Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

SARS-CoV-2 epidemiology, kinetics, and evolution: A narrative review

Since winter 2019, SARS-CoV-2 has emerged, spread, and evolved all around the globe. We explore 4 y of evolutionary epidemiology of this virus, ranging from the applied public health challenges to the more conceptual evolutionary biology perspectives. Through this review, we first present the spread and lethality of the infections it causes, starting from its emergence in Wuhan (China) from the initial epidemics all around the world, compare the virus to other betacoronaviruses, focus on its airborne transmission, compare containment strategies ("zero-COVID" vs. "herd immunity"), explain its phylogeographical tracking, underline the importance of natural selection on the epidemics, mention its within-host population dynamics. Finally, we discuss how the pandemic has transformed (or should transform) the surveillance and prevention of viral respiratory infections and identify perspectives for the research on epidemiology of COVID-19.

Modeling the effects of cross immunity and control measures on competitive dynamics of SARS-CoV-2 variants in the USA, UK, and Brazil

Mutation in the SARS-CoV-2 virus may lead to the evolution of new variants. The dynamics of these variants varied among countries. Identification of the governing factors responsible for distinctions in their dynamics is important for preparedness against future severe variants. This study investigates the impact of cross immunity and control measures on the competition dynamics of the Alpha, Gamma, Delta, and Omicron variants. The following questions are addressed using an n-strain deterministic model: (i) Why do a few variants fail to cause a wave even after winning the competition? (ii) In what scenarios a new variant cannot replace the previous one? The model is fitted and cross-validated with the data of COVID-19 and its variants for the USA, UK, and Brazil. The model analysis highlights implementations of the following measures against any deadlier future variant: (i) an effective population-wide cross-immunity from less lethal strains and (ii) strain-specific vaccines targeting the novel variant. The system exhibits a fascinating dynamical behavior known as an endemic bubble due to Hopf bifurcation. It is observed that the actual situation in which Omicron won the competition from Delta followed by no wave due to Delta may turn into a competitive periodic coexistence of two strains due to substantial disparity in fading rates of cross-immunity. Global sensitivity analysis is conducted to quantify uncertainties of model parameters. It is found that examining the impact of cross-immunity is as crucial as vaccination.

An informed deep learning model of the Omicron wave and the impact of vaccination

The Omicron (B.1.1.529) variant of SARS-CoV-2 emerged in November 2021 and has since evolved into multiple lineages. Understanding its transmission, vaccine efficacy, and potential for reinfection is crucial. This study examines the dynamics of Omicron in Germany, France, and Italy by employing Physics-Informed Neural Networks to estimate the temporal parameters influencing its spread. We validated the performance of our model using the Root Mean Squared Percent Error (RMSPE). Our analysis revealed significant correlations between specific viral mutations-S371F, T376A, D405N, and R408S-and increased transmission rates in all three countries. These mutations, prevalent in the Omicron BA.2 and BA.3 sublineages, are linked to immune evasion and heightened transmissibility.

Defining diverse spike-receptor interactions involved in SARS-CoV-2 entry: Mechanisms and therapeutic opportunities

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped RNA virus that caused the Coronavirus Disease 2019 (COVID-19) pandemic. The SARS-CoV-2 Spike glycoprotein binds to angiotensin converting enzyme 2 (ACE2) on host cells to facilitate viral entry. However, the presence of SARS-CoV-2 in nearly all human organs - including those with little or no ACE2 expression - suggests the involvement of alternative receptors. Recent studies have identified several cellular proteins and molecules that influence SARS-CoV-2 entry through ACE2-dependent, ACE2-independent, or inhibitory mechanisms. In this review, we explore how these alternative receptors were identified, their expression patterns and roles in viral entry, and their impact on SARS-CoV-2 infection. Additionally, we discuss therapeutic strategies aimed at disrupting these virus-receptor interactions to mitigate COVID-19 pathogenesis.

Multiple exposures to SARS-CoV-2 Spike enhance cross-reactive antibody-dependent cellular cytotoxicity against SARS-CoV-1

Vaccination or infection by SARS-CoV-2 elicits a protective immune response against severe outcomes. It has been reported that SARS-CoV-2 infection or vaccination elicits cross-reactive antibodies against other betacoronaviruses. While plasma neutralizing capacity was studied in great detail, their Fc-effector functions remain understudied. Here, we analyzed Spike recognition, neutralization and antibody-dependent cellular cytotoxicity (ADCC) against D614G, a recent Omicron subvariant of SARS-CoV-2 (JN.1) and SARS-CoV-1. Plasma from individuals before their first dose of mRNA vaccine, and following their second, third and sixth doses were analyzed. Despite poor neutralization activity observed after the second and third vaccine doses, ADCC was readily detected. By the sixth dose, individuals could neutralize and mediate ADCC against JN.1 and SARS-CoV-1. Since previous reports have shown that Fc-effector functions were associated with survival from acute infection, these results suggest that ADCC could help in combating future SARS-CoV-2 variants as well as closely related coronaviruses.

Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron's several subvariants and the current rise of KP.3.1.1 and XEC

The recent COVID-19 pandemic is one of the quickest-evolving pandemics in the world history. Therefore, the evolution of SARS-CoV-2 needs to be tracked consistently. Various VOIs, VOCs, and recent subvariants of Omicron have emerged from the dynamically evolving SARS-CoV-2. Various offspring of the Omicron subvariants have emerged since its origin, including lineages such as BA, BQ, and XBB, as well as more recent subvariants like BA.2.86, JN.1, JN.11.1, KP.3, KP.3.1.1, and XEC. The study evaluated the overall and one year evolutionary patterns, genome diversity, divergence event, transmission and geographical distributions, circulating frequency, entropy diversity, mutational diversity, risk mutations in S-protein and mutational fitness of the subvariants. The study estimated the substitution rate of all variants and subvariants of SARS-CoV-2 since its origin (32.001 × 10-4 subs/year). The geographical distributions of the recent KP.3.1.1 and XEC subvariant indicated its distribution in North America, South America, Europe, and Southeast Asia. Simultaneously, genome mutational landscapes were noted, including Spike and RBD mutations. We found that JN.1, JN.1.11.1, KP.3, KP.3.1.1 and XEC subvariants have gained the highest mutational fitness in Europe and North America. Our study indicates that the rapid evolution and highest frequency of mutational fitness have created a variety of subvariants from Omicron. It also indicates a shift from waves to mini-waves. Finally, our possible explanation is that mutation-driven divergent evolution contributes to the emergence of recent subvariants.

Adult Long Coronavirus Disease 2019: Definition, Prevalence Pathophysiology, and Clinical Manifestations

Long coronavirus disease 2019 (COVID-19) is a multisystem disorder with variable manifestations and duration. One in 10 people with a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will develop some manifestation of long COVID-19. Currently, there is no one single etiologic factor for the symptoms and signs of long COVID-19 beyond exposure to the SARS-CoV-2 virus. There are multiple theories about the pathophysiology ranging from viral persistence, reactivation, autoimmunity, and immune depletion. Certain risk factors have been identified including female sex, severe acute/hospitalized COVID-19, previous infections with SARS-CoV-2, and absence of vaccinations.

Comparison of long-term health-related quality of life and symptoms between COVID-19 patients and test-negative controls during the Omicron-predominant period in Japan

BACKGROUND

Persistent symptoms following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affect health-related quality of life (HRQoL) and impose a substantial burden on society. While previous studies showed that both coronavirus disease 2019 (COVID-19) patients and patients with acute respiratory symptoms but negative for SARS-CoV-2 experienced persistent symptoms, evidence comparing the long-term HRQoL of COVID-19 patients with test-negative controls for SARS-CoV-2 remains limited. This study aimed to compare symptoms and HRQoL using EQ-5D-5L in both acute and chronic phases between COVID-19 patients and test-negative controls for SARS-CoV-2 during the Omicron-predominant period in Japan.

