Variant Strains Research Articles

A-synuclein prion strains differentially adapt after passage in mice.

In patients with synucleinopathies, the protein α-synuclein misfolds into multiple conformations, each of which determines whether a patient develops multiple system atrophy (MSA) or one of three Lewy body diseases (LBDs). However, patients may also first present with pure autonomic failure, which strictly impacts autonomic nerves in the periphery, which can then phenoconvert into MSA or a LBD. When neuroinvasion happens, it remains unknown if strain properties are retained or if strain adaptation occurs, even though neuroinvasion of some prion protein (PrP) strains is known to result in the emergence of novel PrP strain variants. To investigate this question in synucleinopathies, we inoculated TgM83+/- mice, which express human α-synuclein with the A53T mutation, with a mouse-passaged MSA patient sample either intracranially (i.c.) or into the sciatic nerve (sc.n.), and compared the biochemical and biological properties of α-synuclein prions in the brains of terminal mice. Importantly, while i.c. and sc.n. transmission studies generated pathogenic α-synuclein with similar properties, both the primary and secondary passaged MSA samples had different infectivity profiles in a panel of α-syn140-YFP cells than the starting MSA patient sample, indicating that MSA prions adapt during initial passage in TgM83+/- mice. Similarly, using i.c. inoculation of A53T preformed fibrils to study strain selection, we found both biochemical and biological evidence that mouse passage exerts a selective pressure on α-synuclein prions in which a sub-population of starting conformations emerges in terminal animals. Together, these findings demonstrate that similar conformational selective pressures known to impact PrP prion replication also impact replication of α-synuclein prions.

Can social media promote vaccination? Strategies and effectiveness of COVID-19 vaccine popularization on Chinese Weibo.

The COVID-19 pandemic has shown a high severity in terms of mortality, and to mitigate the impact of the COVID-19 pandemic, a great deal of reliance has been placed on vaccines with defensive effects. In the context of the transmission of hazardous Omicron variant strains, vaccine popularization and acceptance are very important to ensure world health security. Social media can spread information and increase public confidence in and acceptance of vaccines. In this study, weibos related to "vaccine science popularization" during the COVID-19 pandemic in China were collected, and Weibo publishers were divided into Individuals, Organizations, Media, Government, and Scientists. The communication strategies were analyzed with content analysis from the four dimensions of Issue, Topic, Frame, and Position. SnowNLP was used to mine the audience comments and to assess their emotional tendencies. Finally, hierarchical regression was used to verify the causal relationship between vaccine science popularization strategies and audiences' emotions. We found that the higher the scientific authority of the weibo publisher, the more positive the emotional tendency of the audience toward the weibo. Issues that are scientific, authoritative, and positive topics that positively present the advantages of the COVID-19 vaccine, and frames with detailed narratives, scientific arguments, diversified forms of presentations, and positions in support of the COVID-19 vaccine, positively affect the effect of vaccine popularization. Based on the experience of COVID-19 vaccine promotion in China, the results may serve as a reference for promoting innovative vaccines and handling public health affairs around the world.

Molecular characterization of circulating infectious bursal disease viruses in chickens from different Egyptian governorates during 2023

