Anticipating the future of the COVID-19 pandemic: insights into the emergence of SARS-CoV-2 variant JN.1 and its projected impact on older adults

Real-Time PCR-Based Test as a Research Tool for the Retrospective Detection and Identification of SARS-CoV-2 Variants of Concern in a Sample

The Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), a causative agent of the COVID-19 disease, has been constantly evolving since its first identification. Mutations that are embedded in the viral genomic RNA affect the properties of the virus and lead to the emergence of new variants. During the COVID-19 pandemic, the World Health Organization has identified more than ten variants of the SARS-CoV-2 virus. Five of these-Alpha, Beta, Gamma, Delta, and Omicron-were classified as variants of concern (VOCs), as they caused significant outbreaks of the disease. Additionally, two progeny variants of Omicron, designated JN.1 and KS.1, are still causing new waves of infections. Due to the emergence of various SARS-CoV-2 variants, in some cases, it has become important to identify a particular variant in a sample. Here, we have developed a multiplexed probe-based real-time PCR system for the identification of SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta, Omicron B.1.1.529/BA.1, and Omicron BA.2), as well as modern Omicron variants JN.1 and KS.1. The sensitivity and specificity of the PCR system have been tested using isolated viral genomes and RNA preparations from human nasopharyngeal swabs. The system allows for rapid identification of coronavirus variants in the cryopreserved and fresh samples.

Evaluation of the Content Validity of the COVID-19 Symptoms Daily Diary

Introduction

The COVID-19 Symptoms Daily Diary (CSDD) is a patient-reported outcome measure designed to assess the severity of core COVID-19 symptoms in clinical trials. The preliminary version of the CSDD was developed based on regulatory guidance and the hallmark COVID-19 symptoms identified by the CDC. This study aimed to evaluate CSDD content validity, to determine whether it is fit for the purpose of supporting efficacy endpoints in clinical trials of treatments for COVID-19. This research also sought to evaluate the appropriateness of a newly developed Pre-COVID-19 Symptoms Questionnaire.

Methods

A targeted literature review was completed to evaluate the relevance of concepts included in the diary and to identify any important symptoms that may have been missing. Hybrid (concept elicitation and cognitive debriefing) semistructured qualitative interviews were then conducted across 3 iterative rounds with 30 adults in the United States recently diagnosed with COVID-19.

Results

The CSDD included concepts that were most frequently reported by interview participants, including those identified as most bothersome and most important to treat. During cognitive debriefing, participants described the diary concepts as salient and reported the instructions, recall period, and response options as clear and appropriate. Only 2 of 15 CSDD items were modified across 3 interview rounds; specifically, definitions for the vomiting and diarrhea frequency items were clarified for consistent interpretation and response. Interview participants also reported general ease in understanding and responding to the Pre-COVID-19 questionnaire, with feedback resulting in only minor changes to the reference period and instructions.

Conclusion

The findings of the current study provide strong evidence for the content validity of the CSDD and the appropriateness of each of the items assessed. This rigorous evaluation (aligned with regulatory guidance) indicates that the CSDD is fit for the purpose of supporting efficacy endpoints in planned clinical trials evaluating medications for COVID-19 treatment.

The JN.1 variant of COVID-19: immune evasion, transmissibility, and implications for global health

The emergence of the COVID-19 JN.1 variant has raised global health concerns as it gains prevalence in several regions worldwide. First identified in August 2023, JN.1 evolved from the Omicron lineage's BA.2.86 subvariant. Patients infected with JN.1 commonly exhibit symptoms such as sore throat, fever, dry cough, nausea, and vomiting. While the World Health Organization has labeled JN.1 a Variant of Interest, it currently presents a low global health risk. However, its increased transmissibility, particularly in cold, dry climates, is concerning. This review provides a comprehensive overview of JN.1's biological characteristics, epidemiology, transmissibility, immune evasion, and the efficacy of existing antiviral treatments and vaccination strategies. A literature search across key databases targeted studies from January 2023 to August 2024, emphasizing recent insights into JN.1's spread and clinical impact. Findings reveal that JN.1 exhibits higher infectivity and immune evasion than previous variants, largely due to the L4555 mutation. From November 2023 to March 2024, JN.1 showed an increasing trend in transmission. Previously approved antivirals, including Paxlovid, Veklury, and Lagevrio, demonstrate effectiveness against JN.1, and current vaccines still protect against severe illness from this variant. However, vaccination rates remain low. Monitoring efforts include genomic assessments, wastewater surveillance, and digital tracking to contain the variant's spread. It is essential to encourage the public to maintain vaccination and preventive measures to reduce JN.1's impact. Continued research is critical for understanding and managing the evolving landscape of COVID-19 and its emerging variants.

