow public health officials to make policy decisions in time to reduce morbidity and mortality for sensitive populations such as patients who are immunocompromised or have significant medical comorbidities.

Impact of mutations in SARS-CoV-2 recombinant sub-variant XBB.1.16 on the binding affinity with human ACE2 receptor

Despite the waning threat of the COVID-19 pandemic, its detrimental impact on global health persists. Regardless of natural immunity or immunity obtained through vaccination, emerging variants of the virus continue to undergo mutations and propagate globally. The persistent mutations in SARS-CoV-2, along with the subsequent formation of recombinant sub-variants has become a challenge for researchers and health professionals, raising concerns about the efficacy of current vaccines. Gaining a better understanding of the biochemical interactions between the Spike Protein (RBD) of SARS-CoV-2 variants and the human ACE2 receptor can prove to be beneficial in designing and developing antiviral therapeutics that are equally effective against all strains and emerging variants. Our objective in this study was to investigate the interfacial binding pattern of the SARS-CoV-2 RBD-ACE2 complex of the Wild Type (WT), Omicron, and the Omicron recombinant sub-variant XBB.1.16. We aimed to examine the atomic level factors and observe how mutations influence the interaction between the virus and its host using Molecular Dynamics simulation, MM/GBSA energy calculations, and Principal Component Analysis. Our findings reveal a higher degree of structural deviation and flexibility in XBB.1.16 compared to WT and Omicron. PCA indicated a wider cluster and significant flexibility in the movements of XBB.1.16 which can also be observed in free energy landscapes, while the normal mode analysis revealed converging motions within the RBD-ACE2 complexes which can facilitate the interaction between them. A pattern of decreased binding affinity was observed in case of XBB.1.16 when compared to the WT and Omicron. These observed deviations in XBB.1.16 when compared to its parent lineage Omicron, and WT can be attributed to the mutations specific to it. Collectively, these results enhance our understanding of the impact of mutations on the interaction between this strain and the host, taking us one step closer to designing effective antiviral therapeutics against the continually mutating strains.

SARS-CoV-2 Variants BA.2.86 and EG.5.1 Alongside Scrub Typhus and Nipah in India During the Ongoing Cricket World Cup 2023: Threat Perceptions and Countermeasures

The United States (US), the United Kingdom (UK), and China witnessed rising cases of coronavirus disease 2019 (COVID-19) in 2023. Concerns about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) novel strains amid the sudden surge of COVID cases are growing. Recently, BA.2.86 (Pirola) poses a much greater risk due to its higher transmission rate and spreading across regions. Pirola variant has mutations that set it apart from all earlier known SARS-CoV-2 variants. This variant was designated a variant of interest by the World Health Organization (WHO). Another SARS-CoV-2 variant named "Eris" (EG.5.1) was detected in India and started picking up in the US and the UK. The WHO listed EG.5.1 (variant) as a variant under monitoring. Therefore, it is important to remain vigilant. Further, multiple Nipah virus infections and scrub typhus cases are spreading among humans in India currently. In this situation, the 13th edition of the International Cricket Council (ICC) Men's Cricket World Cup is being held in India this year. With global reach, this big sporting carnival attracts millions of cricket fans from several countries. In light of the multiple public health concerns encountered currently, this gala global sports event needs additional preventive measures.

Current Surge of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Variants in China Could Be Threatening as the Asian Games 2023 Flags Off in September: Foolproof Cautionary Measures Are Suggested

Despite normalcy having almost returned in the lives of people throughout the world post-coronavirus disease-19 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the danger still looms over the fears of development and propagation of a newer SARS-CoV-2 variant. The movement of people globally has reached the pre-pandemic level, and this augmentation increased surveillance regarding the emergence of lethal SARS-CoV-2 variants. International sports events are among the potential avenues where the virus could cause serious impact. Therefore, the organization of such events should be planned and executed meticulously to avoid viral transmission and minimize the health effects of infections on the sportspersons and the local people. Additionally, there could be dissemination of the infections to the native countries of the participants and visitors while they return to their homes. Through this editorial, we prompt caution to the organizers and the event-hosting nation's administration regarding the potential threat and suggest measures to avoid any medical emergencies related to COVID-19.