Infectious bursal disease virus (IBDV) induces severe immunosuppression in chickens, leading to significant economic losses in the global poultry industry. This study investigated 52 chicken flocks, including commercial broilers, layers, and baladi, from various Egyptian governorates in 2023. These flocks exhibited symptoms of depression, along with kidney and bursa lesions, indicative of IBDV infection. Pooled Bursal homogenates were tested using RT-PCR with VP2-specific primers, revealing that 20 flocks tested positive for IBDV. Six representative samples were selected from 20 positive flocks for isolation in embryonated chicken eggs. The embryonic lesions observed included haemorrhage, skull swelling, and liver necrosis with a pale-yellow appearance, in addition to congestion and thickening in the chorioallantoic membrane (CAM). Partial amplification of the VP2 gene from the harvested embryo suspensions of the six IBDV isolates was performed for sequencing. Phylogenetic analysis of the sequences revealed that five IBDV isolates (VV4, VV5, VV6, VV10, and VV16) belonged to the very virulent strain group A3 cluster, whereas one isolate (VV2) clustered with Chinese Variant strains in the A2d group. Sequence analysis of the hypervariable region (HVR) of VP2 compared to that of Egypt-USC-IBD-1-2019 and vvIBDV/Beh21/Egypt/18 highly virulent IBDV strains revealed several amino acid mutations. The VP2 HVR of all isolates maintained the serine-rich heptapeptide sequence SWSASGS, which is adjacent to the major hydrophilic peak B and serves as a virulence marker. Histopathological examination revealed that bursae from chickens infected with vvIBDV exhibited marked interlobular oedema and lymphoid depletion. In contrast, bursae from chickens infected with Variant IBDV showed massive lymphoid depletion, with hyperplasia of the bursal capsule. These findings highlight the circulation of both virulent and Variant IBDV strains in Egyptian chicken flocks, complicating disease control. Consequently, there is a need to update vaccination programs and vaccine strains for IBDV in Egypt.

A new record of avian reovirus genogroup clusters isolated and molecularly characterized in chickens in Egypt

BackgroundThe global poultry industry has been experiencing increasing condemnation at slaughterhouses since 2011, due to the emergence of avian reovirus (ARV) variant strains. Recently seven ARV genogroup clusters were identified based on the σC sequence of the S1 segment that was used as a genetic marker to characterize and classify ARV.ResultsAmong ninety-seven suspected broilers, breeders, and commercial grandparent’s homogenates, ARV was PCR confirmed in thirty-five (36%). Samples were collected from different governorates in Egypt, including Giza–Ismailia–Sharqia–Menoufia, and Behira, between 2020 and 2023. A viral isolation trial was performed on weak positive samples, successfully isolating sixteen samples on the LMH cell line forming the characteristic giant cells of ARV infection. Partial sequencing and phylogenetic analysis of the σC gene of ten ARV PCR positive samples revealed the circulation of ARV genogroup clusters 1, 2, 4, and 5, eight samples being distinguished from commercially available vaccine strains with a low percentage of nucleotides and amino acid identities.ConclusionsThis research demonstrated that the ARV isolates were distinct compared to commercially available vaccine strains based on partial σC sequence. Detection, isolation, and classification of ARV as genogroups 1, 2, 4, and 5 are recorded. A vigilant surveillance to evaluate the ARV situation in Egypt is urgent. We recommend re-evaluating the ARV commercial vaccines by challenging them with circulating Egyptian field isolates, as well as their cross-protection. In addition, the development of autologous vaccines from both classical and variant strains to provide optimal protection.

Prevalence and genetic diversity of porcine epidemic diarrhea virus in Southwest China during 2020–2022

Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), has been frequently occurring in the southwestern region of China over the past few years, continuously affecting the development of the swine industry. However, the genetic diversity and prevalence of PEDV strains circulating in the swine population in southwestern China in recent years have not been well studied. To address this gap, a total of 478 clinical samples were collected from 125 pig farms experiencing piglet diarrhea in 18 cities in southwestern China. The detection results revealed that 227 out of 478 samples tested positive for PEDV nucleic acid, with a positivity rate of 47.49%. Complete S gene sequences of 28 PEDV strains were obtained and classified into four subgroups, G1-a subgroup (classical strain), G1-b subgroup (S-INDEL), and two G2 subgroups (G2-a and G2-b), accounting for 17.86% (5/28), 3.57% (1/28), 35.71% (10/28), 42.86% (12/28) of the total sequenced strains, respectively. The coexistence of multiple genotypes indicates the complex genetic background and prevalence of PEDV in southwest China. Amino acid comparisons of the S proteins showed that the 28 PEDV strains sequenced in the study showed different patterns of variation in the epitope domains compared to vaccine strains belonging to different genotypes and contained many unique amino acid mutations compared to the reference strains, which might lead to immune escape of PEDV. The complex epidemiology of PEDV with multiple subgroups co-circulating in Southwest China underscores the importance of selecting appropriate vaccine strains based on locally prevalent strains and the ongoing need for epidemiological surveillance of PEDV. The emergence of new variant strains also highlights the urgency of developing updated vaccines, and effective management practices remain crucial for controlling PED outbreaks in pig farms.