Fortifying defenses: Tactical safety protocols for COVID-19 sub-variant JN.1 in healthcare and laboratory settings

Introduction

Primary care physicians are crucial in fighting COVID-19, especially with the emergence of the new JN.1 sub-variant.

Measures to Reduce Risk

Given your direct exposure to infected patients, it is imperative to establish a protocol for triaging patients with respiratory symptoms and to uphold a minimum distance of 2 meters between patients and primary care physicians. Patients suspected or diagnosed with the JN.1 sub-variant should be advised to wear surgical masks for their protection and others protection. Primary care physicians must also use personal protective equipment (PPE) and maintain strict hand hygiene practices when dealing with these patients. Patient samples should be treated as high risk for contamination, and laboratory procedures should be meticulously evaluated for potential hazards. PPE should be tailored to the procedure.

Conclusion

To protect the health and well-being of primary care physicians, who play a critical role in addressing the challenges, it is essential to strictly adhere to infection control measures.

A SARS-CoV-2 EG.5 mRNA vaccine induces a broad-spectrum immune response in mice

The emerging of emergent SARS-CoV-2 subvariants has reduced the protective efficacy of COVID-19 vaccines. Therefore, novel COVID-19 vaccines targeting these emergent variants are needed. We designed and prepared CoV072, an mRNA-based vaccine against SARS-CoV-2 Omicron (EG.5) and other emergent SARS-CoV-2 subvariants that encodes the EG.5 spike protein. Six-week-old female BALB/C mice were used to assess humoral and cellular immune responses and cross-reactive neutralizing activity against various SARS-CoV-2 subvariants. Meanwhile different immunization strategies and doses were performed to detect the immunogenicity of this mRNA vaccine. Our results show that two doses of 5 µg CoV072 or a single dose of 15 µg CoV072 both induced broad-spectrum cross-protection ability in mice. Compared with a single dose of 15 µg CoV072, two doses of 5 µg COV072 exhibited higher levels of pseudovirus neutralizing antibody (PNAb) and cross-reactive IgG responses to multiple variants. Moreover, higher levels of neutralizing antibody (NAb) against live XBB and EG.5 variants were also induced. Th1-biased cellular immune response was induced in all vaccination groups. The antigen design and immunization strategy of this study have reference significance for the research of the next generation of COVID-19 vaccine and other vaccines.

Daphnetin may protect from SARS-CoV-2 infection by reducing ACE2

To combat the SARS-CoV-2 pandemic, innovative prevention strategies are needed, including reducing ACE2 expression on respiratory cells. This study screened approved drugs in China for their ability to downregulate ACE2. Daphnetin (DAP) was found to significantly reduce ACE2 mRNA and protein levels in PC9 cells. DAP exerts its inhibitory effects on ACE2 expression by targeting HIF-1α and JAK2, thereby impeding the transcription of the ACE2 gene. The SARS-CoV-2 pseudovirus infection assay confirmed that DAP-treated PC9 cells exhibited decreased susceptibility to viral infection. At therapeutic doses, DAP effectively lowers ACE2 expression in the respiratory systems of mice and humans. This suggests that DAP, already approved for other conditions, could be a new preventive measure against SARS-CoV-2, offering a cost-effective and accessible way to reduce SARS-CoV-2 spread.

