Virology Journal最新文献

{"title":"Risk factors for SARS-CoV-2 pneumonia among renal transplant recipients in Omicron pandemic-a prospective cohort study.","authors":"Sai Zhang, Xiang Ding, Chunmi Geng, Hong Zhang","doi":"10.1186/s12985-024-02591-9","DOIUrl":"10.1186/s12985-024-02591-9","url":null,"abstract":"<p><strong>Background: </strong>The coronavirus disease (COVID-19) pandemic is a global health emergency, and SARS-CoV-2 pneumonia poses significant challenges to health systems worldwide. Renal transplant recipients (RTRs) are a special group and are more vulnerable to viral pneumonia. However, few studies have elucidated the risk factors of SARS-CoV-2 pneumonia in RTRs infected with COVID-19. This study aimed to build a risk prediction model for SARS-CoV-2 pneumonia among RTRs based on demographic and clinical information.</p><p><strong>Methods: </strong>We conducted a prospective cohort study among 383 RTRs (age ≥ 18 years) diagnosed with COVID-19 from December 21, 2022, to March 26, 2023. Patients' demographic and clinical information was collected through a questionnaire survey combined with electronic medical records. A stepwise logistic regression model was established to test the predictors of SARS-CoV-2 pneumonia. We assessed the diagnostic performance of the model by calculating the area under the curve (AUC) of the receiver operating characteristic (ROC) and calibration using the Hosmer-Lemeshow (HL) goodness-of-fit test.</p><p><strong>Results: </strong>Our study showed that the incidence of SARS-CoV-2 pneumonia among RTRs was 31.1%. Older age (OR = 2.08-3.37,95%CI:1.05-7.23), shorter post-transplantation duration (OR = 0.92,95% CI: 0.87,0.99), higher post-transplant Charlson Comorbidity Index (CCI) (OR = 1.84, 95%CI: 1.14,2.98), pulmonary infection history (OR = 3.44, 95%CI: 1.459, 8.099, P = 0.005), fatigue (OR = 2.11, 95%CI: 1.14, 3.90), cough (OR = 2.03, 95%CI: 1.08, 3.81), and lower estimated glomerular filtration rate (eGFR) at COVID-19 diagnosis (OR = 0.98, 95%CI:0.97,0.99) predicted a higher risk for SARS-CoV-2 pneumonia. The model showed good diagnostic performance with Chi-Square = 10.832 (P > 0.05) and AUC = 0.839 (P < 0.001).</p><p><strong>Conclusions: </strong>Our study showed a high incidence of SARS-CoV-2 pneumonia among RTRs, and we built a risk prediction model for SARS-CoV-2 pneumonia based on patients' demographic and clinical characteristics. The model can help identify RTRs infected with COVID-19 at high risk of SARS-CoV-2 pneumonia to inform timely, targeted, and effective prevention and intervention efforts.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"315"},"PeriodicalIF":4.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research trends and hotspots on global influenza and inflammatory response based on bibliometrics.","authors":"Hui Li, Yanping Zong, Jiajie Li, Zheng Zhou, Yonglong Chang, Weibing Shi, Jinchen Guo","doi":"10.1186/s12985-024-02588-4","DOIUrl":"10.1186/s12985-024-02588-4","url":null,"abstract":"<p><p>The influenza virus is considered as a kind of significant zoonotic infectious disease identified to date, with severe infections in humans characterized by excessive inflammation and tissue damage, usually resulting in serious complications. Although the molecular mechanisms underlying inflammation after influenza infection have been extensively studied, bibliometric analysis on the research hotspots and developing trends in this field has not been published heretofore. Articles related to influenza and inflammatory response were retrieved from the Web of Science Core Collection (WoSCC) database (1992-2024) and analyzed using various visualization tools. Finally, this study collected a total of 2,176 relevant articles, involving 13,184 researchers, 2,647 institutions, 78 countries/regions, and published in 723 journals. Most articles were published in the United States (928 articles), China (450 articles) and the United Kingdom (158 articles). Ross Vlahos was the most productive author. Furthermore, some journals, such as PLoS One and Frontiers in Immunology, made much contribution to the topic. The future research trends include airway stem cells and neuroendocrine cells as new directions for the treatment of influenza complications, as well as measures related to prevention, treatment, and research and development based on the COVID-19 pandemic. Through bibliometric analysis and summary of inflammatory response of influenza-related articles, this study ultimately summarizes new directions for preventing and treating influenza.