Novel goose parvovirus in naturally infected ducks suffering from locomotor disorders: molecular detection, histopathological examination, immunohistochemical signals, and full genome sequencing

ABSTRACT In this study, we investigated the pathological effects of novel goose parvovirus (NGPV) infection on the skeletal muscle, brain, and intestine of naturally affected ducks suffering from locomotor dysfunction as a new approach for a deeper understanding of this clinical form. For this purpose, a total of 97 diseased ducks, representing 24 flocks of different duck breeds (14–75 days old), were clinically examined. In total, 72 tissue pools of intestine, brain, and skeletal muscle samples were submitted for molecular identification. Typical clinical signs among the examined ducks suggested parvovirus infection. Regarding postmortem examination, all examined ducks showed muscle emaciation (100%) either accompanied by congestion (34%) or paleness (66%). Slight congestion, either in the brain (82.5%) or intestine (75.25%), was predominantly detected. Based on molecular identification, the intestine had the highest percentage of positive detection (91.7%), followed by the skeletal muscle (70.8%), and the brain (20.8%). The main histopathological alterations were myofibre atrophy and degeneration, marked enteritis accompanied by lymphocytic infiltration in the lamina propria and submucosa, while the affected brains showed vasculitis, diffuse gliosis, and Purkinje cell degeneration in the cerebellum. Next-generation sequencing further confirmed the presence of a variant strain of goose parvovirus (vGPV) that is globally known as NGPV and closely related to Chinese NGPV isolates. Using immunohistochemistry, the NGPV antigen was positively detected in the muscle fibres, enterocytes, and Purkinje cells in the cerebellum. These findings provided proof of the involvement of virus replication in the locomotor disorders linked to NGPV infection in ducks.

Development of a new platform for testing antiviral drugs using coronavirus-infected human nasal mucosa organoids

To establish a coronavirus (CoV) infection model using human nasal mucosa organoids for testing antiviral drugs and evaluate the feasibility of using human nasal mucosa organoids with viral infection as platforms for viral research and antiviral drug development. Human nasal mucosa organoids were tested for susceptibility to SARS-CoV-2 and HCoV-OC43 pseudoviruses. In a P3 laboratory, nasal mucosa organoids were infected with the original strain of SARS-CoV-2 and 4 variant strains, and the infection conditions were optimized. The viral loads in the culture supernatants were measured at different time points using RT-qPCR, and immunofluorescence assay was employed to localize SARS-CoV-2 nucleocapsid protein to determine the type of the infected cells. In the optimized nasal mucosa viral infection model, the antiviral effects of camostat and bergamot extract (which were known to inhibit SARS-CoV-2) were tested and the underlying molecular mechanisms were explored. In the optimized nasal mucosa organoid models infected with SARS-CoV-2 and HCoV-OC43 pseudoviruses, the viral load in the culture supernatants increased significantly during the period of 2 to 24 h following the infection, which confirmed infection of the organoids by both of the pseudoviruses. The nasal mucosa organoids could be stably infected by the original SARS-CoV-2 strain and its 4 variant strains, validating successful establishment of the viral infection model, in which both camostat and bergamot extract exhibited dose-dependent antiviral effects. Human nasal mucosa organoids with SARS-CoV-2 infection can serve as platforms for screening and testing antiviral drugs, particularly those intended for nasal administration.

Research progress of spike protein mutation of SARS-CoV-2 mutant strain and antibody development.