METHODS

Individuals aged ≥18 years tested for SARS-CoV-2 with COVID-19-like symptoms at a clinic in Tokyo, Japan, between January 2022 and January 2023, were invited an online survey. Individuals who tested positive and negative for SARS-CoV-2 were both included. Participants retrospectively recorded their physical and mental symptoms, and completed EQ-5D-5L questionnaires during the acute phase, and at months 1, 3, and 6, which were compared between COVID-19 patients and test-negative controls. Additionally, the mean EQ-5D-5L utility score was compared between male and female COVID-19 patients.

RESULTS

A total of 302 COVID-19 patients and 77 test-negative controls were included (median age: 42 years; 41.2% male; 13.2% with underlying medical conditions). At month 3, 19.9% (60/302) of COVID-19 patients and 9.1% (7/77) of test-negative controls reported ongoing symptoms. Mental symptoms and fatigue persisted for over three months among COVID-19 patients. The mean EQ-5D-5L utility score during the acute phase for COVID-19 patients was 0.615 (95% confidence interval [CI]: 0.586-0.645), and 0.874 (95% CI: 0.826-0.921) for test-negative controls, with a mean difference of -0.258 (95% CI: -0.324 to -0.193). COVID-19 patients consistently exhibited lower EQ-5D-5L utility scores than controls for over six months post-infection. Female COVID-19 patients showed lower EQ-5D-5L utility scores compared to male patients throughout the period (acute phase mean difference: -0.091; 95% CI: -0.151 to -0.031).

CONCLUSIONS

COVID-19 patients experienced more symptoms three months post-testing compared to test-negative controls, with lower EQ-5D-5L utility scores persisting for over six months. Female COVID-19 patients exhibited lower EQ-5D-5L utility scores than their male counterparts throughout the period.

Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana

The coronavirus disease 2019 pandemic has highlighted the importance and challenges of the sample collection component of the diagnostic cycle. Although combined nasopharyngeal and oropharyngeal swabs (NOS) have historically been the gold standard of sampling, the saline gargle (SG) sampling method has been evaluated and implemented in multiple jurisdictions for respiratory pathogen detection. It has proven to be user-acceptable to patients, simple to collect, and highly sensitive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by molecular methods when compared to swabs. We performed a prospective cross-sectional study to evaluate the SG collection method against the NOS collection method for molecular detection and next-generation sequencing (NGS) of SARS-CoV-2 in Botswana. Paired SG and NOS samples were collected and underwent nucleic acid extraction prior to molecular detection. The SG had an overall sensitivity of 81.3% (95% CI: 68.8%%-96.0%), while the NOS had an overall sensitivity of 96.9% (95% CI: 84.3-99.4). Paired samples with a mean crossing threshold value of <35 also underwent NGS. SG specimens had a median genome coverage of 94.7% (interquartile range [IQR] 87.0%-99.2%) and NOS specimens had a median genome coverage of 99.6% (IQR 90.0%-99.6%). Bioinformatics analysis showed the 15 successfully matched pairs belong to clades BA.1 and BA.2 indicative of the Omicron variant. Further analysis at the nucleotide level showed a mean similarity of 99.998% ± 0.00465% between NOS and SG. This method has the potential to overcome the challenges that come with swab-based sampling for SARS-CoV-2 testing and may be an alternative in testing for other viral pathogens.

IMPORTANCE

During the coronavirus disease 2019 (COVID-19) pandemic, a major challenge has been inadequate sampling for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients posed additional challenges with sample collection, and they and others are also at risk of rare complications from swab collection. Saline gargle (SG) sampling method has been evaluated and introduced as an alternative to swab collection in several jurisdictions. Our study affirms the acceptable performance of the saline gargle method for the molecular detection of SARS-CoV-2 and also establishes that SG samples do not pose an obstacle for genomic sequencing of SARS-CoV-2. The SG method may be a reliable alternative for SARS-CoV-2 detection and next-generation sequencing, facilitating COVID-19 surveillance efforts in resource-constraint settings.

Comparison of the pathogenicity of multiple SARS-CoV-2 variants in mouse models

BACKGROUND

New variants of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)continue to drive global epidemics and pose significant health risks. The pathogenicity of these variants evolves under immune pressure and host factors. Understanding these changes is crucial for epidemic control and variant research.

METHODS

Human angiotensin-converting enzyme 2(hACE2) transgenic mice were intranasally challenged with the original strain WH-09 and the variants Delta, Beta, and Omicron BA.1, while BALB/c mice were challenged with Omicron subvariants BA.5, BF.7, and XBB.1. To compare the pathogenicity differences among variants, we conducted a comprehensive analysis that included clinical symptom observation, measurement of viral loads in the trachea and lungs, evaluation of pulmonary pathology, analysis of immune cell infiltration, and quantification of cytokine levels.

RESULTS

In hACE2 mice, the Beta variant caused significant weight loss, severe lung inflammation, increased inflammatory and chemotactic factor secretion, greater macrophage and neutrophil infiltration in the lungs, and higher viral loads with prolonged shedding duration. In contrast, BA.1 showed a significant reduction in pathogenicity. The BA.5, BF.7, and XBB.1 variants were less pathogenic than the WH-09, Beta, and Delta variants when infected in BALB/c mice. This was evidenced by reduced weight loss, diminished pulmonary pathology, decreased secretion of inflammatory factors and chemokines, reduced macrophage and neutrophil infiltration, as well as lower viral loads in both the trachea and lungs.

CONCLUSION

In hACE2 mice, the Omicron variant demonstrated the lowest pathogenicity, while the Beta variant exhibited the highest. Pathogenicity of the Delta variant was comparable to the original WH-09 strain. Among BALB/c mice, Omicron subvariants BA.5, BF.7, and XBB.1 showed no statistically significant differences in virulence.

Design of Entry Inhibitor Peptides Covalently Bonding SARS-CoV-2 Variants in Wastewater

Design of inhibitors with universal blocking activities for variants of concern is highly demanded in fighting against the COVID-19 pandemic. We proposed an in silico-aided design of entry inhibitor peptides that block protein-protein interaction between SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (hACE2). First, we screened affinity peptides by identifying hot spot residues of hACE2 that interact with the prototype RBD. Then, equipped with sulfur(VI) fluoride exchange reaction modifications and added with a PEG12 spacer arm, the entry inhibitor peptides could form irreversible bonds with the RBD in a wide range, potentially overcoming the inhibition escape of SARS-CoV-2 variants with RBD mutations. Combined with magnetic beads, the entry inhibitor peptides were used as enrichment materials to preconcentrate SARS-CoV-2 pseudovirus in different water matrices, showing recoveries of 15-75% even in 102-107 copies/mL wastewater. The entry inhibitor peptides may serve as a starting point for the development of new viral capturing, enrichment, and detection technologies in the field of environmental monitoring.

Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residences

BACKGROUND

Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the University of California San Diego (UC San Diego) facilitated the return of students to campus with comprehensive testing, vaccination, masking, wastewater surveillance, and isolation policies.

METHODS

We performed molecular epidemiological and phylogeographic analysis of 4418 SARS-CoV-2 genomes sampled from UC San Diego students during the Omicron waves between December 2021 and September 2022, representing 58% of students with confirmed SARS-CoV-2 infection. We overlaid these analyses across on-campus residential information to assess the spread and persistence of SARS-CoV-2 within university residences.

FINDINGS

Within campus residences, SARS-CoV-2 transmission was frequent among students residing in the same room or suite. However, a quarter of pairs of suitemates with concurrent infections had distantly related viruses, suggesting separate sources of infection during periods of high incidence in the surrounding community. Students with concurrent infections residing in the same building were not at substantial increased probability of being members of the same transmission cluster. Genetic network and phylogeographic inference indicated that only between 3.1 and 12.4% of infections among students could be associated with transmission within buildings outside of individual suites. The only super-spreading event we detected was related to a large event outside campus residences.

INTERPRETATION

We found little evidence for sustained SARS-CoV-2 transmission within individual buildings, aside from students who resided in the same suite. Even in the face of heightened community transmission during the 2021-2022 Omicron waves, congregate living did not result in a heightened risk for SARS-CoV-2 transmission in the context of the multi-pronged mitigation strategy.

