Virus Variants Research Articles

Identification of raccoon rabies virus variant in a stray kitten: the role of veterinary practitioners in detection and reporting of a non-native zoonotic pathogen-Nebraska, 2023.

Rabies is a fatal encephalitic disease affecting all mammals. This report describes identification of raccoon rabies virus variant isolated from a stray kitten in an urban Midwestern city that is nonendemic for this virus variant. The kitten originally presented with nonspecific neurologic abnormalities. Astute veterinary, wildlife, and public health professionals played a critical role in the identification of this fatal zoonotic disease and the extensive public health and wildlife management response that ensued. This case serves as an important reminder of the risk of rabies in unvaccinated animals or those without known vaccination status, including stray animals.

An Active-Learning Framework for Educating Medical Students on SARS-CoV-2 Variants and COVID-19 Epidemiology

Background The emergence of multiple Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) variants presented an escalated risk to public health globally and prompted epidemiologic monitoring and classification. Health professionals are vital for patient education regarding Coronavirus Disease 2019 (COVID-19), discussing patient concerns, and providing guidance. Students enrolled in professional healthcare programs benefit from being adept with the evolution and spread of SARS-CoV-2 variants, and a team-based learning module can be helpful for applying foundational concepts to clinical problems. Methods This team-based learning (TBL) framework was developed in response to the COVID-19 pandemic and the emergence of viral variants. It was placed at the end of a hematology block within the first semester of year one of the medical school during the academic years 2021–2022. It consists of a 7-question readiness assurance process and a four-question application exercise. Results The average score increased from 58.8% (iRAT) to 85.9% (tRAT) (n=104). The post-session survey data showed an increase in students’ understanding of the classification of COVID-19 variants and the role of genetic mutations in viral pathogenesis. Qualitative data yielded positive feedback for the session, notably in students' ability to interpret phylogenetic trees and understand the role of variants. Conclusions This TBL framework cultivates higher-order thinking skills among medical students and effectively integrates virology, epidemiology, and pathology. Additionally, it provides a framework for developing a robust and up-to-date platform for the discussion of novel variants of COVID-19 or other infectious diseases.

Association of mRNA COVID-19 vaccination and reductions in Post-COVID Conditions following SARS-CoV-2 infection in a US prospective cohort of essential workers.

While there is evidence that COVID-19 vaccination protects against development of post-COVID conditions (PCC) after severe infection data are limited on whether vaccination reduces the risk after cases of less-severe non-hospitalized COVID-19 disease with more recent SARS-CoV-2 variant viruses. This study assessed whether COVID-19 vaccination was protective against subsequent development of PCC in persons with predominantly mild initial infections during both Delta and Omicron variant predominance. This study utilized a case-control design, nested within the HEROES-RECOVER cohort. Participants aged ≥18 years with PCR-confirmed SARS-CoV-2 infection between 6/28/2021 and 9/14/2022 were surveyed for PCC, defined by symptoms lasting >1 month after initial infection Cases were participants self-reporting PCC and controls were participants that did not self-report PCC. The exposure was mRNA COVID-19 vaccination (2 or 3 monovalent doses) versus no COVID-19 vaccination. Logistic regression was used to compare the odds of PCC among vaccinated and unvaccinated persons; additional analyses evaluating PCC subtypes were also performed. A total of 936 participants with documented SARS-CoV-2 infection were included; of these 23.6% (221) reported PCC and 83.3% (779) were vaccinated. Participants who received a 3rd COVID-19 monovalent mRNA dose prior to infection had lower odds of PCC-related gastrointestinal, neurological, and other symptoms compared to unvaccinated participants (aOR: 0.37; 95% CI: 0.16-0.85; aOR: 0.56; 95% CI: 0.32-0.97; aOR:0.48; 95% CI: 0.25-0.91). COVID-19 vaccination protected against development of PCC among persons with mild infection during both Delta and Omicron variant predominance, supporting vaccination as an important tool for PCC prevention.

Local and Noninvasive Glyco-Virus Checkpoint Nanoblockades Restrict Sialylation for Prolonged Broad-Spectrum Epidemic Virus Therapy.