The coronavirus disease 2019 (COVID-19) is a respiratory disease with a very high infectious rate caused by the Severe Acute Respiratory Syndrome Coronavirus-2(SARS-CoV-2). Because SARS-CoV-2 is easy to mutate, the continuous emergence of SARS-CoV-2 variant strains not only enhances the infectivity of the SARS-CoV-2 but also brings great obstacles to the treatment of COVID-19. Neutralizing antibodies have achieved good results in the clinical application of the novel coronavirus pneumonia, which can be used for pre-infection protection and treatment of novel coronavirus patients. This review makes a detailed introduction to the mutation characteristics of SARS-CoV-2, focusing on the molecular mechanism of mutation affecting the infectivity of SARS-CoV-2, and the impact of mutation on monoclonal antibody therapy, providing scientific reference for the prevention of SARS-CoV-2 variant strains and the research and development of antibody drugs.

Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization.

The evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profound comprehension of potential variations is crucial to effectively mitigate the impact of viral evolution. Yet, this task still faces considerable challenges. This study introduces DARSEP, a method based on Deep learning Associates with Reinforcement learning for SARS-CoV-2 Evolution Prediction, combined with self-game sequence optimization and RetNet-based model. DARSEP accurately predicts evolutionary sequences and investigates the virus's evolutionary trajectory. It filters spike protein sequences with optimal fitness values from an extensive mutation space, selectively identifies those with a higher likelihood of evading immune detection, and devises a superior evolutionary analysis model for SARS-CoV-2 spike protein sequences. Comprehensive downstream task evaluations corroborate the model's efficacy in predicting potential mutation sites, elucidating SARS-CoV-2's evolutionary direction, and analyzing the development trends of Omicron variant strains through semantic changes. Overall, DARSEP enriches our understanding of the dynamic evolution of SARS-CoV-2 and provides robust support for addressing present and future epidemic challenges.

Production of a monoclonal antibody targeting the SARS-CoV-2 Omicron spike protein and analysis of SARS-CoV-2 Omicron mutations related to monoclonal antibody resistance

SARS-CoV-2 mutations have resulted in the emergence of multiple concerning variants, with Omicron being the dominant strain presently. Therefore, we developed a monoclonal antibody (mAb) against the spike (S) protein of SARS-CoV-2 Omicron for therapeutic applications. We established the 1E3H12 mAb, recognizing the receptor binding domain (RBD) of the Omicron S protein, and found that the 1E3H12 mAb can efficiently recognize the Omicron S protein with weak affinity to the Alpha, Beta, and Mu variants, but not to the parental strain and Delta variant. Based on in vitro assays, the mAb demonstrated neutralizing activity against Omicron BA.1, BA.4/5, BQ.1.1, and XBB. A humanized antibody was further produced and proved to have neutralizing activity. To verify the potential limitations of the 1E3H12 mAb due to viral escape of SARS-CoV-2 Omicron variants, we analyzed the emergence of variants by whole genome deep sequencing after serial passage in cell culture. The results showed a few unique S protein mutations in the genome associated with resistance to the mAb. These findings suggest that this antibody not only contributes to the therapeutic arsenal against COVID-19 but also addresses the ongoing challenge of antibody resistance among the evolving subvariants of SARS-CoV-2 Omicron.

T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome.

As SARS-CoV-2 variants continue to emerge capable of evading neutralizing antibodies, it has become increasingly important to fully understand the breadth and functional profile of T cell responses to determine their impact on the immune surveillance of variant strains. Here, sampling healthy individuals, we profiled the kinetics and polyfunctionality of T cell immunity elicited by mRNA vaccination. Modeling of anti-spike T cell responses against ancestral and variant strains of SARS-CoV-2 suggested that epitope immunodominance and cross-reactivity are major predictive determinants of T cell immunity. To identify immunodominant epitopes across the viral proteome, we generated a comprehensive map of CD4+ and CD8+ T cell epitopes within non-spike proteins that induced polyfunctional T cell responses in convalescent patients. We found that immunodominant epitopes mainly resided within regions that were minimally disrupted by mutations in emerging variants. Conservation analysis across historical human coronaviruses combined with in silico alanine scanning mutagenesis of non-spike proteins underscored the functional importance of mutationally-constrained immunodominant regions. Collectively, these findings identify immunodominant T cell epitopes across the mutationally-constrained SARS-CoV-2 proteome, potentially providing immune surveillance against emerging variants, and inform the design of next-generation vaccines targeting antigens throughout SARS-CoV-2 proteome for broader and more durable protection.