FUNDING

SEARCH Alliance: Centers for Disease Control and Prevention (CDC) BAA (75D301-22-R-72097) and the Google Cloud Platform Research Credits Program. J.O.W.: NIH-NIAID (R01 AI135992). T.I.V.: Branco Weiss Fellowship and Newkirk Fellowship. L.L.: University of California San Diego.

Structural Basis of SARS-CoV-2 Nsp13-Derived Peptide-Mediated NK Cell Activation

As pivotal effectors of antiviral immunity, natural killer (NK) cells are crucial for controlling the spread of COVID-19. The nonstructural protein 13 of SARS-CoV-2 can encode a viral peptide (Nsp13232-240) preventing human leukocyte antigen E (HLA-E) from recognizing inhibitory receptor NKG2A, thereby activating NK cells. The underlying molecular mechanisms of Nsp13232-240 remain unclear. Therefore, we compared the interaction discrepancy between the self-peptide and Nsp13232-240, theoretically predicting its source. Results indicate that electrostatic interaction energy provides the main source of binding, and its attenuation greatly promotes binding affinity differences. Nsp13232-240 disrupts the hydrogen bond network between CD94 and HLA-E, impacting the binding of hot-spot residues, including Q112CD94 and E161HLA-E. Moreover, Nsp13232-240 breaks the salt bridges formed by K217NKG2A and K199NKG2A with HLA-E. Conformational changes induced by Nsp13232-240 lead to diminished atomic contacts and an unstable binding pattern. These findings provide novel insights into the immunomodulatory role of Nsp13232-240 and may inform future NK cell-mediated strategies targeting SARS-CoV-2.

SARS-CoV-2 spike protein: structure, viral entry and variants

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a devastating global pandemic for 4 years and is now an endemic disease. With the emergence of new viral variants, COVID-19 is a continuing threat to public health despite the wide availability of vaccines. The virus-encoded trimeric spike protein (S protein) mediates SARS-CoV-2 entry into host cells and also induces strong immune responses, making it an important target for development of therapeutics and vaccines. In this Review, we summarize our latest understanding of the structure and function of the SARS-CoV-2 S protein, the molecular mechanism of viral entry and the emergence of new variants, and we discuss their implications for development of S protein-related intervention strategies.

Use of allele-specific qPCR and PCR-RFLP analysis for rapid detection of the SARS-CoV-2 variants in Tunisia: A cheap flexible approach adapted for developing countries

Monitoring the emergence and propagation of SARS-COV2 variants, especially Omicron variants, remains a major concern in developing countries, including Tunisia. We here report lessons of simple approaches used to track prevalent Omicron variants in the city and district of Sfax, Tunisia, between June 2022 and April 2023. Initially, the screening approach was designed by selecting and verifying key SARS-CoV-2 mutations using publicly available sequencing data. Then, the analytical performance of the screening tests was rigorously assessed before being implemented on 227 confirmed COVID-19 cases. In a first stage, from June to September 2022, allele-specific (AS)-qPCR detection of deletions ΔHV69-70 (S gene) and ΔKSF141-143 (ORF1a gene) allowed identification of BA.5 as the predominant variant (128 out of 165 cases; 77.5%) which quickly replaced the pre-existing lineages BA.4 (15.7%) and BA.2 (6.7%). In a second stage, from October 2022 to April 2023, circulation of additional variants was demonstrated using concomitant detection of new relevant mutations by PCR-RFLP (n=62). Detection of mutations Y264H (ORF1b) and V445P/G446S (S gene) resulted in the identification of 38 cases of the BQ.1 variant and 14 cases of the XBB variant, respectively. Further restriction analysis of the S gene was conducted to screen more recent sublineages, including CH.1.1. For all sequenced cases (n=115), our rapid detection assays showed perfect concordance with sequencing results in identifying SARS-CoV-2 variants. These findings highlight the potential of simple, cheap and proven methods for rapid genotyping and monitoring of SARS-COV2 variants. Therefore, these methods appear as valuable tools for effective infection control and prevention in developing countries.

Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States

The COVID-19 pandemic has been marked by continuous emergence of novel SARS-CoV-2 variants. Questions remain about the mechanisms with which those variants establish themselves in new geographic areas. We performed a discrete phylogeographic analysis on 18,529 sequences of the SARS-CoV-2 Omicron BA.5 sublineage sampled during February-June 2022 to elucidate emergence of that sublineage in different regions of the United States. The earliest BA.5 sublineage introductions came from Africa, the putative variant origin, but most were from Europe, matching a high volume of air travelers. In addition, we discovered extensive domestic transmission between different US regions, driven by population size and cross-country transmission between key hotspots. We found most BA.5 virus transmission within the United States occurred between 3 regions in the southwestern, southeastern, and northeastern parts of the country. Our results form a framework for analyzing emergence of novel SARS-CoV-2 variants and other pathogens in the United States.

Advances in Engineered Phages for Disease Treatment

Phage therapy presents a promising solution for combating multidrug-resistant (MDR) bacterial infections and other bacteria-related diseases, attributed to their innate ability to target and lyse bacteria. Recent clinical successes, particularly in treating MDR-related respiratory and post-surgical infections, validated the therapeutic potential of phage therapy. However, the complex microenvironment within the human body poses significant challenges to phage activity and efficacy in vivo. To overcome these barriers, recent advances in phage engineering have aimed to enhance targeting accuracy, improve stability and survivability, and explore synergistic combinations with other therapeutic modalities. This review provides a comprehensive overview of phage therapy, emphasizing the application of engineered phages in antibacterial therapy, tumor therapy, and vaccine development. Furthermore, the review highlights the current challenges and future trends for advancing phage therapy toward broader clinical applications.

The impact of pre-existing immunity on the emergence of within-host immune-escape mutations in Omicron lineages

The Omicron variant of SARS-CoV-2 circulating amongst highly immunized populations is anticipated to induce immunological pressures, potentially compromising existing immunity. This study investigates vaccine-induced immunity's impact on within-host diversity of Omicron variants and evaluates sub-consensus mutations at spike protein antigenic sites. Next-generation sequencing assessed the within-host diversity of 728 Omicron-positive samples (421 vaccinated; 307 unvaccinated). Quantitative analysis revealed limited vaccine impact, regardless of lineage, vaccine type or doses. Non-lineage mutations (39, 33 and 25 in BA.2*, BA.4* and BA.5* lineages, respectively) were detected, some showing higher incidence in vaccinated individuals. Six mutations detected at sub-consensus levels at antigenic sites suggest increased immune pressure on the spike protein in vaccinated individuals. Four high-prevalence antigenic mutations, absent from global GISAID sequences, were identified. Although within-host diversity did not significantly differ between vaccination statuses, detected mutations suggest that vaccine-induced immunity may influence within-host mutation patterns.

The consequences of SARS-CoV-2 within-host persistence

SARS-CoV-2 causes an acute respiratory tract infection that resolves in most people in less than a month. Yet some people with severely weakened immune systems fail to clear the virus, leading to persistent infections with high viral titres in the respiratory tract. In a subset of cases, persistent SARS-CoV-2 replication results in an accelerated accumulation of adaptive mutations that confer escape from neutralizing antibodies and enhance cellular infection. This may lead to the evolution of extensively mutated SARS-CoV-2 variants and introduce an element of chance into the timing of variant evolution, as variant formation may depend on evolution in a single person. Whether long COVID is also caused by persistence of replicating SARS-CoV-2 is controversial. One line of evidence is detection of SARS-CoV-2 RNA and proteins in different body compartments long after SARS-CoV-2 infection has cleared from the upper respiratory tract. However, thus far, no replication competent virus has been cultured from individuals with long COVID who are immunocompetent. In this Review, we consider mechanisms of viral persistence, intra-host evolution in persistent infections, the connection of persistent infections with SARS-CoV-2 variants and the possible role of SARS-CoV-2 persistence in long COVID. Understanding persistent infections may therefore resolve much of what is still unclear in COVID-19 pathophysiology, with possible implications for other emerging viruses.