The coronavirus disease 2019 (COVID-19) pandemic has driven major advances in virus research. The role of glycans in viral infection has been revealed, with research demonstrating that terminal sialic acids are key receptors during viral attachment and infection into host cells. However, there is an urgent demand for universal tools to study the mechanism of sialic acids in viral infections, as well as to develop therapeutic agents against epidemic viruses through the downregulation of terminal sialic acid residues on glycans acting as a glyco-virus checkpoint to accelerate virus clearance. In this study, we developed a robust sialic acids blockade tool termed local and noninvasive glyco-virus checkpoint nanoblockades (LONG NBs), which blocked cell surface sialic acids by endogenously and continuously inhibiting the de novo sialic acids biosynthesis pathway. Furthermore, LONG NBs could accurately characterize the sialic acid-dependent profiles of multiple virus variants and protected the host against partial SARS-CoV-2, rotavirus, and influenza A virus infections after local and noninvasive administration. Our results suggest that LONG NBs represent a promising tool to facilitate in-depth research on the mechanism of viral infection, and serve as a broad-spectrum protectant against existing and emerging viral variants via glyco-virus checkpoint blockade.

Burden of post-acute COVID-19 sequelae in healthcare workers and its course over a 30-month period-results from a prospective multicentre cohort.

As healthcare workers (HCW) have been disproportionally affected by COVID-19, its post-acute sequelae (PASC) in HCW can impact healthcare systems. We assessed the burden and course of PASC in HCW over a 30-month period. In a prospective multicentre HCW cohort in Switzerland, PASC surveys were conducted in 03/2021, 09/2021, 06/2022, 04/2023, and 10/2023. Stratified by viral variant at first infection, the prevalence of PASC symptoms, self-experienced PASC and the Post-COVID Functional Status (PCFS) were analysed cross-sectionally in 10/2023, self-perceived success of therapeutic measures used was assessed. The evolution of PASC symptoms and PCFS in Wild-type and non-Wild-type infected HCW compared to uninfected controls was analysed longitudinally across all surveys. In cross-sectional analysis, 1704 HCW (median age 47years, 82.2% female) were included. Thereof, 30.7% reported ≥ 1 PASC symptom in 10/2023, with 115 (6.7%) stating to have or have had PASC. Both were most common after Wild-type infection compared to other variants. Overall, 17/115 (15%) indicated relevant/severe restrictions in their daily activities and of 85 (74%) that tried ≥ 1 measure against their symptoms, 69 (81%) reported having benefitted. Longitudinal analysis (n = 653) showed a significantly higher proportion of Wild-type infected HCW to report PASC symptoms compared to controls in 03/2021 (+ 21%, 95% CI 4-39), with decreasing trend (+ 7%, 95%CI -10-25 in 10/2023). This effect was not evident for non-Wild-type infected HCW. Over a 30month period, overall PASC burden in our HCW cohort decreased, although 1% still experience relevant restrictions in their daily life; Wild-type infected individuals show the highest disease burden.

Genotypic and phylogeographic insights into a pre-epidemic variant of Wesselsbron virus detected in sylvatic Aedes mcintoshi from Semuliki Forest, Uganda.