Pseudorabies virus infection triggers mitophagy to dampen the interferon response and promote viral replication.

Pseudorabies virus (PRV) utilizes multiple strategies to inhibit type I interferon (IFN-I) production and signaling to achieve innate immune evasion. Among several other functions, mitochondria serve as a crucial immune hub in the initiation of innate antiviral responses. It is currently unknown whether PRV inhibits innate immune responses by manipulating mitochondria. In this study, we found that PRV infection damages mitochondrial structure and function, as shown by mitochondrial membrane potential depolarization, reduction in mitochondrial numbers, and an imbalance in mitochondrial dynamics. In addition, PRV infection triggered PINK1-Parkin-mediated mitophagy to eliminate the impaired mitochondria, which resulted in a suppression of IFN-I production, thereby promoting viral replication. Furthermore, we found that mitophagy resulted in the degradation of the mitochondrial antiviral signaling protein, which is located on the mitochondrial outer membrane. In conclusion, the data of the current study indicate that PRV-induced mitophagy represents a previously uncharacterized PRV evasion mechanism of the IFN-I response, thereby promoting virus replication.IMPORTANCEPseudorabies virus (PRV), a pathogen that induces different disease symptoms and is often fatal in domestic animals and wildlife, has caused great economic losses to the swine industry. Since 2011, different PRV variant strains have emerged in Asia, against which current commercial vaccines may not always provide optimal protection in pigs. In addition, there are indications that some of these PRV variant strains may sporadically infect people. In the current study, we found that PRV infection causes mitochondria injury. This is associated with the induction of mitophagy to eliminate the damaged mitochondria, which results in suppressed antiviral interferon production and signaling. Hence, our study reveals a novel mechanism that is used by PRV to antagonize the antiviral host immune response, providing a theoretical basis that may contribute to the research toward and development of new vaccines and antiviral drugs.

Identification of a new Clostridium perfringens variant with a chromosomally encoded enterotoxin gene in a suspected persistent food poisoning outbreak in Eritrea.

Clostridium perfringens is a causative agent of various human and animal enteric diseases including food poisoning. In this study, we describe an interesting case of a persistent food poisoning outbreak among Finnish peacekeepers in Eritrea, possibly caused by Clostridium perfringens carrying a new variant of the chromosomally encoded enterotoxin gene. C. perfringens strains causing food poisoning carry the enterotoxin gene, cpe, in its chromosome (c-cpe) or on a plasmid (p-cpe). PCR assays are widely used for toxinotype C. perfringens strains. The integration sites for the cpe gene are highly conserved, and PCR assays targeting the cpe gene and the adjacent IS elements (the IS1470 in c-cpe and the IS1470-like or IS1151 in p-cpe strains) are used to further determine the genetic location of the cpe gene. We sequenced nine enteropathogenic C. perfringens strains related to a persistent food poisoning outbreak among Finnish peacekeepers in Eritrea. Six of these strains produced non-typeable cpe results in the standard PCR assay due to divergence in the enterotoxin integration site. The gene order of the new variant of the chromosomal cpe insertion site with an additional IS1470 element impairing genotyping PCR assay for the location of cpe is described. In addition, variant c-cpe strains carried 58-81 copies of IS1470 in their genomes, compared to 9-23 copies found in previously described c-cpe strains. Thus, the present study represents an untraditional type of C. perfringens food poisoning caused by variant c-cpe strains, and the sequenced strains bring geographic variation to the existing strain collection of sequenced C. perfringens.