Molecular mechanistic exploration of conformational shifts induced by class IV anti-RBD antibody IY2A

The SARS-CoV-2 virus mutates rapidly, reducing the effectiveness of antibodies. The novel Class IV antibody IY2A partially unfolds the receptor-binding domain (RBD), allowing tolerance of antigenic variations and effectively neutralizing Omicron variants. In this study, we used molecular dynamics simulations and alanine scanning combined with interaction entropy method to elucidate how IY2A maintains its binding affinity across Omicron variants. We compared IY2A with EY6A and evaluated how mutations affect IY2A inhibition. The findings revealed that the IY2A adopted a closer conformation when binding to Omicron variants than to the WT. Energy calculations indicate that van der Waals interactions primarily drive IY2A binding to the RBD. Following unfolding, IY2A interacts with the RBD via interatomic hydrogen bonds and hydrophobic contacts involving LEU368, PHE377, LYS378, and SER383. This study provides theoretical insights to guide the development of Class IV antibodies against emerging and future Omicron variants.

Principles and implementation strategies for equitable and representative academic partnerships in global health informatics research

OBJECTIVE

Developing equitable, sustainable informatics solutions is key to scalability and long-term success for projects in the global health informatics (GHI) domain. This paper presents key strategies for incorporating principles of health equity in the GHI project lifecycle.

MATERIALS AND METHODS

The American Medical Informatics Association (AMIA) GHI Working Group organized a collaborative workshop at the 2023 AMIA Annual Symposium that included the presentation of five case studies of how principles of health equity have been incorporated into projects situated in low-and-middle-income countries and with Indigenous communities in the U.S. and best practices for operationalizing these principles into other informatics projects.

RESULTS

We present five principles: (1) Inclusion and Participation in Ethical, Sustainable Collaborations; (2) Engaging Community-Based Participatory Research Approaches; (3) Stakeholder Engagement; (4) Scalability and Sustainability; (5) Representation in Knowledge Creation, along with strategies that informatics researchers may use to incorporate these principles into their work.

DISCUSSION

Presented case studies and subsequent focus groups yielded key concepts and strategies to promote health equity that may be operationalized across GHI projects.

CONCLUSION

Equitable, sustainable, and scalable GHI projects require intentional integration of community and stakeholder perspectives in project development, implementation, and knowledge creation processes.

Large-scale screening of SARS-CoV-2 variants in Tokyo, Japan: A 3-year and 9-month longitudinal survey

Over nearly four years (March 10, 2021-December 31, 2024), we performed a comprehensive longitudinal analysis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants among patients in a single hospital in Tokyo, Japan. Using RT-qPCR and Sanger sequencing, complemented by whole-genome sequencing, we tested nasopharyngeal swab samples (n = 4,628) and tracked the emergence and evolution of variants of concern (VOCs). The findings demonstrate the utility of a hospital-based SARS-CoV-2 variant surveillance system for informing clinical decision-making and public health settings, including: i) serving as a reference for selecting appropriate treatments, ii) enabling early detection of VOCs, iii) contributing to the development of hospital infection control guidelines, iv) fostering cooperation with local governments, v) supporting cohort studies, and vi) identifying long-term SARS-CoV-2 infections. This work underscores the importance of real-time variant monitoring for mitigating the effects of pandemics and provides essential epidemiological and clinical data that can guide future outbreak management and policy development.

Study on the detection rate, genetic polymorphism, viral load, persistent infection capacity, and pathogenicity of human papillomavirus type 33

BACKGROUND

There is a lack of research on the relations among genetic polymorphisms, viral load, adaptability, persistent infection ability, and pathogenicity of human papillomavirus (HPV) type 33. Understanding these relations is crucial for revealing its pathogenic mechanisms and formulating prevention strategies.

METHODS

Exfoliated cervical cells were harvested from female participants in three hospitals located in the southwestern region of China (Guizhou, Sichuan, and Chongqing). Real-time fluorescence PCR technology was used for HPV genotyping and genomic quantification, and Sanger sequencing was used to obtain the gene sequence. then, changing trends in HPV33 detection rates and E6/E7 allele frequencies were compared. Positive selection, viral load, pathogenicity, and persistent infection capacity of different E6/E7 variants/mutations were analyzed.

RESULTS

Among 239,743 samples, HPV detection number was 56,681, the HPV33 detection rate was 3.72% (2,110/56,681) among all detected HPV genotypes. Between 2009 and 2023, a downward trend in the HPV33 detection rate was observed. The E6 + E7 prototype (E6 + E7 on the same variant is consistent with the reference sequence) was the dominant variant, with a significantly increased allele frequency. This dominant variant showed a significantly higher relative risk in causing persistent infection and cervical diseases (cervical intraepithelial neoplasia and cervical cancer). The viral load in the cervical disease group was significantly higher than that in the lesion-free group, and the viral load in the persistent infection group was significantly higher than that in the viral clearance group. There was no correlation between viral load and major genetic variants/mutations.

CONCLUSIONS

The E6 + E7 prototype has a significant impact on the pathogenicity and persistent infection capacity of HPV33. Viral load is positively correlated with pathogenicity and persistent infection capacity. It may serve as a biomarker for predicting disease progression during HPV33 screening. Other mechanisms underlying allele replacement require further investigation.

SARS-CoV-2 infection in the Indigenous Pataxó community of Southern Bahia, Brazil: second wave of transmission and vaccine effects

Indigenous people are at risk of several infectious diseases, including viruses that affect the respiratory system. In a previous study, we demonstrated how the Pataxó ethnic group, in the southernmost region of Bahia State, Brazil, was disproportionately affected during the first wave of COVID-19. Here, we provide an overview of how this community was affected by the second wave of the disease, evaluating the impact of vaccination on SARS-CoV-2 transmission. Prospective study data was grouped by Epidemiological Weeks 3/2021-43/2022, during which vaccine effects were analyzed and new variants of concern (VOC) emerged. The second wave produced a decreasing trimodal moving average curve, with an incidence rate of 4,407.2/100,000 inhabitants. Mobility and precarious work situations linked to tourism and craft trade increased infection rates in some villages. Risk factors for infection and severity (female sex, older age, and comorbidities) were determinants, but mortality was lower. Individuals with two doses of vaccine (Vac) developed more symptoms than the unvaccinated, but were less likely to have dyspnea. The mean time for COVID-19 symptoms to develop was longer in those with Vac (x̅ = 27 weeks) compared to those who received only one dose (x̅ = 12 weeks, p ≤ 0.001). Vac individuals who received booster shots, VacB1 and VacB2, had infection rates of 7.4% and 0%, respectively. The detrimental impact of COVID-19 once again highlights the persistence of health and socioeconomic inequities in this ethnic group. Moreover, the vaccines failed to prevent transmission, possibly due to mutated VOCs, but they may have protected this group against severe symptoms and extended the transmission period.

Comparative analysis of environmental persistence of SARS-CoV-2 variants and seasonal coronaviruses

Conducting persistence studies of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on environmental surfaces may require a biosafety level 3 (BSL-3) laboratory. We aimed to compare the environmental persistence of BSL-2 level human coronaviruses (229E, NL63, and OC43) and bovine coronavirus (BoCoV) with three SARS-CoV-2 variants (WA-1, Delta, and Omicron). OC43 (1.8 TCID50/mL) and BoCoV (1.0 TCID50/mL) had lower detection thresholds in cell culture assays compared to 229E (150 TCID50/mL) and NL63 (2,670 TCID50/mL) and were used for persistence tests at room temperature. Viable OC43 became undetectable (>5.2log10) after 48 hours on stainless steel and plastic coupons but exhibited extended persistence up to 72 hours on touchscreen glass coupons. In contrast, BoCoV remained viable for up to 120 hours with <1.8 log10 infectivity loss. Both OC43 and BoCoV showed a reduction of >5 log10 on vinyl coupons after 48 hours. On stainless steel coupons, the viability of all three SARS-CoV-2 variants became undetectable (>2.3 log10 reduction) after 48 hours, with minor differences in reduction levels at 24 hours, whereas on touchscreen glass coupons, the viable virus could be detected for up to 48 hours for WA-1 and Omicron and 72 hours for the Delta variant. Regardless of coupon or virus type, viral RNA titers increased <4.5 Ct values after 120 hours. Our data demonstrate distinct persistence characteristics between BoCoV and OC43, with neither fully mimicking SARS-CoV-2 variants. This variability along with the impact of surface types on viral persistence underscores the need for caution when using these viruses as surrogates for SARS-CoV-2.IMPORTANCEIn this study, we evaluated three human seasonal coronaviruses (OC43, NL63, and 229E) and one bovine coronavirus (BoCoV) as potential surrogate viruses for SARS-CoV-2. Our data suggest that among the four surrogate viruses tested, OC43 and BoCoV were the most promising candidates due to their assay sensitivity, ease of handling, and high genetic similarity to SARS-CoV-2. However, neither BoCoV nor OC43 fully mimicked the environmental persistence characteristics of SARS-CoV-2 variants highlighting the potential limitations of using surrogate viruses.