Wesselsbron virus (WSLV) is a neglected mosquito-borne virus within the yellow fever subgroup in the genus Orthoflavivirus of the Flaviviridae family. Despite being primarily a veterinary pathogen able to cause stillbirths, congenital malformations, and mortality in ruminants, WSLV also infects humans, causing a usually self-limiting febrile illness, or may lead to neurological complications in rare cases. WSLV causes sporadic outbreaks in Southern Africa, but findings in mosquitoes from other African countries suggest a wider distribution. Here, we report the detection and isolation of WSLV from an Aedes mcintoshi mosquito collected in a pristine ecosystem within Semuliki National Park, western Uganda. The detected strain M5937-UG-2018 was impaired in infectivity, replication, and production of infectious particles in cell lines derived from different hosts compared to an epidemic reference strain, SA H177. Full-genome sequencing by next-generation sequencing from the mosquito homogenate revealed a maximum nucleotide identity of 98.1% to a WSLV isolate from a human sample collected in South Africa in 1996. M5937-UG-2018 grouped in phylogenetic analyses with strains from South Africa and Senegal. Reconstruction of the temporal and spatial dispersal of WSLV across Africa estimated a likely origin of WSLV in South Africa in the early 19th century and spread in Southern Africa in the following decades. Long-distance movement toward Western and Eastern Africa was modeled to have occurred in the early 21st century. However, displacing the origin of M5937-UG-2018 did not decrease the likelihood of the model supporting the hypothesis that WSLV is widely distributed in Africa.IMPORTANCEWSLV is a neglected mosquito-borne virus causing teratogenicity in ruminants and febrile illness in humans. WSLV is mainly endemic to Southern Africa, but findings in other regions suggest a wider distribution on the continent. Knowledge of the distribution of WSLV is impaired as differential diagnostics are rarely performed in livestock and humans presenting with symptoms compatible with WSLV infection. Our work investigating viral infections in mosquitoes from a remote tropical rainforest region demonstrates that WSLV is endemic in Uganda. The isolated virus was less infective and showed lower replication ability in vitro compared to an epidemic isolate from South Africa. Phylogeographic reconstruction of spatial and temporal movements, along with the displacement of the origin of the newly detected strain, suggests that WSLV may be widely distributed across Africa. Our data show that the geographic distribution of WSLV and its impact on human and animal health are likely underestimated.

Quantifying the impact of vaccination on transmission and diversity of influenza A variants in pigs.

Global evolutionary dynamics of influenza A virus (IAV) are fundamentally driven by the extent of virus diversity generated, transmitted, and shaped in individual hosts. How vaccination affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs is unknown. To evaluate the effect of vaccination on the transmission of genetically distinct IAV variants and their diversity after transmission in pigs, we examined the whole genome of IAV recovered from the nasal cavities of pigs vaccinated with different influenza immunization regimens after being infected simultaneously by H1N1 and H3N2 IAVs using a seeder pig model. We found that the seeder pigs harbored more diversified virus populations than the contact pigs. Among contact pigs, H3N2 and H1N1 viruses recovered from pigs vaccinated with a single dose of an unmatched modified live vaccine generally accumulated more extensive genetic mutations than non-vaccinated pigs. Furthermore, the non-sterilizing immunity elicited by the single-dose-modified live vaccine may have exerted positive selection on H1 antigenic regions as we detected significantly higher nonsynonymous but lower synonymous evolutionary rates in H1 antigenic regions than non-antigenic regions. In addition, we observed that the vaccinated pigs shared significantly less proportion of H3N2 variants with seeder pigs than unvaccinated pigs. These results indicated that vaccination might reduce the impact of transmitted influenza variants on the overall diversity of IAV populations harbored in recipient pigs and that within-host genetic selection of IAV is more likely to occur in pigs vaccinated with improperly matched vaccines.IMPORTANCEUnderstanding how vaccination shapes the diversity of influenza variants that transmit and propagate among pigs is essential for designing effective IAV surveillance and control programs. Current knowledge about the transmission of IAV variants has primarily been explored in humans during natural infection. However, how immunity elicited by improperly matched vaccines affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs at the whole-genome level is unknown. We analyzed IAV sequences from samples collected daily from experimentally infected pigs vaccinated with various protocols in a field-represented IAV co-infection model. We found that vaccine-induced non-sterilizing immunity might promote genetic variation on the IAV genome and drive positive selection at antigenic sites during infection. In addition, a smaller proportion of H3N2 viral variants were shared between seeder pigs and vaccinated pigs, suggesting the influence of vaccination on shaping the virus genomic diversity in recipient pigs during the transmission events.

Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study-the COVIDKID study.