TMT-based quantitative proteomic analysis of IBDV-infected CEF cells reveals a favorable role of chicken IRF10 in IBDV replication via suppressing type-I interferon expression

Infectious bursal disease (IBD) is an acute, highly contagious disease caused by infectious bursal disease virus (IBDV), causing huge economic losses to the poultry industry worldwide. Currently, the emerging variant strains of IBDV and new recombinants in the field are circulating in many countries and poses severe threats to the development of poultry industry. Elucidation of the pathogenesis of IBDV infection will be of great help to the development of vaccines for control of IBDV infection. In this study, liquid chromatography tandem-mass spectrometry (LC–MS/MS) combined with tandem mass tag (TMT) labeling was performed to determine the expressions of nucleus proteins in IBDV-infected chicken embryonic fibroblast (CEF) cells 24 h post-infection (hpi). Our data show that a total of 236 nucleus proteins were differentially expressed in IBDV-infected cells vs mock-infected controls, and that among those proteins, 171 were significantly upregulated while 65 downregulated. Bioinformatics analysis reveals that the differentially expressed proteins (DEPs) were mainly involved in immune response, DNA replication, mismatch repair, and RIG-I-like receptor (RLR) signaling. Consistently, the expression of ten selected upregulated genes (IRF10, IRF7, IRF1, STAT1, ATF3, GTF3A, CSRP3, RARB, BASP1, and NF-κB1) markedly increased as examined by quantitative real‐time PCR (qRT-PCR). Furthermore, the expression of IRF10 was upregulated both in the cytoplasm and nucleus of DF-1 cells as examined by Western Blot. Moreover, knockdown of IRF10 remarkably inhibited IBDV replication via promoting IFN-I response, and overexpression of IRF10 significantly suppressed type I interferon and ISGs expression in both mock and IBDV-infected cells, suggesting that IRF10 serve as a negative regulator for host antiviral response. These results provide clues to further investigation into host–IBDV interactions and the underlying mechanisms of IBDV infection.

Broad immunogenicity to prior SARS-CoV-2 strains and JN.1 variant elicited by XBB.1.5 vaccination in nursing home residents.

SARS-CoV-2 vaccination has reduced hospitalization and mortality for nursing home residents (NHRs) but emerging variants and waning immunity challenge vaccine effectiveness. This study assesses the immunogenicity of the most recent XBB.1.5 monovalent vaccine to variant strains among NHRs. Participants were subset of a longitudinal study of consented NHRs and Healthcare workers (HCWs) who have received serial blood draws to assess immunogenicity with each SARS-CoV-2 mRNA vaccine dose. We report data on participants who received the XBB.1.5 monovalent vaccine post-FDA approval in Fall 2023. NHRs were categorized by whether they had an interval SARS-CoV-2 infection between their first bivalent vaccine dose and their XBB.1.5 monovalent vaccination. The sample included 61 NHRs [median age 76 (IQR 68-86), 51% female] and 28 HCWs [median age 45 (IQR 31-58), 46% female). After XBB.1.5 vaccination, a robust geometric mean fold rise (GMFR) in XBB.1.5-specific neutralizing antibody titers was observed:17.3 (95% confidence interval [CI] 9.3, 32.4) and NHRs with interval infection and 11.3 (95% CI 5, 25.4) in those without and 13.6 (95% CI 8.4,22) in HCWs. For JN.1-specific titers, GMFRs were 14.9 (95% CI 7.9, 28) and 6.5 (95% CI 3.3, 13.1) in NHRs with and without interval infection, and 11.4 (95% CI 6.2, 20.9) in HCWs. NHRs with interval SARS-CoV-2 infection had higher titers across all analyzed strains analyzed. The XBB.1.5 vaccine significantly elevates Omicron-specific neutralizing antibody titers to XBB.1.5 and JN.1 strains in both NHRs and HCWs with more pronounced in those previously infected with SARS-CoV-2 since bivalent vaccination.

Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus (PEDV) during 2020-2022 and Isolation of a Variant Recombinant PEDV Strain.