Emerging SARS-CoV-2 Variants in Uganda in the Era of COVID-19 Vaccination

The emergence of SARS-CoV-2 variants has heightened concerns about vaccine efficacy, posing challenges in controlling the spread of COVID-19. As part of the COVID-19 Vaccine Effectiveness and Variants (COVVAR) study in Uganda, this study aimed to genotype and characterize SARS-CoV-2 variants in patients with COVID-19-like symptoms who tested positive on a real-time PCR. Amplicon deep sequencing was performed on 163 oropharyngeal/nasopharyngeal swabs collected from symptomatic patients. Genome assembly, lineage classification and phylogenetic analysis was performed using the Edge Bioinformatics pipeline version 2.4.0, Pangolin version 4.3.1 and iqtree version 2.3.6 software respectively. Of the 163 deep sequences analyzed between April 2023 and March 2024, the most common were XBB.1 lineages and sublineages (113, 69.3%), followed by JN.1* (12, 7.4%), XBB.2* (11, 6.7%) and FL* (11, 6.7%), EG* (7, 4.3%), others (BQ.1.1, FY.4.1, FY.4.1.2, GY.2.1, HK.27.1) (5, 3.1%) and CM* (4, 2.5%). XBB.1* dominated from April to July 2023; thereafter, other variants, including JN.1* were increasingly detected. There was no statistically significant association between vaccine status and lineage assignment (Fisher's exact test, p-value = 0.994). Our findings showed that the Omicron variant, specifically the XBB.1* lineage, was the dominant circulating virus. However, the emergence of the JN.1 variant that exhibits a significant spike protein mutation profile could impact COVID-19 transmission in Uganda.

SARS-CoV-2 and Environmental Changes: The Perfect Storm

The COVID-19 pandemic has had a significant impact on the global economy. It also provided insights into how the looming global climate crisis might be addressed, as there are several similarities between the challenges proposed by COVID-19 and those expected from the coming climate emergency. COVID-19 is an immediate health threat, but climate change represents a more gradual and insidious risk that will lead to long-term consequences for human health. Research shows that climate change, air pollution and the pandemics have a negative impact on health. Recent studies show that COVID-19 mortality increases with climate extremes. The goal of our review is to analyze the clinical findings of COVID-19 and how they are affected by the climate change, while also providing insight into the emergence of new variants and their ability to evade the immune system. We selected and synthesized data from primary studies, reviews, meta-analyses, and systematic reviews. Selection was based on rigorous methodological and relevance criteria. Indeed, a new variant of SARS-CoV-2, named JN.1, has emerged as the dominant, first in the United States and then worldwide; the variant has specific mutations in its spike proteins that increase its transmissibility. According to the World Health Organization (WHO), JN.1 is currently the most reported variant of interest (VOI), having been identified in 132 countries. We highlight the link between climate change and pandemics, emphasizing the need for global action, targeted medical approaches and scientific innovation.

Enhancing COVID-19 Vaccination Awareness and Uptake in the Post-PHEIC Era: A Narrative Review of Physician-Level and System-Level Strategies

Following the World Health Organization's declaration that the COVID-19 pandemic is no longer a public health emergency of international concern (PHEIC), COVID-19 remains an ongoing threat to human health and healthcare systems. Vaccination plays a crucial role in reducing the disease's incidence, mitigating its severity, and limiting transmission, contributing to long-term public health resilience. However, incomplete vaccination coverage and vaccine hesitancy exist. This narrative review investigates strategies at the system and physician levels aimed at sustaining awareness and uptake of COVID-19 vaccination in a post-PHEIC era. Through an examination of the existing literature, this review explores the effectiveness of diverse approaches utilized by healthcare systems and individual providers. These approaches address every component of the 5C model of vaccine hesitancy: confidence, complacency, constraints/convenience, calculation, and collective responsibility. Physician-level approaches include appropriate message framing, persuasive communication containing safety and personal/social benefit information, sharing of personal stories, creating a safe space for discussion, harnessing co-administration with annual influenza vaccines, and use of decision aids and visual messages. System-level approaches include messaging, mass media for health communication, on-site vaccine availability, pharmacist delivery, healthcare protocol integration, incentives, and chatbot use.

COVID-19: vaccination, therapeutics and a review of the science and public health

COVID-19, stemming from the SARS-CoV-2 virus, has initiated a worldwide respiratory pandemic. Remarkable headway has been made in the realm of vaccination, as nearly every nation has initiated COVID-19 vaccine deployment. However, a mere 32.6% of individuals in low-income countries have received only a single vaccine dose. Unprecedented research and development endeavors have yielded over 170 COVID-19 vaccines, several of which are now in practical use. These vaccines have demonstrated remarkable efficacy in averting severe illness, hospitalization, and fatalities from COVID-19, even against emerging variants. Research pursuits persist, concentrating on novel vaccine technologies, oral and nasal vaccines, broader coronavirus protection, and vaccine combinations. In the realm of therapeutics, there have been significant strides in developing oral antiviral medications and monoclonal antibodies. Nonetheless, challenges in COVID-19 vaccination persist, encompassing issues of hesitancy, accessibility, financial barriers, knowledge gaps, and logistical hindrances. Robust monitoring via global agencies and reporting systems remains pivotal. Strategies for enhancing vaccination efficacy are rooted in fostering trust, countering misinformation, and expanding access. As for therapeutics, the approach involves dedicated research, clinical trials, regulatory streamlining, stockpiling, and international collaboration. Telemedicine and public awareness campaigns play integral roles in this effort, with coordination being the linchpin for preserving lives and mitigating the disease's impact. The global campaign against COVID-19 has witnessed substantial advancements, with an ongoing research focus on developing vaccines and therapeutics that are not only more accessible and affordable but also more effective, particularly for populations in low-income countries and vulnerable communities.