Limited data on SARS-CoV-2 seroprevalence in rural areas of northern Germany necessitate comprehensive cohort studies. We aimed to evaluate the seroprevalence, silent infection (SI) rates and risk factors for infections among children and adolescents in Western Pomerania from December 2020 to August 2022. In this cross-sectional study, serum or plasma samples from children and adolescents (6 months to 17 years) were collected during routine blood draw. SARS-CoV-2 specific antibodies (S1 and nucleocapsid) and their neutralizing capacity were analyzed using commercially available enzyme-linked immunosorbent and neutralization assays. Socio-demographic data and information about SARS-CoV-2 infection or vaccination were obtained. Multivariable logistic regression was used to identify independent risk factors for SARS-CoV-2 infections and SI. A total of 1,131 blood samples were included into the study. Overall, SARS-CoV-2 seroprevalence was 25.1%, strongly influenced by the pandemic course, predominant virus variants, age and approval of vaccination. SI rate was 5.4% (95%-CI [3.7%-6.8%]) among unvaccinated and undiagnosed children over the entire study period with highest rates among adolescents. Main risk factor despite the time at risk for silent infections was an infected household member (Odds ratio = 9.88, 95%-CI [4.23-22.9], p<0.001). Factors associated with overall infections (known and silent) also include the infection of a household member (Odds ratio = 17.8, 95%-CI [10.7-29.6], p<0.001). We believe that the introduction of governmental measures and systematic test strategies in schools strongly impacted on the SI rate, as we suspect that asymptomatic cases have already been identified, resulting in surprisingly low SI identified in our study.

Comparing strategies for the mitigation of SARS-CoV-2 airborne infection risk in tiered auditorium venues

The COVID-19 pandemic demonstrated that reliable risk assessment of venues is still challenging and resulted in the indiscriminate closure of many venues worldwide. Therefore, this study used an experimental, numerical and analytical approach to investigate the airborne transmission risk potential of differently ventilated, sized and shaped venues. The data were used to assess the magnitude of effect of various mitigation measures and to develop recommendations. Here we show that, in general, positions in the near field of an emission source were at high risk, while the risk of infection from positions in the far field varied depending on the ventilation strategy. Occupancy, airflow rate, residence time, virus variants, activity level and face masks affected the individual and global infection risk in all venues. The global infection risk was lowest for the displacement ventilation case, making it the most effective ventilation strategy for keeping airborne transmission and the number of secondary cases low, compared to mixing or natural ventilation.

Comparative analysis of whole-genome sequences of African swine fever virus (Asfarviridae: Asfivirus) isolates сollected on the territory of the left bank of the Dnieper River in 2023.

The lack of data on the whole-genome sequences of African swine fever virus (ASFV) variants circulating on the territory of the left bank of the Dnieper River complicates the understanding of the molecular evolution of the virus and the character of the epidemic process development in Russia and Ukraine. Understanding the genetic divergence and phylogenetic relatedness of isolates can largely adjust the strategy of general and specific prevention of the disease. The aim of the study - search and description of unique mutations (deletions/insertions/substitutions) in isolates collected from domestic pigs in Donetsk, Luhansk and Zaporozhye regions in 2023; determination of relatedness and level of homology with reference strains of ASFV genotype II; sub-genotyping and clustering of isolates based on whole-genome analysis. The samples used were a culture suspension of porcine bone marrow (PBM) cells containing ASFV isolates obtained from pathologic material from domestic pig carcasses. Genomic DNA was prepared by purification and concentration of virus followed by phenol-chloroform extraction of total nucleic acid. The high-throughput sequencing process was performed using MGI technology. Consensus sequences were assembled by mapping reads to the reference genome of strain Georgia 2007/1. All isolates are assigned to genotype II, have a monophyletic origin, are phylogenetically close to the clusters «Europe» (4/5) and «Bryansk 2021» (1/5), and are divergent from the original parental genetic variants that make up the enlarged clades. In addition, numerous substitutions in the loci of the multigene family MGF 110, 505, and 360, encoding virulence proteins, were detected in 4 isolates from Donetsk and Zaporozhye regions. The phylogeny of the genotype II ASFV, which originated from the reference strain Georgia 2007/1, is shown to be sufficient for isolate differentiation. The presented data are of theoretical and practical importance for domestic and international ASFV surveillance.