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"313"},"PeriodicalIF":4.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142772782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of circulating infectious bursal disease viruses in chickens from different Egyptian governorates during 2023.","authors":"Amr H Abd El-Fatah, Dalia Ayman, Mahmoud Samir, Soad Eid, Mahmoud Elgamal, A A El-Sanousi, Mahmoud Ibrahim, M AlKhazindar, M M Ali, Amira Afify","doi":"10.1186/s12985-024-02559-9","DOIUrl":"https://doi.org/10.1186/s12985-024-02559-9","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"312"},"PeriodicalIF":4.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11607947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142772780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating clinical data and genetic susceptibility to elucidate the relationship between systemic lupus erythematosus and human cytomegalovirus infection.","authors":"Xin Luo, Liuliu Quan, Qingting Lin, Huiteng Rong, Yue Liu, Jiaqi Meng, Xin You","doi":"10.1186/s12985-024-02578-6","DOIUrl":"10.1186/s12985-024-02578-6","url":null,"abstract":"<p><strong>Background: </strong>Viral infections are known to induce the occurrence and pathogenesis of systemic lupus erythematosus (SLE). Previous studies have indicated a possible relationship between SLE and human cytomegalovirus (HCMV) infection and have attributed HCMV to be associated with various autoantibodies; however, these studies were constrained by variations in sample size and potential selection bias. Therefore, in the present study, we aimed to elucidate the relationship between HCMV and autoantibodies in patients with SLE by integrating clinical data and genetic susceptibility.</p><p><strong>Methods: </strong>Using various statistical methods, we conducted a retrospective analysis of the spectrum of SLE autoantibodies and HCMV infections among patients hospitalized at our center over the past 10 years. Machine learning modeling was used to predict active HCMV infections based on the antinuclear (ANA) spectrum. Moreover, Mendelian randomization (MR) was used to investigate the causal relationship between SLE and HCMV infection.</p><p><strong>Results: </strong>In the HCMV group, the levels of ANA, anti-dsDNA, anti-histone antibody (AHA), and anti-nucleosome antibody (ANuA) were significantly increased (P < 0.001) and were linked to the presence of CMV-pp65-antigen-positive polymorphonuclear leukocytes (P < 0.001). A weak correlation was observed between the titers of anti-CMV IgM and ANA (P < 0.001). The ANA spectrum demonstrated a strong predictive performance for active HCMV infection based on principal component analysis (Adonis and ANOSIM P < 0.001) as well as support vector machine and extreme gradient boosting modeling. MR analyses of inverse-variance weighted, weighted mean, MR-Egger, and weighted mode revealed that patients with SLE were at a higher risk of developing HCMV infection (P < 0.05). However, HCMV infection did not have a causal effect on SLE (P > 0.05).</p><p><strong>Conclusion: </strong>The ANA spectrum in patients with SLE can be used to predict HCMV infection status. Due to the inherent susceptibility of patients with SLE to HCMV infection, we propose for the first time that if a patient with SLE exhibits high serum titers of ANA, anti-dsDNA, ANuA, and AHA, caution should be exercised for HCMV infection, which can contribute to the clinical assessment of SLE and improve patient prognosis.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"311"},"PeriodicalIF":4.