A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein

The Coronavirus Immunotherapeutic Consortium (CoVIC) conducted side-by-side comparisons of over 400 anti-SARS-CoV-2 spike therapeutic antibody candidates contributed by large and small companies as well as academic groups on multiple continents. Nine reference labs analyzed antibody features, including in vivo protection in a mouse model of infection, spike protein affinity, high-resolution epitope binning, ACE-2 binding blockage, structures, and neutralization of pseudovirus and authentic virus infection, to build a publicly accessible dataset in the database CoVIC-DB. High-throughput, high-resolution binning of CoVIC antibodies defines a broad and predictive landscape of antibody epitopes on the SARS-CoV-2 spike protein and identifies features associated with durable potency against multiple SARS-CoV-2 variants of concern and high in vivo efficacy. Results of the CoVIC studies provide a guide for selecting effective and durable antibody therapeutics and for immunogen design as well as providing a framework for rapid response to future viral disease outbreaks.

Dynamic Changes in Antibodies and Proteome in Breast Milk of Mothers Infected with Wild-Type SARS-CoV-2 and Omicron: A Longitudinal Study

Background: Breast milk confers essential passive immunity to infants, particularly during viral pandemics. This study investigates dynamic changes in SARS-CoV-2-specific antibodies and proteome in the breast milk of mothers infected with either the wild-type or Omicron variants, addressing gaps in longitudinal dynamics and conserved or variant-specific immune responses. Methods: A prospective cohort of 22 lactating mothers infected with Omicron variant (December 2022-January 2023) was analyzed alongside a published dataset of wild-type-infected mothers (January-May 2020). Breast milk samples were collected at eight time points (1, 4, 7, 14, 21, 28, 35, 42 days post-infection) from the Omicron cohort for ELISA quantification of SARS-CoV-2-specific IgA, IgG, and IgM. Proteomic analysis was conducted for both cohorts. Results: Macronutrient composition remained stable throughout the post-infection period. SARS-CoV-2-specific IgA and IgG demonstrated biphasic kinetics, rapidly rising by day 14 (IgA: 0.03 to 0.13 ng/mL; IgG: 0.91 to 37.00 ng/mL) and plateauing through day 42. In contrast, IgM levels remained unchanged. Proteomic profiling identified 135 proteins associated with IgA/IgG dynamics, including variant-specific and conserved proteins. Conclusions: Breast milk maintains nutritional integrity while mounting robust immune responses during SARS-CoV-2 infection. These findings underscore breastfeeding as a safe and protective practice during COVID-19.

Deaths "due to" COVID-19 and deaths "with" COVID-19 during the Omicron variant surge, among hospitalized patients in seven tertiary-care hospitals, Athens, Greece

In Greek hospitals, all deaths with a positive SARS-CoV-2 test are counted as COVID-19 deaths. Our aim was to investigate whether COVID-19 was the primary cause of death, a contributing cause of death or not-related to death amongst patients who died in hospitals during the Omicron surge and were registered as COVID-19 deaths. Additionally, we aimed to analyze the factors associated with the classification of these deaths. We retrospectively re-viewed all in-hospital deaths, that were reported as COVID-19 deaths, in 7 hospitals, serving Athens, Greece, from January 1, 2022, until August 31, 2022. We retrieved clinical and laboratory data from patient records. Each death reported as COVID-19 death was characterized as: (A) death "due to" COVID-19, or (B) death "with" COVID-19. We reviewed 530 in-hospital deaths, classified as COVID-19 deaths (52.4% males; mean age 81.7 ± 11.1 years). We categorized 290 (54.7%) deaths as attributable or related to COVID-19 and in 240 (45.3%) deaths unrelated to COVID-19 In multivariable analysis The two groups differed significantly in age (83.6 ± 9.8 vs. 79.9 ± 11.8, p = 0.016), immunosuppression history (11% vs. 18.8%, p = 0.027), history of liver disease (1.4% vs. 8.4%, p = 0.047) and the presence of COVID-19 symptoms (p < 0.001). Hospital stay was greater in persons dying from non-COVID-19 related causes. Among 530 in-hospital deaths, registered as COVID-19 deaths, in seven hospitals in Athens during the Omicron wave, 240 (45.28%) were reassessed as not directly attributable to COVID-19. Accuracy in defining the cause of death during the COVID-19 pandemic is of paramount importance for surveillance and intervention purposes.

Beyond the Pandemic Era: Recent Advances and Efficacy of SARS-CoV-2 Vaccines Against Emerging Variants of Concern

Vaccination has been instrumental in curbing the transmission of SARS-CoV-2 and mitigating the severity of clinical manifestations associated with COVID-19. Numerous COVID-19 vaccines have been developed to this effect, including BioNTech-Pfizer and Moderna's mRNA vaccines, as well as adenovirus vector-based vaccines such as Oxford-AstraZeneca. However, the emergence of new variants and subvariants of SARS-CoV-2, characterized by enhanced transmissibility and immune evasion, poses significant challenges to the efficacy of current vaccination strategies. In this review, we aim to comprehensively outline the landscape of emerging SARS-CoV-2 variants of concern (VOCs) and sub-lineages that have recently surfaced in the post-pandemic years. We assess the effectiveness of existing vaccines, including their booster doses, against these emerging variants and subvariants, such as BA.2-derived sub-lineages, XBB sub-lineages, and BA.2.86 (Pirola). Furthermore, we discuss the latest advancements in vaccine technology, including multivalent and pan-coronavirus approaches, along with the development of several next-generation coronavirus vaccines, such as exosome-based, virus-like particle (VLP), mucosal, and nanomaterial-based vaccines. Finally, we highlight the key challenges and critical areas for future research to address the evolving threat of SARS-CoV-2 subvariants and to develop strategies for combating the emergence of new viral threats, thereby improving preparedness for future pandemics.

Structural and Energetic Insights into SARS-CoV-2 Evolution: Analysis of hACE2-RBD Binding in Wild-Type, Delta, and Omicron Subvariants

The evolution of SARS-CoV-2, particularly the emergence of Omicron variants, has raised questions regarding changes in its binding affinity to the human angiotensin-converting enzyme 2 receptor (hACE2). Understanding the impact of mutations on the interaction between the receptor-binding domain (RBD) of the spike protein and hACE2 is critical for evaluating viral transmissibility, immune evasion, and the efficacy of therapeutic strategies. Here, we used molecular dynamics (MD) simulations and binding energy calculations to investigate the structural and energetic differences between the hACE2- RBD complexes of wild-type (WT), Delta, and Omicron subvariants. Our results indicate that the Delta and the first Omicron variants showed the highest and the second-highest binding energy among the variants studied. Furthermore, while Omicron variants exhibit increased structural stability and altered electrostatic potential at the hACE2-RBD interface when compared to the ancestral WT, their binding strength to hACE2 does not consistently increase with viral evolution. Moreover, newer Omicron subvariants like JN.1 exhibit a bimodal conformational strategy, alternating between a high-affinity state for hACE2 and a low-affinity state, which could potentially facilitate immune evasion. These findings suggest that, in addition to enhanced hACE2 binding affinity, other factors, such as immune evasion and structural adaptability, shape SARS-CoV-2 evolution.