JN.1 and the ongoing battle: unpacking the characteristics of a new dominant COVID-19 variant

In the fourth year of the COVID-19 occurrence, a new COVID-19 variant, JN.1, has emerged and spread globally and become the dominant strain in several regions. It has some specific mutations in its spike proteins, empowering it with higher transmissibility. Regarding the significance of the issue, understanding the clinical and immunological traits of JN.1 is critical for enhancing health strategies and vaccination efforts globally, with the ultimate goal of bolstering our collective response to the pandemic. In this study, we take a look at the latest findings of JN.1 characteristics and mutations as well as its consequences on bypassing immune system. We demonstrate the importance of continual surveillance and strategic adaptation within healthcare frameworks along with the significance of wastewater sampling for the rapid identification of emerging SARS-CoV-2 variants.

SARS-CoV-2 JN.1 variant: a short review

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded, positive-sense RNA virus. The SARS-CoV-2 virus is evolving continuously, and many variants have been detected over the last few years. SARS-CoV-2, as an RNA virus, is more prone to mutating. The continuous evolution of the SARS-CoV-2 virus is due to genetic mutation and recombination during the genomic replication process. Recombination is a naturally occurring phenomenon in which two distinct viral lineages simultaneously infect the same cellular entity in an individual. The evolution rate depends on the rate of mutation. The rate of mutation is variable among the RNA viruses, with the SARS-CoV-2 virus exhibiting a lower rate of mutation than other RNA viruses. The novel 3'-to-5' exoribonuclease proofreading machinery is responsible for a lower rate of mutation. Infection due to the SARS-CoV-2, influenza, and respiratory syncytial virus has been reported from around the world during the same period of fall and winter, resulting in a "tripledemic." The JN.1 variant, which evolved from the predecessor, the omicron variant BA.2.86, is currently the most dominant globally. The impact of the JN.1 variant on transmissibility, disease severity, immune evasion, and diagnostic and therapeutic escape will be discussed.

Characteristics and clinical manifestations of patients, including organ transplant patients, during the surge of JN.1: Insights from Saudi Arabia

BACKGROUND

Amidst the persistent global health threat posed by the evolving SARS-CoV-2 virus throughout the four-year-long COVID-19 pandemic, the focus has now turned to the Omicron variant and its subvariant, JN.1, which has rapidly disseminated worldwide. This study reports on the characteristics and clinical manifestations of patients during the surge of the JN.1 variant in Saudi Arabia; it also investigates the evolution of SARS-CoV-2 variants in organ transplant patients and identifies patient risk factors.

METHODS

A total of 151 nasopharyngeal samples from patients with PCR-confirmed SARS-CoV-2 infection were collected between September 2023 and January 2024. Demographic and clinical data of the patients were obtained from electronic health records. All confirmed positive samples underwent sequencing using Ion GeneStudio and the Ion AmpliSeq™ SARS-CoV-2 panel.

RESULTS

During the surge of the JN.1 variant, the average age of the patients was 40 years, ranging from 3 to 93 years, and nearly 50% of the patients were male. Our investigation revealed that the J.N variant predominantly infected patients with comorbidities or organ transplant recipients (57.6%). Moreover, patients with comorbidities or organ transplants exhibited a higher number of mutations. In our organ transplant cohort, an increased total number of spike mutations was associated with a lower risk of developing severe disease (OR = 0.96, 95% CI: 0.93-0.98).

CONCLUSIONS

Although JN.1 may not prove to be particularly harmful, it is crucial to recognize the persistent emergence of concerning variants, which create new pathways for the virus to evolve. The ongoing evolution of SARS-CoV-2 is evident in the continuous divergence of these variants from the original strain that marked the onset of the pandemic nearly four years ago.