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11607911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142755716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Obtaining HBV core protein VLPs carrying SARS-CoV-2 nucleocapsid conserved fragments as vaccine candidates.","authors":"Yadira Lobaina, Alexis Musacchio, Panchao Ai, Rong Chen, Edith Suzarte, Glay Chinea, Miaohong Zhang, Zhiqiang Zhou, Yaqin Lan, Ricardo Silva, Gerardo Guillén, Ke Yang, Wen Li, Yasser Perera, Lisset Hermida","doi":"10.1186/s12985-024-02583-9","DOIUrl":"10.1186/s12985-024-02583-9","url":null,"abstract":"<p><p>The Hepatitis B core antigen (HBcAg) has been used as a carrier of several heterologous protein fragments based on its capacity to form virus-like particles (VLPs) and to activate innate and adaptive immune responses. In the present work, two chimeric proteins were designed as potential pancorona vaccine candidates, comprising the N- or C- terminal domain of SARS-CoV-2 nucleocapsid (N) protein fused to HBcAg. The recombinant proteins, obtained in E. coli, were named CN-1 and CND-1, respectively. The final protein preparations were able to form 10-25 nm particles, visualized by TEM. Both proteins were recognized by sera from COVID-19 convalescent donors; however, the antigenicity of CND-1 tends to be higher. The immunogenicity of both proteins was studied in Balb/C mice by intranasal route without adjuvant. After three doses, only CND-1 elicited a positive immune response, systemic and mucosal, against SARS-CoV-2 N protein. CND-1 was evaluated in a second experiment mixed with the CpG ODN-39 M as nasal adjuvant. The induced anti-N immunity was significantly enhanced, and the antibodies generated were cross-reactive with N protein from Omicron variant, and SARS-CoV-1. Also, an anti-N broad cellular immune response was detected in spleen, by IFN-γ ELISpot. The nasal formulation composed by CND-1 and ODN-39 M constitutes an attractive component for a second generation coronavirus vaccine, increasing the scope of S protein-based vaccines, by inducing mucosal immunity and systemic broad humoral and cellular responses against Sarbecovirus N protein.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"310"},"PeriodicalIF":4.0,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11606075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tomato yellow leaf curl virus (TYLCV) in Kuwait and global analysis of the population structure and evolutionary pattern of TYLCV.","authors":"Abrar Akbar, Hanadi Al Hashash, Ebtisam Al-Ali","doi":"10.1186/s12985-024-02540-6","DOIUrl":"10.1186/s12985-024-02540-6","url":null,"abstract":"<p><p>Tomato yellow leaf curl virus (Family Geminiviridae, Genus Begomovirus) is a serious menace in the cultivation of tomato causing Tomato leaf curl disease (ToLCD). Recently, we presented the TYLCV isolates having additional genomic features (nucleotides insertions) characterized from the tomato fields of Kuwait adding up to the genetic diversity repertoire of these viruses. The widespread prevalence of disease in tropics across the continents, emergence of genetic variants and ever increasing complete genome sequences of virus isolates in public database warrant a global analysis to infer the genetic diversity, evolutionary pattern so as to devise suitable disease control stratagems. Molecular phylogeny suggested the monophyletic origin of the TYLCV Kuwait isolates and TYLCV reported from Asian countries revealing their genetic relatedness. Though genetic diversity of TYLCV reported from elsewhere (TYLCV others) is two folds higher (0.11765) than TYLCV Kuwait, a relatively high number of polymorphic sites in the latter imply their inherent genetic diversity. Neutrality tests of TYLCV as a whole suggest the operation of phenomenon of purifying selection indicating deleterious mutations are being weeded out from the population. Recombination analysis discloses that TYLCV Kuwait isolates are potential genetic recombinants or involved in the generation of potential recombinants as parents. The results of the neutrality tests were further strengthened by the outcome of codon substitution analysis indicating the operation of purifying selection in the codons of C1 ORF of TYLCV population as a whole and in the sub-group TYLCV Kuwait. The implications of these results are discussed.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"308"},"PeriodicalIF":4.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel polyomavirus in the endangered garden dormouse Eliomys quercinus.","authors":"Emilija Vasiliūnaitė, Monika Repšytė, Eva Marie Kramer, Johannes Lang, Christine Jelinek, Rainer G Ulrich, Christopher B Buck, Alma Gedvilaitė","doi":"10.1186/s12985-024-02581-x","DOIUrl":"10.1186/s12985-024-02581-x","url":null,"abstract":"<p><strong>Background: </strong>The garden dormouse (Eliomys quercinus) has experienced a significant population decline across Europe in recent decades. While habitat loss and climate change are often cited as primary factors, pathogen exposure, either to novel or to previously known, may play a role in such a decline. This study aimed to investigate the presence of polyomaviruses in garden dormice, given that these viruses are highly prevalent and can cause disease, particularly in immunocompromised individuals.