Post-Omicron SARS-CoV-2 antibody prevalence in Sierra Leone: A cross-sectional, nationally representative, follow-up serosurvey

Based on a serosurvey conducted in March 2021, Barrie and colleagues published the first nationally representative SARS-CoV-2 serosurvey in Africa, estimating a SARS-CoV-2 seroprevalence of 2.6% in Sierra Leone, 43 times higher than the reported number of cases at that time. Over the following two years, increasingly transmissible variants-specifically Delta and Omicron-proliferated across the globe, and their impact in Africa is poorly understood. Additional nationally representative seroprevalence data are therefore necessary to understand the pandemic's progression on the continent and for evaluating containment measures and future preparedness. Our follow-up nationally representative survey was conducted in Sierra Leone from February to March 2023. We returned to the 120 Enumeration Areas throughout the country collecting blood samples from one or more individuals per household as well as information on sociodemographic characteristics, history of COVID-19 infection and immunization, and attitudes towards vaccination. The weighted overall seroprevalence (vaccinated and/or SARS-CoV-2 infection) for individuals >19 years of age was 33% (95% CI 29-37). Using the data and distributions from our previous serosurvey, the weighted predicted seroprevalence (any prior SARS-CoV-2 infection) for the general population was 28% (95% CI 15-41). The weighted predicted seroprevalence was ~11 times higher than the pre-Delta/Omicron prevalence. It was also over 300 times higher than the reported number of cases. Despite this, overall seroprevalence was low compared with countries in Europe and the Americas (pointing towards lower transmission in Sierra Leone). In addition, our results suggest the following regarding prevention campaigns claiming to have vaccinated 70% of adults in Sierra Leone as of December 2022: 1) they resulted in limited seroconversion; 2) there was significant waning of immunity; and/or 3) many less individuals were vaccinated than reported. Regardless of the cause, the utility of COVID-19 Vaccine Delivery Partnership (CoVDP) efforts three years into the pandemic is called into question.

Design, synthesis and in vitro validation of bivalent binders of SARS-CoV-2 spike protein: Obeticholic, betulinic and glycyrrhetinic acids as building blocks

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic, which caused over 6.7 million deaths worldwide. The Spike protein plays a crucial role in the infection process, mediating the binding of the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2), and its subsequent entry into target cells. Previous studies identified, through virtual screening, several natural products capable of binding to two distinct pockets of the Spike protein: triterpenoids binding to pocket 1 and bile acid derivatives binding to pocket 5. Building on these findings, our study advances the field by developing bivalent compounds 1-4 that through a spacer combine a triterpenoid (betulinic acid or glycyrrhetinic acid) with a semisynthetic bile acid derivative (obeticholic acid). These bivalent compounds are designed to simultaneously bind both pockets of the Spike protein, offering significant advantages over single molecules or the combination of the two natural products. In vitro cell assays using pseudotyped recombinant lentiviral particles with selected SARS-CoV-2 Spike proteins demonstrated that 1 and 2 exhibit enhanced activity in reducing viral entry into target cells compared to individual natural products, thus highlighting their potential as superior antiviral agents with reduced side effects.

Role of antiviral CD8+ T cell immunity to SARS-CoV-2 infection and vaccination

The COVID-19 pandemic has greatly enhanced our understanding of CD8+ T cell immunity and their role in natural infection and vaccine-induced protection. Rapid and early SARS-CoV-2-specific CD8+ T cell responses have been associated with efficient viral clearance and mild disease. Virus-specific CD8+ T cell responses can compensate for waning, morbidity-related, and iatrogenic reduction of humoral immunity. After infection or vaccination, SARS-CoV-2-specific memory CD8+ T cells are formed, which mount an efficient recall response in the event of breakthrough infection and help to protect from severe disease. Due to their breadth and ability to target mainly highly conserved epitopes, SARS-CoV-2-specific CD8+ T cells are also able to cross-recognize epitopes of viral variants, thus maintaining immunity even after the emergence of viral evolution. In some cases, however, CD8+ T cells may contribute to the pathogenesis of severe COVID-19. In particular, delayed and uncontrolled, e.g., nonspecific and hyperactivated, cytotoxic CD8+ T cell responses have been linked to poor COVID-19 outcomes. In this minireview, we summarize the tremendous knowledge about CD8+ T cell responses to SARS-CoV-2 infection and COVID-19 vaccination that has been gained over the past 5 years, while also highlighting the critical knowledge gaps that remain.

An In-Depth Characterization of SARS-CoV-2 Omicron Lineages and Clinical Presentation in Adult Population Distinguished by Immune Status

This retrospective study analyzed SARS-CoV-2 Omicron variability since its emergence, focusing on immunocompromised (IPs) and non-immunocompromised adult people (NIPs). Phylogenetic analysis identified at least five major Omicron lineage groups circulating in Central Italy, from December 2021 to December 2023: (a) BA.1 (34.0%), (b) BA.2 + BA.4 (25.8%), (c) BA.5 + BF (10.8%), (d) BQ + BE + EF (9.2%), and (e) Recombinants (20.2%). The BA.2 + BA.4 lineages were more common in IPs compared to NIPs (30.9% vs. 17.8%, respectively; p = 0.011); conversely, Recombinants were less prevalent in IPs than in NIPs (16.0% vs. 27.1%, respectively; p = 0.018). High-abundant single nucleotide polymorphisms (SNPs; prevalence ≥ 40%) and non-synonymous SNPs (prevalence ≥ 20%) increased during the emergence of new variants, rising from BA.1 to Recombinants (54 to 92, and 43 to 70, respectively, both p < 0.001). Evaluating the genetic variability, 109 SNPs were identified as being involved in significant positive or negative associations in pairs (phi > 0.70, p < 0.001), with 19 SNPs associated in 3 distinct clusters (bootstrap > 0.96). Multivariate regression analysis showed that hospitalization was positively associated with one specific cluster, including S686R and A694S in Spike and L221F in Nucleocapsid (AOR: 2.74 [95% CI: 1.13-6.64, p = 0.025]), and with increased age (AOR:1.03 [95% CI: 1.00-1.06], p = 0.028). Conversely, negative associations with hospitalization were observed for female gender and previous vaccination status (AORs: 0.34 [95% CI: 0.14-0.83], p = 0.017 and 0.19 (95% CI: 0.06-0.63, p = 0.006, respectively). Interestingly, the S686R SNP located in a furin cleavage site suggests its potential pathogenetic role. The results show how Omicron genetic diversification significantly influences disease severity and hospitalization, together with age, sex, and vaccination status as key factors.

A live attenuated SARS-CoV-2 vaccine constructed by dual inactivation of NSP16 and ORF3a

BACKGROUND

Live attenuated vaccines against SARS-CoV-2 activate all phases of host immunity resembling a natural infection and they block viral transmission more efficiently than existing vaccines in human use. In our prior work, we characterised an attenuated SARS-CoV-2 variant, designated d16, which harbours a D130A mutation in the NSP16 protein, inactivating its 2'-O-methyltransferase function. The d16 variant has demonstrated an ability to induce both mucosal and sterilising immunity in animal models. However, further investigation is required to identify any additional modifications to d16 that could mitigate concerns regarding potential virulence reversion and the suboptimal regulation of the proinflammatory response.

METHODS

Mutations were introduced into molecular clone of SARS-CoV-2 and live attenuated virus was recovered from cultured cells. Virological, biochemical and immunological assays were performed in vitro and in two animal models to access the protective efficacies of the candidate vaccine strain.

FINDINGS

Here we describe evaluation of a derivative of d16. We further modified the d16 variant by inverting the open reading frame of the ORF3a accessory protein, resulting in the d16i3a strain. This modification is anticipated to enhance safety and reduce pathogenicity. d16i3a appeared to be further attenuated in hamsters and transgenic mice compared to d16. Intranasal vaccination with d16i3a stimulated humoural, cell-mediated and mucosal immune responses, conferring sterilising protection against SARS-CoV-2 Delta and Omicron variants in animals. A version of d16i3a expressing the XBB.1.16 spike protein further expanded the vaccine's protection spectrum against circulating variants. Notably, this version has demonstrated efficacy as a booster in hamsters, providing protection against Omicron subvariants and achieving inhibition of viral transmission.

INTERPRETATION

Our work established a platform for generating safe and effective live attenuated vaccines by dual inactivation of NSP16 and ORF3a of SARS-CoV-2.