Porcine epidemic diarrhea (PED) is an acute, highly contagious, and infectious disease caused by porcine epidemic diarrhea virus (PEDV). PEDV can affect pigs of all ages, with 50~100% mortality in neonatal piglets and substantial economic losses in the swine industry. In the present study, 347 fecal and intestinal samples were collected from seven regions in China during 2020-2022. A comprehensive molecular investigation of the spike (S) gene of PEDV strains was carried out, which included phylogenetic analysis of the obtained PEDV sequences. Epidemiological surveillance data indicate that the GIIc subgroup strains are widely distributed among pigs. A PEDV strain was successfully isolated from positive small intestine samples and identified through RT-PCR detection using specific N gene primers of PEDV, indirect immunofluorescence assay (IFA), TEM analysis, genome sequencing, and full-length S gene analysis, named PEDV/SC/2022. RDP and SimPlot analysis showed that the isolate originated from the recombination of PEDV/AH2012 and PEDV/AJ1102. In conclusion, our findings contribute to the current understanding of PEDV epidemiology and provide valuable information for the control of PED outbreaks in China.

MiR-181a Negatively Regulates Claudin-3 to Facilitate Lateolabrax maculatus Iridovirus Replication in Lateolabrax maculatus Astroglia Cells.

Lateolabrax maculatus iridovirus (LMIV) is a variant strain of red sea bream iridovirus (RSIV), causing serious economic losses in aquaculture. Claudins (CLDNs) are major components of tight junctions (TJs) forming an important line of defense against pathogens. Our pilot miRNA-mRNA joint analysis indicated the degradation of CLDN3, as well as its interaction with miR-181a during LMIV infection. To elucidate the miR-181a/CLDN3/LMIV interactions, in vitro assays were carried out on LMB-L cells. We first confirmed that LMIV infection could decrease the expression of CLDN3, accompanied by the enhancement of permeability, suggesting the dysfunction of TJs. Contrary to the inhibition of CLDN3, the activation of miR-181a was proved, presenting a negative correlation between miR-181a and CLDN3 (Pearson r = -0.773 and p < 0.01). In addition, the influence of CLDN3 on LMIV replication was analyzed by knockdown and over-expression of CLDN3. When CLDN3 was silenced in LMB-L cells with siCLDN3-623 at 9 days post transfection (dpt), LMIV copies and titers were significantly up-regulated by 1.59-fold and 13.87-fold, respectively. By contrast, LMIV replication in LMB-L cells was reduced by 60% and 71%, post transfection with pcDNA3.1-CLDN3 over-expressed plasmid at 6 dpt and 9 dpt, respectively. Ultimately, the regulatory relationship between miR-181a and CLDN3 was further validated by dual luciferase reporter assays. Taking into account the above-described results, we proposed a "miR-181a/CLDN3/LMIV" regulatory relationship. This study provides a new insight for understanding the mechanism of LMIV replication.

Shift in Demographic Involvement and Clinical Characteristics of COVID-19 From Wild-Type SARS-CoV-2 to the Delta Variant in the Indian Population: In Silico Analysis.