</p><p><strong>Methods: </strong>The carcasses of garden dormice (n = 89) were collected throughout Germany. Kidney samples were tested for the presence of polyomavirus DNA using nested degenerate and specific diagnostic PCRs. Seroprevalence was assessed from chest cavity fluid samples through an enzyme-linked immunosorbent assay using polyomavirus VP1 virus-like particles produced in yeast.</p><p><strong>Results: </strong>A new polyomavirus, related to chimpanzee (Pan troglodytes) polyomaviruses 4 and 5 and human Merkel cell polyomavirus, was identified in the garden dormouse. Two 5,380 bp-length complete viral genomes were sequenced from dormice kidney samples (sequences PQ246041 and PQ246042). Genes encoding the putative structural proteins VP1, VP2, and VP3, as well as the Large, Middle, and small T antigens, containing conserved functional domains were identified. Polyomavirus DNA was detected in 2 of 74 dormice (2.7%, 95% confidence interval: 0-6.4%) through PCR, while 12 of 69 animals (17.4%, 95% confidence interval: 8.4-26.3%) tested positive for polyomavirus-specific antibodies.</p><p><strong>Conclusions: </strong>In conclusion, here we describe a novel polyomavirus in the garden dormouse with molecular and serological detection. Pairwise sequence comparison and phylogenetic analysis suggest that this novel virus may represent a novel species within the genus Alphapolyomavirus. Future work should examine if this virus is garden dormouse-specific and whether it is associated with disease in dormice.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"309"},"PeriodicalIF":4.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive seroepidemiology of dengue and chikungunya arboviruses in Iran, 2020-2023.","authors":"Seyed-Mahmood Seyed-Khorami, Ehsan Mostafavi, Sepideh Gerdooei, Seyed Marzieh Sajadi, Laya Farhan Asadi, Tahmineh Jalali, Mohammad Hassan Pouriayevali, Fatemeh Nikpour, Abdolreza Mirolyaei, Ahmad Raeisi, Shahnam Arshi, Mohammad Mehdi Gouya, Ahmadali Enayati, Morteza Zaim, Mostafa Salehi-Vaziri","doi":"10.1186/s12985-024-02574-w","DOIUrl":"10.1186/s12985-024-02574-w","url":null,"abstract":"<p><strong>Aim: </strong>Dengue virus (DENV) and Chikungunya virus (CHIKV) are the most common arthropod-borne viruses (Arboviruses) globally. So far, no autochthonous cases of DENV and CHIKV infections have been reported in Iran. Nevertheless, due to the recent identification of Aedes aegypti in the south and Aedes albopictus in the north of Iran, the country is at a serious risk of local outbreaks of these infections.</p><p><strong>Methods: </strong>Between 2020 and 2023, a comprehensive cross-sectional study was conducted to explore the anti-DENV and CHIKV IgG antibodies in the general populations of both southern and northern regions of Iran using ELISA.</p><p><strong>Results: </strong>A total of 11,192 participants were included, of whom 2.3% (256 individuals) and 0.1% (11 cases) were DENV seropositive and CHIK seropositive, respectively. Across the eight examined provinces, Sistan and Baluchestan province displayed the highest prevalence of dengue seropositive cases (6.80%) (P < 0.001). Samples collected in 2022 demonstrated a notably higher seropositive rate of 5.5% (P < 0.001). Interestingly, all 11 CHIKV seropositive cases were from Sistan and Baluchestan province.</p><p><strong>Conclusion: </strong>The seroprevalence of DENV was notably higher in southern regions, particularly in Sistan and Baluchestan province and CHIKV seropositive cases were exclusively found in Sistan and Baluchestan province. This study furnishes crucial insights into the seroepidemiology of DENV and CHIKV in Iran, which in conjunction with the presence of Ae. aegypti in the south and Ae. albopictus in the north of Iran, emphasizes the requirement of improving integrated surveillance and control systems in the whole of the country, especially in the south of Iran.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"305"},"PeriodicalIF":4.