Variability of non-structural proteins of HIV-1 sub-subtype A6 (Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1, sub-subtype A6) variants circulating in different regions of the Russian Federation.

HIV-1 non-structural proteins are promising targets for vaccine development and for creating approaches to personalized medicine. HIV-1 sub-subtype A6 has become the dominating strain in Russia. However, the geographic, economic and demographic characteristics of the country can contribute to the formation of differences between A6 variants circulating in different regions. The aim of the study is a comparative analysis of the consensus sequences of non-structural proteins in A6 variants circulating in the Amur Region, in Arkhangelsk, Irkutsk and Murmansk. 48 whole blood samples obtained from HIV-infected patients without experience of therapy observed at the AIDS Centers in Arkhangelsk, Irkutsk, Murmansk and Amur Region were analyzed. HIV-1 whole-genome nucleotide sequences were obtained and were subtyped. Consensus sequences of sub-subtype A6 variants non-structural proteins for each analyzed region were formed. Furthermore, reference sequences of sub-subtype A6 non-structural proteins were formed based on whole-genome sequences retrieved from the international Los Alamos database. Comparison of consensus sequences and references was performed using the MEGA v.10.2.2 and the PSIPRED programs. Vif, Vpr and Nef reference sequences have been obtained for HIV-1 sub-subtype A6. There was not difference in consensus sequences of Vpr in different regions. Characteristic features were found for consensus sequences of Tat, Rev, Vpu, Vif and Nef proteins in different regions. A limitation of the study is a small sample size. Overall, the results demonstrate the existing diversity of non-structural proteins in sub-subtype A6 variants in different regions and indicate the relevance of studying the polymorphism of non-structural proteins of virus variants in different regions.

Evaluation of the effectiveness of chemical inactivation and immunogenicity of the Omicron variant of the SARS-CoV-2 virus

The rapid spread of coronavirus infection COVID-19 among the population of many countries around the world has contributed to the emergence of many genetic variants of SARS-CoV-2. Compared to previous coronavirus variants, the new Omicron variants have shown a noticeable degree of mutation. Virus inactivation is one of the most important steps in the development of inactivated vaccines. The chemical inactivation agents currently used are β-propiolactone and formaldehyde, but there is no uniform standard for designing and specifying the inactivation process. Evaluation and comparison of the effectiveness of chemical inactivation of two agents, formaldehyde and β-propiolactone against immunogenicity of the Omicron variant of the SARS-CoV-2 virus. Nasopharyngeal swabs were used to obtain the SARS-CoV-2 Omicron variant virus. Vero cell culture was used to isolate, reproduce, titrate the virus, and perform a neutralization reaction. The kinetics of studying the inactivation of the virus by chemical agents such as formaldehyde and β-propiolactone was carried out. Studies have been conducted to comparatively evaluate the effectiveness of chemical agents used to inactivate the SARS-CoV-2 virus of the Omicron variant, planned for use in the production of an inactivated whole-virion vaccine. Formaldehyde and β-propiolactone were used as inactivation agents in concentrations of 0.05, 0.1, 0.5% of the total volume of the virus suspension. It has been established that complete inactivation of the virus by formaldehyde in the concentrations used at a temperature of 37 °C occurs within up to 2 hours, and when using beta-propiolactone, within up to 12 hours. Inactivated virus samples have different antigenic activity depending on the concentration of the inactivation agents used. The most pronounced antigenic activity is manifested in samples of the pathogen that were treated with an inactivation agent at a mild concentration of 0.05%. Increasing the concentration of inactivation agent by 5 or more times leads to a significant decrease in the antigenicity of the SARS-CoV-2 virus. With the inactivation modes used, the loss of biological activity of the virus occurs faster and antigenicity is retained largely when treated with formaldehyde.