Evolving immune evasion and transmissibility of SARS-CoV-2: The emergence of JN.1 variant and its global impact

The continuous evolution of SARS-CoV-2 variants constitutes a significant impediment to the public health. The World Health Organization (WHO) has designated the SARS-CoV-2 variant JN.1, which has evolved from its progenitor BA.2.86, as a Variant of Interest (VOI) in light of its enhanced immune evasion and transmissibility. The proliferating dissemination of JN.1 globally accentuates its competitive superiority and the potential to instigate fresh surges of infection, notably among cohorts previously infected by antecedent variants. Notably, prevailing evidence does not corroborate an increase in pathogenicity associated with JN.1, and antiviral agents retain their antiviral activity against both BA.2.86 and JN.1. The sustained effectiveness of antiviral agents offers a beacon of hope. Nonetheless, the variant's adeptness at eluding the immunoprotective effects conferred by extant vaccines highlights the imperative for the development of more effective vaccines and therapeutic approaches. Overall, the distinct evolutionary trajectories of BA.2.86 and JN.1 underscore the necessity for ongoing surveillance and scholarly inquiry to elucidate their implications for the pandemic's evolution, which requires the international communities to foster collaboration through the sharing of data, exchange of insights, and collective scientific endeavors.

Next-generation treatments: Immunotherapy and advanced therapies for COVID-19

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in 2019 following prior outbreaks of coronaviruses like SARS and MERS in recent decades, underscoring their high potential of infectivity in humans. Insights from previous outbreaks of SARS and MERS have played a significant role in developing effective strategies to mitigate the global impact of SARS-CoV-2. As of January 7, 2024, there have been 774,075,242 confirmed cases of COVID-19 worldwide. To date, 13.59 billion vaccine doses have been administered, and there have been 7,012,986 documented fatalities (https://www.who.int/) Despite significant progress in addressing the COVID-19 pandemic, the rapid evolution of SARS-CoV-2 challenges human defenses, presenting ongoing global challenges. The emergence of new SARS-CoV-2 lineages, shaped by mutation and recombination processes, has led to successive waves of infections. This scenario reveals the need for next-generation vaccines as a crucial requirement for ensuring ongoing protection against SARS-CoV-2. This demand calls for formulations that trigger a robust adaptive immune response without leading the acute inflammation linked with the infection. Key mutations detected in the Spike protein, a critical target for neutralizing antibodies and vaccine design -specifically within the Receptor Binding Domain region of Omicron variant lineages (B.1.1.529), currently dominant worldwide, have intensified concerns due to their association with immunity evasion from prior vaccinations and infections. As the world deals with this evolving threat, the narrative extends to the realm of emerging variants, each displaying new mutations with implications that remain largely misunderstood. Notably, the JN.1 Omicron lineage is gaining global prevalence, and early findings suggest it stands among the immune-evading variants, a characteristic attributed to its mutation L455S. Moreover, the detrimental consequences of the novel emergence of SARS-CoV-2 lineages bear a particularly critical impact on immunocompromised individuals and older adults. Immunocompromised individuals face challenges such as suboptimal responses to COVID-19 vaccines, rendering them more susceptible to severe disease. Similarly, older adults have an increased risk of severe disease and the presence of comorbid conditions, find themselves at a heightened vulnerability to develop COVID-19 disease. Thus, recognizing these intricate factors is crucial for effectively tailoring public health strategies to protect these vulnerable populations. In this context, this review aims to describe, analyze, and discuss the current progress of the next-generation treatments encompassing immunotherapeutic approaches and advanced therapies emerging as complements that will offer solutions to counter the disadvantages of the existing options. Preliminary outcomes show that these strategies target the virus and address the immunomodulatory responses associated with COVID-19. Furthermore, the capacity to promote tissue repair has been demonstrated, which can be particularly noteworthy for immunocompromised individuals who stand as vulnerable actors in the global landscape of coronavirus infections. The emerging next-generation treatments possess broader potential, offering protection against a wide range of variants and enhancing the ability to counter the impact of the constant evolution of the virus. Furthermore, advanced therapies are projected as potential treatment alternatives for managing Chronic Post-COVID-19 syndromeand addressing its associated long-term complications.