FUNDING

This work was supported by National Key Research and Development Program of China (2021YFC0866100, 2023YFC3041600, and 2023YFE0203400), Hong Kong Health and Medical Research Fund (COVID190114, CID-HKU1-9, and 23220712), Hong Kong Research Grants Council (C7142-20GF and T11-709/21-N), Hong Kong Innovation and Technology Commission grant (MHP/128/22), Guangzhou Laboratory (EKPG22-01) and Health@InnoHK (CVVT). Funding sources had no role in the writing of the manuscript or the decision to submit it for publication.

Viral escape-inspired framework for structure-guided dual bait protein biosensor design

A generalizable computational platform, CTRL-V (Computational TRacking of Likely Variants), is introduced to design selective binding (dual bait) biosensor proteins. The iteratively evolving receptor binding domain (RBD) of SARS-CoV-2 spike protein has been construed as a model dual bait biosensor which has iteratively evolved to distinguish and selectively bind to human entry receptors and avoid binding neutralizing antibodies. Spike RBD prioritizes mutations that reduce antibody binding while enhancing/ retaining binding with the ACE2 receptor. CTRL-V's through iterative design cycles was shown to pinpoint 20% (of the 39) reported SARS-CoV-2 point mutations across 30 circulating, infective strains as responsible for immune escape from commercial antibody LY-CoV1404. CTRL-V successfully identifies ~70% (five out of seven) single point mutations (371F, 373P, 440K, 445H, 456L) in the latest circulating KP.2 variant and offers detailed structural insights to the escape mechanism. While other data-driven viral escape variant predictor tools have shown promise in predicting potential future viral variants, they require massive amounts of data to bypass the need for physics of explicit biochemical interactions. Consequently, they cannot be generalized for other protein design applications. The publicly availably viral escape data was leveraged as in vivo anchors to streamline a computational workflow that can be generalized for dual bait biosensor design tasks as exemplified by identifying key mutational loci in Raf kinase that enables it to selectively bind Ras and Rap1a GTP. We demonstrate three versions of CTRL-V which use a combination of integer optimization, stochastic sampling by PyRosetta, and deep learning-based ProteinMPNN for structure-guided biosensor design.

Variable rates of SARS-CoV-2 evolution in chronic infections

An important feature of the evolution of the SARS-CoV-2 virus has been the emergence of highly mutated novel variants, which are characterised by the gain of multiple mutations relative to viruses circulating in the general global population. Cases of chronic viral infection have been suggested as an explanation for this phenomenon, whereby an extended period of infection, with an increased rate of evolution, creates viruses with substantial genetic novelty. However, measuring a rate of evolution during chronic infection is made more difficult by the potential existence of compartmentalisation in the viral population, whereby the viruses in a host form distinct subpopulations. We here describe and apply a novel statistical method to study within-host virus evolution, identifying the minimum number of subpopulations required to explain sequence data observed from cases of chronic infection, and inferring rates for within-host viral evolution. Across nine cases of chronic SARS-CoV-2 infection in hospitalised patients we find that non-trivial population structure is relatively common, with five cases showing evidence of more than one viral population evolving independently within the host. The detection of non-trivial population structure was more common in severely immunocompromised individuals (p = 0.04, Fisher's Exact Test). We find cases of within-host evolution proceeding significantly faster, and significantly slower, than that of the global SARS-CoV-2 population, and of cases in which viral subpopulations in the same host have statistically distinguishable rates of evolution. Non-trivial population structure was associated with high rates of within-host evolution that were systematically underestimated by a more standard inference method.

SARS-CoV-2: The Interplay Between Evolution and Host Immunity

The persistence of SARS-CoV-2 infections at a global level reflects the repeated emergence of variant strains encoding unique constellations of mutations. These variants have been generated principally because of a dynamic host immune landscape, the countermeasures deployed to combat disease, and selection for enhanced infection of the upper airway and respiratory transmission. The resulting viral diversity creates a challenge for vaccination efforts to maintain efficacy, especially regarding humoral aspects of protection. Here, we review our understanding of how SARS-CoV-2 has evolved during the pandemic, the immune mechanisms that confer protection, and the impact viral evolution has had on transmissibility and adaptive immunity elicited by natural infection and/or vaccination. Evidence suggests that SARS-CoV-2 evolution initially selected variants with increased transmissibility but currently is driven by immune escape. The virus likely will continue to drift to maintain fitness until countermeasures capable of disrupting transmission cycles become widely available.

Comparison of the pathogenicity and neutrophil and monocyte response between SARS-CoV-2 prototype and Omicron BA.1 in a lethal mouse model

BACKGROUND

SARS-CoV-2, first identified in late 2019, has given rise to numerous variants of concern (VOCs), posing a significant threat to human health. The emergence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022. At present, the lethal mouse model for the study of SARS-CoV-2 needs supplementation, and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated.

METHODS

Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 prototype and Omicron BA.1, respectively. The pathogenicity of the two strains was evaluated by observing clinical symptoms, viral load and pathology. Complete blood count, immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains.

RESULTS

Our findings revealed that Omicron BA.1 exhibited significantly lower virulence compared to the SARS-CoV-2 prototype in the mouse model. Additionally, we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1. We found that the proportion of monocytes increased at first and then decreased. The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar.

CONCLUSION

Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1. SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.

RBD-depleted SARS-CoV-2 spike generates protective immunity in cynomolgus macaques

The SARS-CoV-2 pandemic revealed the rapid evolution of circulating strains. This led to new variants carrying mostly mutations within the receptor binding domain, which is immunodominant upon immunization and infection. In order to steer the immune response away from RBD epitopes to more conserved domains, we generated S glycoprotein trimers without RBD and stabilized them by formaldehyde cross-linking. The cryoEM structure demonstrated that SΔRBD folds into the native prefusion conformation, stabilized by one specific cross-link between S2 protomers. SΔRBD was coated onto lipid vesicles, to produce synthetic virus-like particles, SΔRBD-LV, which were utilized in a heterologous prime-boost strategy. Immunization of cynomolgus macaques either three times with the mRNA Comirnaty vaccine or two times followed by SΔRBD-LV showed that the SΔRBD-LV boost induced similar antibody titers and neutralization of different variants, including omicron. Upon challenge with omicron XBB.3, both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes conferred similar overall protection from infection for both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes. However, the SΔRBD-LV boost indicated better protection against lung infection than the Comirnaty strategy alone. Together our findings indicate that SΔRBD is highly immunogenic and provides improved protection compared to a third mRNA boost indicative of superior antibody-based protection.

Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses

DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among merbecoviruses and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. We defined the molecular determinants of receptor species tropism and identified a single amino acid mutation enabling HKU5 to utilize human ACE2, providing proof of principle for machine-learning-assisted outbreak preparedness. We show that MERS-CoV and HKU5 have markedly distinct antigenicity and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution, as several merbecovirus clades independently evolved ACE2 utilization, and pave the way for developing countermeasures against viruses poised for human emergence.

SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19

BACKGROUND

The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.

METHOD

From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.

RESULTS

Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.

CONCLUSION

Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.

National investment case development for pathogen genomics

Sustaining and expanding genomic surveillance capacity requires broader investment in genomics that target both novel and pandemic pathogens. Currently, there is no standardized methodology to evaluate the cost and benefit of a multi-pathogen surveillance system. We propose a framework for pathogen genomic surveillance that links public health and systems considerations to a stepwise approach.

The evolution and epidemiology of H3N2 canine influenza virus after 20 years in dogs

The H3N2 canine influenza virus (CIV) emerged from an avian reservoir in Asia to circulate entirely among dogs for the last 20 years. The virus was first seen circulating outside Asian dog populations in 2015, in North America. Utilizing viral genomic data in addition to clinical reports and diagnostic testing data, we provide an updated analysis of the evolution and epidemiology of the virus in its canine host. CIV in dogs in North America is marked by a complex life history - including local outbreaks, regional lineage die-outs, and repeated reintroductions of the virus (with diverse genotypes) from different regions of Asia. Phylogenetic and Bayesian analysis reveal multiple CIV clades, and viruses from China have seeded recent North American outbreaks, with 2 or 3 introductions in the past 3 years. Genomic epidemiology confirms that within North America the virus spreads very rapidly among dogs in kennels and shelters in different regions - but then dies out locally. The overall epidemic therefore requires longer-distance dispersal of virus to maintain outbreaks over the long term. With a constant evolutionary rate over 20 years, CIV still appears best adapted to transmission in dense populations and has not gained properties for prolonged circulation among dogs.

Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates

In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account for the time passing since the divergence of pathogen variants in individuals, which is problematic in viruses with high within-host evolutionary rates. This prompted us to consider possible transmission pairs in terms of phylogenetic data and additional estimates of time since infection derived from clinical biomarkers. We develop Bayesian mixture models with an evolutionary clock as a signal component and additional mixed effects or covariate random functions describing the mixing weights to classify potential pairs into likely and unlikely transmission pairs. We demonstrate that although sources cannot be identified at the individual level with certainty, even with the additional data on time elapsed, inferences into the population-level sources of transmission are possible, and more accurate than using only phylogenetic data without time since infection estimates. We apply the proposed approach to estimate age-specific sources of HIV infection in Amsterdam tranamission networks among men who have sex with men between 2010 and 2021. This study demonstrates that infection time estimates provide informative data to characterize transmission sources, and shows how phylogenetic source attribution can then be done with multi-dimensional mixture models.

Distinct Responses of Cystic Fibrosis Epithelial Cells to SARS-CoV-2 and Influenza A Virus

The coronavirus disease (COVID-19) pandemic has underscored the impact of viral infections on individuals with cystic fibrosis (CF). Initial observations suggested lower COVID-19 rates among CF populations; however, subsequent clinical data have presented a more complex scenario. This study aimed to investigate how bronchial epithelial cells from individuals with and without CF, including various CFTR (CF transmembrane conductance regulator) mutations, respond to in vitro infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and SARS-CoV. Comparisons with the influenza A virus (IAV) were included based on evidence that patients with CF experience heightened morbidity from IAV infection. Our findings showed that CF epithelial cells exhibited reduced replication of SARS-CoV-2, regardless of the type of CFTR mutation or SARS-CoV-2 variant, as well as the original 2003 SARS-CoV. In contrast, these cells displayed more efficient IAV replication than non-CF cells. Interestingly, the reduced susceptibility to SARS-CoV-2 in CF was not linked to the expression of ACE2 (angiotensin-converting enzyme 2) receptor or to CFTR dysfunction, as pharmacological treatments to restore CFTR function did not normalize the viral response. Both SARS-CoV-2 infection and CFTR function influenced the concentrations of certain cytokines and chemokines, although these effects were not correlated. Overall, this study reveals a unique viral response in CF epithelial cells, characterized by reduced replication for some viruses like SARS-CoV-2, while showing increased susceptibility to others, such as IAV. This research offers a new perspective on CF and viral interactions, emphasizing the need for further investigation into the mechanisms underlying these differences.

The Compensatory Effect of S375F on S371F Is Vital for Maintaining the Infectivity of SARS-CoV-2 Omicron Variants

The emergence of Omicron variants dramatically changed the transmission rate and infection characteristics compared to previously prevalent strains, primarily due to spike protein mutations. However, the impact of individual mutations remained unclear. Here, we used virus-like particle (VLP) pseudotyped to investigate the functional contributions by 12 common mutations in the spike protein. We found that the S371F mutation in the receptor binding domain (RBD) of spike protein led to a 5- and 10-fold decrease of ACE2 utilization efficiency and viral infectivity, respectively, accompanied by a 5- to 11-fold reduction of neutralization sensitivity to monoclonal antibodies. However, the S375F mutation in the RBD had a compensatory effect, rescuing the infectivity of the S371F Omicron variant. Based on molecular dynamics simulations, we proposed a "tug of war" model to explain this compensation phenomenon. These results provide a comprehensive and dynamic perspective on the evolution of this important pandemic virus.

Planning and adjusting the COVID-19 booster vaccination campaign to reduce disease burden

As public health policies shifted in 2023 from emergency response to long-term COVID-19 disease management, immunization programs started to face the challenge of formulating routine booster campaigns in a still highly uncertain seasonal behavior of the COVID-19 epidemic. Mathematical models assessing past booster campaigns and integrating knowledge on waning of immunity can help better inform current and future vaccination programs. Focusing on the first booster campaign in the 2021/2022 winter in France, we used a multi-strain age-stratified transmission model to assess the effectiveness of the observed booster vaccination in controlling the succession of Delta, Omicron BA.1 and BA.2 waves. We explored counterfactual scenarios altering the eligibility criteria and inter-dose delay. Our study showed that the success of the immunization program in curtailing the Omicron BA.1 and BA.2 waves was largely dependent on the inclusion of adults among the eligible groups, and was highly sensitive to the inter-dose delay, which was changed over time. Shortening or prolonging this delay, even by only one month, would have required substantial social distancing interventions to curtail the hospitalization peak. Also, the time window for adjusting the delay was very short. Our findings highlight the importance of readiness and adaptation in the formulation of routine booster campaign in the current level of epidemiological uncertainty.

Delta and Omicron SARS-CoV-2 pneumonia: Comparison of clinical and radiological features

BACKGROUND

Computed tomography (CT) is a critical tool for the diagnosis of pneumonia caused by SARS-CoV-2. The Delta and Omicron variants show distinct clinical features, but the radiological differences between pneumonia caused by these variants have not been extensively studied in patients with oxygen-dependent pneumonia.

OBJECTIVE

To compare the radiological and clinical features of pneumonia in patients hospitalized with oxygen-dependent SARS-CoV-2 infection caused by the Delta and Omicron variants.

METHODS

We performed a retrospective single-center study, including patients hospitalized with oxygen-dependent SARS-CoV-2 pneumonia between October 2021 and February 2022. Clinical and radiological data were collected and compared between patients infected with the Delta variant and those with the Omicron variant. CT scans were reviewed by a radiologist and a pulmonologist blinded to clinical and variant information.

RESULTS

A total of 135 patients with the Delta variant and 48 with the Omicron variant were included. Patients infected with Omicron were older (median age 75 years [68-83.2] vs 69 years [62-77.5], p = 0.004), more immunocompromised (52 % vs. 25 %, p < 0.001), and had higher vaccination rates (73 % vs. 51 %, p = 0.009). Radiologically, ground-glass opacities were present in 95 % of patients. There were no significant differences in the degree of lung involvement, type of lesions and their predominance. Unilateral lung involvement was more common in Omicron-infected patients (8.3 % vs 0.74 %, p = 0.02).

CONCLUSION

While Omicron oxygen-dependent pneumonia occurred in older and more comorbid patients, its clinical and radiological features were largely indistinguishable from those caused by the Delta variant, except for a higher rate of unilateral lung involvement.

A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves

The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic. We aimed to identify the key processes relevant to COVID-19 transmission dynamics and thereby develop a model that could quantify relevant epidemiological parameters. The pipeline's advantages include markedly increased speed, an expressive application programming interface, the transparency of open-source development, easy access to a broad range of calibration and optimisation tools and consideration of the full workflow from input manipulation through to algorithmic generation of the publication materials. Extending the base model to include mobility effects slightly improved model fit to data, with this approach selected as the model configuration for further epidemiological inference. Under our assumption of widespread immunity against severe outcomes from recent vaccination, incorporating an additional effect of the main vaccination programs rolled out during 2022 on transmission did not further improve model fit. Our simulations suggested that one in every two to six COVID-19 episodes were detected, subsequently emerging Omicron subvariants escaped 30-60% of recently acquired natural immunity and that natural immunity lasted only one to eight months on average. We documented our analyses algorithmically and present our methods in conjunction with interactive online code notebooks and plots. We demonstrate the feasibility of integrating a flexible domain-specific syntax library with state-of-the-art packages in high performance computing, calibration, optimisation and visualisation to create an end-to-end pipeline for infectious disease modelling. We used the resulting platform to demonstrate key epidemiological characteristics of the transition from the emergency to the endemic phase of the COVID-19 pandemic.