Genomic characteristics, disease outcome and heterologous vaccine effectiveness among cases with SARS CoV-2 infection

BackgroundIn the pursuit of global health security, continuous monitoring of vaccine effectiveness across various viral strains emerges as a crucial imperative. The emergence of SARS-CoV-2 major variants of concern (VOCs), including Alpha, Beta, Delta, and Omicron, has added complexity to the COVID-19 vaccination landscape.ObjectivesTo assess illness severity, evaluate vaccine efficacy across varying doses and types, and determine effectiveness against major VOCs within the population.MethodsThis retrospective cohort study, conducted in Abu Dhabi, United Arab Emirates, focuses on a cohort of 44,073 SARS-CoV-2 positive cases from February 2021 to May 2022, dominated by the Delta and Omicron variants. The study employed a nested case-control design, analyzing hospital admissions for confirmed SARS-CoV-2 infection.ResultsVaccine effectiveness was higher among heterologus-boosted individuals at 87% (95% CI:79%-93%) compared to homologus-boosted individuals at 59% (95% CI: 48%-68%) and fully vaccinated, non-boosted adults at 53% (95% CI: 46%-59%). These findings highlight the importance of heterologous boosting, particularly against rapidly evolving viral variants, offering valuable insights for refining pandemic response strategies.ConclusionThe study underscores the critical need for ongoing assessment and adaptation of vaccination strategies to the evolving viral landscape.

Recombinant characterization and pathogenicity of a novel L1C RFLP-1-4-4 variant of porcine reproductive and respiratory syndrome virus in China

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant diseases affecting the pig industry worldwide and is caused by the PRRS virus (PRRSV), which has complex genetic variation due to frequent mutations, indels, and recombination. The emergence of PRRSV L1C.5 in 2020 in the United States has raised worldwide concerns about PRRSV with the RFLP 1-4-4 pattern and lineage 1C. However, studies on the pathogenic characteristics, epidemiological distribution, and effectiveness of vaccines against PRRSV with L1C and RFLP1-4-4 pattern in China are still insufficient. In this study, a novel recombinant variant of PRRSV with RFLP 1-4-4 and lineage 1C features, different from L1C.5 in the United States, was isolated in China in 2021. In pathogenicity experiments in specific pathogen-free piglets or farm piglets, 60–100% of artificially infected experimental piglets died with high fever and respiratory symptoms. Inflammatory cytokine and chemokine levels were upregulated in infected piglets. A commercially modified live vaccine against highly pathogenic PRRSV did not provide effective protection when the vaccinated piglets were challenged with the novel L1C-1-4-4 variant. Therefore, this strain merits special attention when devising control and vaccine strategies. These findings suggest that extensive joint surveillance is urgently needed and that vaccine strategies should be updated to prevent the disease from spreading further.

Safety and Immunogenicity of Intranasal Razi Cov Pars as a COVID-19 Booster Vaccine in Adults: Promising Results from a Groundbreaking Clinical Trial

Protective antibodies in the upper respiratory tract prevent the spread of COVID-19 in the community. Intranasal vaccines could raise the specific secretory IgA and IgG levels. This is a single-center, randomized, double-blind, placebo-controlled clinical trial to evaluate the safety and immunogenicity of Razi Cov Pars (RCP) intranasal recombinant protein subunit COVID-19 vaccine as a booster in adults. We compared specific IgG and IgA levels in the intranasal RCP group (n = 97) versus placebo (n = 96) in serum, saliva, and nasal mucosal secretions on days 0 and 14 and reported their Geometric Mean Ratios (GMR) and 95% confidence intervals (CI). We showed significant increases in IgA and IgG anti-RBD in the nasal mucosa in the RCP group, but their increase was not detectable in the serum and saliva. Anti-spike IgA in the nasal mucosa also increased in the RCP group compared to the placebo. This increase against the COVID-19 variant Omicron was also similar to that of the Wuhan. We detected no serious adverse reactions or anaphylaxis and all adverse events resolved completely during the follow-up period and were similar in both groups. Intranasal RCP is safe, stimulates the respiratory mucosal immunity, and could be a booster on various COVID-19 vaccines and be effective against new virus variants.

Effect of wild-type vaccine doses on BA.5 hybrid immunity, disease severity, and XBB reinfection risk.