The Delta variant (B.1.617.2) was considered the most dangerous SARS-CoV-2 strain; however, in-depth studies on its impact based on demographic and clinical characteristics of COVID-19 are scarce. We aimed to investigate the shift in demographic and clinical characteristics of the COVID-19 pandemic with the emergence of the SARS-CoV-2 Delta variant compared with the wild-type (WT) strain (B.1). A cross-sectional study of COVID-19 cases in the Indian population caused by the WT strain (B.1) and Delta variant of SARS-CoV-2 was performed. The viral genomic sequence metadata containing demographic, vaccination, and patient status details (N=9500, NDelta=6238, NWT=3262) were statistically analyzed. With the Delta variant, in comparison with the WT strain, a higher proportion of young individuals (<20 years) were infected (0-9 years: Delta: 281/6238, 4.5% vs B.1: 75/3262, 2.3%; 10-19 years: Delta: 562/6238, 9% vs B.1: 229/3262, 7%; P<.001). The proportion of women contracting infection increased (Delta: 2557/6238, 41% vs B.1: 1174/3262, 36%; P<.001). However, it decreased for men (Delta: 3681/6238, 59% vs B.1: 2088/3262, 64%; P<.001). An increased proportion of the young population developed symptomatic illness and were hospitalized (Delta: 27/262, 10.3% vs B.1: 5/130, 3.8%; P=.02). Moreover, an increased proportion of the women (albeit not men) from the young (Delta: 37/262, 14.1% vs B.1: 4/130, 3.1%; P<.001) and adult (Delta: 197/262, 75.2% vs B.1: 72/130, 55.4%; P<.001) groups developed symptomatic illness and were hospitalized. The mean age of men and women who contracted infection (Delta: men=37.9, SD 17.2 years; women=36.6, SD 17.6 years; P<.001; B.1: men=39.6, SD 16.9 years; women=40.1, SD 17.4 years; P<.001) as well as developing symptoms or being hospitalized (Delta: men=39.6, SD 17.4 years; women=35.6, SD 16.9 years, P<.001; B.1: men=47, SD 18 years; women=49.5, SD 20.9 years, P<.001) were considerably lower with the Delta variant than the B.1 strain. The total mortality was about 1.8 times higher with the Delta variant than with the WT strain. With the Delta variant, compared with B.1, mortality decreased for men (Delta: 58/85, 68% vs B.1: 15/20, 75%; P<.001); in contrast, it increased for women (Delta: 27/85, 32% vs B.1: 5/20, 25%; P<.001). The odds of death increased with age, irrespective of sex (odds ratio 3.034, 95% CI 1.7-5.2, P<.001). Frequent postvaccination infections (24/6238) occurred with the Delta variant following complete doses. The increased involvement of young people and women, the lower mean age for illness, higher mortality, and frequent postvaccination infections were significant epidemiological concerns with the Delta variant.

Prevalence of Human Adenovirus Type 3 Associated with Pharyngoconjunctival Fever in Children in Osaka, Japan during and after the COVID-19 Pandemic.

The incidence and type distribution of human adenovirus (HAdV) infections among children with pharyngoconjunctival fever (PCF) in Osaka, Japan between 2019 and 2023 were analyzed to assess the effect of the coronavirus disease 2019 (COVID-19) pandemic. The number of reported PCF cases in Osaka decreased from 2020 to 2022, followed by an unprecedented increase in 2023. HAdV-C strains, including types C1, C2, and C5, were detected in throughout the study period. Conversely, HAdV-B3 was not detected for 2 years and 9 months from March 2020 to December 2022, but the number of detections increased from July 2023. Overall, HAdV-B3 was the most frequently detected type (27 of 52 strains), and genetic analysis of its hexon hypervariable regions showed that, except for one strain, the HAdV-B3 strains identified after 2022 had different amino acid substitutions to those identified in 2019 and 2020. These results suggest that the PCF epidemic in 2023 was predominantly caused by variant strains of HAdV-B3, and that children were susceptible owing to a lack of exposure to HAdV-B3 between 2020 and 2022. Ongoing surveillance is needed to evaluate the impact of COVID-19 on the prevalence of HAdV infection.

Aging brought additional immune response alterations after breakthrough infections with the Omicron BA.5/BF.7 variants: Protein immune mechanism

The global spread of the Omicron variant strain BA.5/BF.7 has led to an increase in breakthrough infections. The elderly population shows different immune responses after infection due to the aging of the immune system, which has not been fully studied. The aim of this study was to investigate the effect of aging on immune response after breakthrough infection of Omicron BA.5/BF.7 variant, especially the changes of protein immune mechanism. The study analyzed the concentration of antibodies in serum and their ability to neutralize the mutant strain by comparing the immune response of the elderly population and the young population after infection. Proteomics techniques were used to assess differences in the expression of key proteins in immune cells of different age groups. The study found that older subjects produced lower levels of antibodies after infection than younger subjects and showed a significantly reduced ability to neutralize against BA.5/BF.7. In addition, proteomic analysis showed that the expression of proteins related to inflammation and apoptosis significantly increased in the immune cells of the elderly, while the proteins related to antiviral response and cell repair significantly decreased. These findings provide new ideas for immune intervention strategies in the elderly population, and emphasize the targeted research of anti-virus vaccines.