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142732995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple third-generation recombinants formed by CRF55_01B and CRF07_BC in newly diagnosed HIV-1 infected patients in Shenzhen city, China.","authors":"Yan Jiao, Minghui An, Nan Zhang, Hui Zhang, Chenli Zheng, Lin Chen, Hao Li, Yan Zhang, Yongxia Gan, Jin Zhao, Hong Shang, Xiaoxu Han","doi":"10.1186/s12985-024-02563-z","DOIUrl":"10.1186/s12985-024-02563-z","url":null,"abstract":"<p><p>In the evolution landscape of HIV, the coexistence of multiple subtypes has led to new, complex recombinants, posing public health challenges. CRF55_01B, first identified among MSM in Shenzhen, China, has spread rapidly across China. In this study, 47 plasma samples from newly diagnosed HIV-1 CRF55_01B patients in Shenzhen, of which the genotype was only identified by the routine HIV drug resistance test, were collected. Multiple gene regions were acquired using Sanger and next-generation sequencing methods, followed by the phylogenetic reconstruction, recombination breakpoint scanning, Bayesian molecular clock, and the prediction of coreceptors. From 47 samples, we found seven new unique recombinants formed by CRF55_01B and CRF07_BC, which shared similar breakpoints in certain gene regions and primarily utilized CCR5 receptors. All of the most recent common ancestors of subregions for these recombinants were estimated to be later than CRF55_01B and CRF07_BC, potentially suggesting they are the third-generation recombinants formed by CRF55_01B and CRF07_BC as parents. The continuous emergence of new recombinants highlights the increasing complexity of circulating strains in Shenzhen, and also suggests that subtype analysis using partial pol gene may lead to an overestimation of the major subtype strains and an underestimation of new complex HIV recombinants. Consequently, to effectively address and mitigate the complex HIV epidemic, there is an urgent need for expanded monitoring and the optimization of testing methodologies.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"306"},"PeriodicalIF":4.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142732999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epidemiological characteristics of respiratory pathogens infections among children after the removal of non-pharmaceutical interventions in central China.","authors":"Shun Liu, Yao Lei, Xiuxiu Chen, Zihan Wen, Bing Mei","doi":"10.1186/s12985-024-02579-5","DOIUrl":"10.1186/s12985-024-02579-5","url":null,"abstract":"<p><strong>Background: </strong>During the COVID-19 pandemic between 2020 and 2022 in China, various non-pharmaceutical interventions (NPIs) were implemented to reduce the spread of SARS-CoV-2 and other respiratory pathogens. From 2023, China downgraded the management of COVID-19, and compliance with NPIs was no longer mandatory. This study aimed to reveal the epidemiological characteristics of respiratory pathogens in 2023 after the removal of NPIs in central China.</p><p><strong>Methods: </strong>Respiratory specimens of children with acute respiratory infections (ARIs) were obtained to detect seven common respiratory pathogens, including influenza A (FluA), influenza B (FluB), adenovirus (ADV), human rhinovirus (HRV), human respiratory syncytial virus (HRSV), human metapneumovirus (HMPV), Mycoplasma pneumoniae (MP). From January 2022 to December 2023, a total of 5423 specimens were collected, including 1122 children in 2022 and 4301 children in 2023.</p><p><strong>Results: </strong>One or more pathogens were detected in 62.50% specimens in 2023, significantly higher than that in 2022 (44.12%). HRV (13.81%) was the most common pathogen in 2022, whereas MP (24.67%) was predominant in 2023. There was no significant difference in the overall prevalence of HRV, HRSV and HMPV between 2022 and 2023. HRSV was the most common pathogen in the < 1 years children both in 2022 and 2023. However in the ≥ 7 years group, FluB was the predominant pathogen in 2022 whereas MP ranked first in 2023. Co-detection were significantly more frequent in 2023 compared to 2022.</p><p><strong>Conclusions: </strong>The removal of NPIs significantly increased the infection rates of the respiratory pathogens among children. Some NPIs, such as wearing mask and hand hygiene are necessary to decrease the prevalence of certain pathogens.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"303"},"PeriodicalIF":4.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}