Vaccination against the wild-type (WT) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus did not produce detectable levels of neutralizing antibodies (NAbs) against the BA.5 strain before it emerged. However, coronavirus disease-2019 (COVID-19) severity varied highly between unvaccinated, partially vaccinated, and fully vaccinated individuals, for unknown reasons. We assessed the severity of BA.5 infection and the risk of XBB strain reinfection and measured serum levels of NAbs against WT, BA.5, and XBB.1.9.1 SARS-CoV-2 strains at varying time points in 1,373 individuals who received zero, one, two, or three WT vaccine doses. We found that two to three WT doses significantly increased WT and BA.5 NAb levels and reduced the incidence of COVID-19-associated pneumonia upon BA.5 strain infection compared to zero to one dose. Regarding XBB reinfection, those who received two to three doses and were infected with the BA.5 variant exhibited a significantly lower reinfection risk compared to those who received zero to one dose. RNA analysis revealed that the differentially expressed genes between the two to three dose and unvaccinated groups were enriched in B cell activation, cytokine-cytokine receptor interaction, complement, and monocyte activation functions-indicating that vaccination increased the antibody response and reduced inflammation. Our results suggest that multiple antigen exposures to either matched or unmatched SARS-COV-2 variants, through vaccination or infection, may be necessary to achieve significant immune imprinting.IMPORTANCEThe administration of coronavirus disease-2019 (COVID-19) vaccines that do not perfectly match the viral strains that individuals become infected with has been found to impact the resultant illness severity-although the precise mechanism underlying this phenomenon remains unclear. We assessed viral clearance, as well as serum levels of inflammatory cytokines and neutralizing antibodies (NAbs) against wild-type, BA.5, and XBB.1.9.1 variants of the severe acute respiratory syndrome coronavirus 2 among individuals who received varying doses of such strain-mismatched vaccines. Notably, vaccination with ≥2 doses of strain-mismatched COVID-19 vaccines appeared to stimulate the production of specific NAbs during infection with new variants, as well as attenuate the inflammatory response and enhance viral clearance. Such vaccination regimens can also reduce the risk of reinfection. These findings may be important for guiding the development of future COVID-19 vaccination strategies that target both matched and mismatched viral variants.

How well do different COVID-19 vaccines protect against different viral variants? A systematic review and meta-analysis.

While the efficacy of coronavirus disease 2019 (COVID-19) vaccines has been evaluated in numerous trials, comprehensive evidence on how protection by different vaccines has varied over time remains limited. We aimed to compare protective effects of different vaccines against different viral variants. To achieve this, we searched Medline, Cochrane Library and Embase for randomized controlled trials assessing the efficacy of COVID-19 vaccines. Forest plots using Mantel-Haenszel and random-effects models were generated showing risk ratios (RRs) and 95% CIs by vaccines and variants. We included 36 studies with 90 variant-specific primary outcomes. We found a RR of 0.26 (95% CI 0.21 to 0.31) against all variants overall, with the highest protective effects against the wild-type (RR 0.13; 95% CI 0.10 to 0.18), followed by Alpha (RR 0.26; 95% CI 0.18 to 0.36), Gamma (RR 0.34; 95% CI 0.21 to 0.55), Delta (RR 0.39; 95% CI 0.28 to 0.56) and Beta (RR 0.49; 95% CI 0.40 to 0.62) variants. Nucleic acid vaccines showed the highest protection levels against all variants (RR 0.11; 95% CI 0.08 to 0.15), followed by protein subunit, inactivated virus and viral vector. In conclusion, we found high but heterogenous levels of protection for most COVID-19 vaccines, with decreasing protective effects for vaccines based on traditional technologies as SARS-CoV-2 variants emerged over time. Novel nucleic acid-based vaccines offered substantially higher and more consistent protection.

Virulence‐Free Reconstituted Synthetic Nanopathogen Empowered by Timely‐Activating TLR Agonist Promotes Heterologous Cancer Immunotherapy with Depletion of Tumor‐Specific Treg Cells

AbstractThe heterologous immunity of live pathogens leads to the emergence of this approach as a pivotal component in cancer immunotherapy. However, virulence, inflammatory‐related toxicity, and the induction of Treg cells after treatment hinder their clinical translation. Here, to exploit the heterologous immunity of live pathogens without risks, a virulence‐free reconstituted synthetic nanopathogen (RSnP) is developed by the cell wall skeleton of disrupted Mycobacterium bovis and the incorporation of timely‐activating Toll‐like receptor 7/8 agonists of which multifaceted activities can be promoted by endolysosomal enzymes. Immunization with RSnP, even without tumor‐specific antigens, exhibits potent antitumor efficacy against melanoma, breast cancer, and bladder cancer by promoting antitumor effector cells (CD8+ T cells, NK cells, M1 macrophages, and Th17 cells) and proinflammatory cytokines (IL‐12p70, TNF‐α, and IL‐6) while simultaneously mitigating immunosuppressive myeloid cells (MDSCs and M2 macrophages) in the tumor microenvironment, surpassing the therapeutic efficacies of approved live‐BCG drug and mRNA vaccine. The increase in CCR8+Foxp3+ Treg cells induced to counteract RSnP treatment can be attenuated by anti‐CCR8 antibody, a depletion antibody for tumor‐specific Treg cells, to synergize therapeutic efficacy with relieved autoimmunity. RSnP can be a therapeutic nanomedicine platform across heterologous cancers and emerging infectious virus variants with minimized toxicity.

Programmable DNA-based nanostructure sensors for mutation detection coupled with asymmetric amplification in precision genome profiling

We introduce a DNA-based nanostructure sensor for the rapid, precise identification of single-nucleotide polymorphisms (SNPs), a key factor in determining disease susceptibility and tailoring medical treatment. The proposed two-state sensor design facilitates multiplexed, sequence-specific detection of double-stranded genomic DNA (gDNA), overcoming traditional obstacles presented by base pairing interference. Utilizing detector strands with binding penalties, the sensor achieves high SNP specificity, discernible by distinct gel electrophoresis band positions. Coupled with asymmetric PCR (asy-PCR), our integrated system amplifies genetic profiling effectiveness, especially in clinical biopsies, enhancing gDNA detection sensitivity and specificity for concurrent multiple mutation identifications. This cost-effective method ($0.41 per test) streamlines mutation screening, enabling high-throughput analysis with limited equipment—requiring only a single staining agent and a unified electrophoresis apparatus. Validated clinically with 70 colorectal cancer samples, the system boasts a 98.57% sensitivity and 95.71% specificity for KRAS mutations, surpassing traditional PCR detection and uncovering low-frequency mutations untraceable by direct sequencing. Our findings suggest this asy-PCR enhanced DNA-based nanostructure sensor system has the potential to revolutionize genetic diagnostics, offering expansive applications in detecting viral variants and microbial strains, thus advancing personalized genetic testing.

Fighting Mutations with Mutations: Evolutionarily Adapting a DNA Aptamer for High‐Affinity Recognition of Mutated Spike Proteins of SARS‐CoV‐2

AbstractAn on‐going challenge with COVID‐19, which has huge implications for future pandemics, is the rapid emergence of viral variants that makes diagnostic tools less accurate, calling for rapid identification of recognition elements for detecting new variants caused by mutations. We hypothesize that we can fight mutations of the viruses with mutations of existing recognition elements. We demonstrate this concept via rapidly evolving an existing DNA aptamer originally selected for the spike protein (S‐protein) of wildtype SARS‐CoV‐2 to enhance the interaction with the same protein of the Omicron variants. The new aptamer, MBA5SA1, has acquired 22 mutations within its 40‐nucleotide core sequence and improved its binding affinity for the S‐proteins of diverse Omicron subvariants by &gt;100‐fold compared to its parental aptamer (improved from nanomolar to picomolar affinity). Deep sequencing analysis reveals dynamic competitions among several MBA5SA1 variants in response to increasing selection pressure imposed during in vitro selection, with MBA5SA1 being the final winner of the competition. Additionally, MBA5SA1 was implemented into an enzyme‐linked aptamer binding assay (ELABA), which was applied for detecting Omicron variants in the saliva of infected patients. The assay produced a sensitivity of 86.5 % and a specificity of 100 %, which were established with 83 clinical samples.