VirusDisease最新文献

{"title":"Phylogenetic analysis of the partial sequences of the env and tax BLV genes reveals the presence of genotypes 1 and 3 in dairy herds of Antioquia, Colombia","authors":"Cristina Úsuga-Monroy, F. J. Díaz, Luis Gabriel González-Herrera, José Julián Echeverry-Zuluaga, Albeiro López-Herrera","doi":"10.1007/s13337-023-00836-9","DOIUrl":"https://doi.org/10.1007/s13337-023-00836-9","url":null,"abstract":"Abstract Bovine leukemia virus (BLV) is a retrovirus that primarily infects dairy cows. Although few studies have also used the tax gene, phylogenetic studies of BLV use mostly the env gene. The aim of this work was to establish the circulating genotypes of BLV in specialized dairy cattle from Antioquia, Colombia. Twenty blood samples from Holstein Friesian cows were collected, and their DNA was isolated. A PCR was performed for a partial region of the env and tax genes. A phylogenetic analysis was carried out using the maximum likelihood and Bayesian methods for both genes. Nineteen sequences were identified as genotype 1 by env and tax genes. Only one sequence was clustered with genotype 3 and had the highest proportion of different nucleotide sites compared to other strains. Four amino acid substitutions in the 134 amino acid residue fragment of the Env protein were identified in the Colombian sequences, and three new amino acid substitutions were reported in the 296 amino acid residue fragment of the Tax protein. R43K (Z finger), A185T (Activation domain), and L105F changes were identified in the genotype 3 sample. This genotype has been reported in the United States, Japan, Korea, and Mexico, but so far, not in Colombia. The country has a high rate of imported live animals, semen, and embryos, especially from the United States. Although it is necessary to evaluate samples from other regions of the country, the current results indicate the presence of two BLV genotypes in specialized dairy herds.","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136295608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Outcomes of COVID-19 in immunocompromised patients: a single center experience.","authors":"Masoud Mardani, Jafar Mohammadshahi, Roghayeh Teimourpour","doi":"10.1007/s13337-023-00832-z","DOIUrl":"10.1007/s13337-023-00832-z","url":null,"abstract":"<p><p>Malignancy, bone marrow and organ transplantation are associated with deficient and defective immune systems. Immunocompromised patients are at risk for severe and chronic complication of COVID-19 infection. However, the pathogenesis, diagnosis and management of this comorbidity remain to be elucidated. The purpose of the present study was to describe key aspects of COVID-19 infection in immunocompromised patients. In this retrospective, cross-sectional study, lab findings and outcomes of 418 COVID-19 patients with secondary immunodeficiency disorders admitted to Taleghani Hospital in Tehran, from March 2020 to September 2022 were investigated. Of the 418 immunocompromised patients with COVID-19, 236 (56.5%) ‌ were male and the median age of all studied patients was 56.6 ± 16.4 with range of 14 to 92 years. Totally, 198 (47.4%) of the patients died during hospitalization. Remdesivir was used for treatment of all patients. Mortality rate among patients admitted to ICU ward (86.8%) was significantly higher than non ICU admission (<i>p</i> < 0.001). The death rate in patients with CKD was substantially higher than other underlying disease (<i>p</i> < 0.001). In terms of laboratory finding, there was a significant relationship between ICU admission and worse outcome with WBC count (HR = 1.94, 95% CI = 1. 46-2.59, <i>p</i> < 0.001), PMN count (HR = 1.93, 95% CI = 1.452.56, <i>p</i> < 0.001), Hb (HR = 1.49, 95% CI = 1.042.13, <i>p</i> = 0.028), AST (HR = 2.55, 95% CI = 1.913.41, <i>p</i> < 0.001), BUN (HR = 2.56, 95% CI = 2.063.69, <i>p</i> < 0.001), Cr (HR = 2.63, 95% CI = 1.89-3.64, <i>p</i> < 0.001), Comorbidities index (HR = 1.71, 95% CI = 1.29-2.27, <i>p</i> < 0.001) and aging (HR = 1.91, 95% CI = 1.4-2.54, <i>p</i> < 0.001). Immunocompromised status increased the risk of mortality or worse outcome in patients diagnosed with COVID-19. Our finding showed outcome predicting markers in whom the waned immune system encounter new emerging disease and improved our understanding of COVID-19 virus behavior in immunocompromised individuals.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"373-382"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41103603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First molecular detection of avian polyomavirus from captive psittacine birds in Bangladesh, together with confirmation of beak and feather disease virus co-infection.","authors":"Chandan Nath, Md Saddam Hossain, Md Ahaduzzaman","doi":"10.1007/s13337-023-00829-8","DOIUrl":"10.1007/s13337-023-00829-8","url":null,"abstract":"<p><p>Avian polyomavirus (APV) is an emerging pathogen in many parts of the world responsible for causing significant mortality in captive psittacine birds. The virus spreads slowly, and transboundary movement of birds is one of the potential risk factors for the virus introduction in the naïve population. Bangladesh allows the import of birds, however there is currently no surveillance to screen for APV. Since we confirmed beak and feather disease virus (BFDV) infection in the captive population in our earlier investigation, we hypothesized that APV may also be circulating in Bangladesh. Feather samples were collected from 100 birds (90 psittacine and 10 non-psittacine). The polymerase chain reaction (PCR) was used to detect viral DNA together with sequencing and phylogenetic analysis. This first pilot study confirmed the presence (7%, 7/100) of APV in captive psittacine birds of Bangladesh and almost half (4%, 4/100) of the APV positive birds had the BFDV co-infection. All the PCR-positive birds were asymptomatic and found in live bird markets (LBMs). No significant variation was observed in the detection rate considering species (<i>P</i> = 0.94), age (<i>P</i> = 0.39) or sex (<i>P</i> = 0.55) of birds. According to the results of the phylogenetic study, the APV isolates found in Bangladesh appear to be unrelated to isolates from other geographical areas. These findings provide an evidence of APV circulating in Bangladesh, with or without the co-infection of BFDV. Additional studies are needed to investigate the occurrence of APV/BFDV co-infection in the larger population of Bangladesh and in countries where transboundary bird interaction with Bangladesh may be possible.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"440-445"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Significance of CMV reactivation in non-allogeneic stem cell transplant patients with cancers: experience of single tertiary care cancer institute.","authors":"Uzma Rasool Mahar, Mussadique Ali Jhatial, Romena Qazi, Usman Ahmed, Bushra Ahsan, Syed Waqas Imam Bokhari","doi":"10.1007/s13337-023-00839-6","DOIUrl":"10.1007/s13337-023-00839-6","url":null,"abstract":"<p><p>CMV reactivation is rare in hematological as well as solid organ malignancies in non-allogeneic stem cell transplant settings. An increasing number of patients undergoing active treatment or follow-up and diagnosed with CMV reactivation in recent years prompted us to investigate the risk factors and outcomes of CMV reactivation or disease. This was a hospital-based retrospective study that included 174 cancer patients suspected of CMV reactivation. Among them, forty-one tested positive for CMV viremia. The risk factors for CMV reactivation included the use of steroids in 78% of patients, active cancer in 43.9%, use of a monoclonal antibody rituximab in 31.7%, a history of radiation in 26.8%, and autologous stem cell transplant in 12% of patients. The median age was 36 years, and the most common clinical feature was fever (58.5%; n = 24), followed by GI symptoms (12.1%; n = 5), respiratory symptoms (14.6%; n = 6), cytopenia (7.3%; n = 3), and visual/neurological symptoms (4.8%; n = 2). The mean CMV viral load was 37,332 copies/ml (range: 75.00-633,000.00 copies/ml). Nineteen patients received CMV treatment with an average treatment duration of 81.5 days. The median overall survival was 2 months, with 12.0% of patients alive at 5 years. CMV reactivation is associated with significant morbidity and mortality. We recommend vigilant monitoring of CMV-related symptoms, with a low threshold for testing and treatment, for patients with multiple risk factors for CMV reactivation.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"383-388"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41149769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity of viruses infecting cnidium plants (<i>Cnidium officinale</i>) in Japan.","authors":"Kazuma Iwai, Tatsuya Kon, Yuito Fujita, Haruki Abe, Hiroshi Honma, Naoki Kawasumi, Hiroko Kawakami, Midori Kawashimo, Miki Sakurai, Shin-Ichi Fuji","doi":"10.1007/s13337-023-00835-w","DOIUrl":"10.1007/s13337-023-00835-w","url":null,"abstract":"<p><p>Cnidium vein yellowing virus (CnVYV), cnidium virus X (CnVX), cucumber mosaic virus (CMV) and cnidium virus 1 (CnV1) were detected at extremely high levels in <i>Cnidium officinale</i> plants showing viral symptoms collected from Iwate and Hokkaido Prefectures, Japan. The complete nucleotide sequence of the newly detected CnVYV and CnV1, and genetic diversity of the cnidium-infecting viruses (CnVYV, CnVX, and CnV1) indicated that South Korean and Japanese cnidium plants had close relationship with each other. All three viruses can infect vegetatively propagated perennials and are vertically transmitted once infection occurs.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13337-023-00835-w.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"431-439"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41152850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Utility of CDC DENV1-4 real time PCR assay and trioplex assay for the diagnosis of dengue in patients with acute febrile illness.","authors":"Subhabrata Sarkar, Ishani Bora, Parakriti Gupta, Gajanan Sapkal, Shveta Shethi, Kanwalpreet Kaur, Radha Kanta Ratho","doi":"10.1007/s13337-023-00831-0","DOIUrl":"10.1007/s13337-023-00831-0","url":null,"abstract":"<p><p>Nucleic acid amplification tests (NAATs) have revolutionized reliable detection of dengue virus (DENV) during acute phase of infection. The study evaluated performance of CDC DENV-1-4 real-time assay, trioplex RT-PCR and heminested conventional RT-PCR assay in the diagnosis of DENV. The three NAATs were performed on 107 consecutive samples collected from patients suspected of DENV infection during acute phase of illness. Their performance was compared against composite reference standard, consisting of DENV NS1 antigen ELISA and DENV IgM ELISA. 88/107 study samples were positive by DENV ELISA, either NS1Ag (80), IgM (3) or both (5). The overall sensitivity of CDC DENV-1-4 RT-PCR assay, trioplex RT-PCR assay and conventional multiplex RT-PCR was 68.18%, 54.55% and 38.64%, respectively in diagnosing dengue during acute phase, with an area under the curve of 0.841, 0.773 and 0.693 respectively when compared against composite reference standard. The sensitivity was 82.93%, 73.17% and 51.22%, respectively within three days of illness and 60%, 42.86% and 28.57%, respectively between 4 and 5th day of illness. All the three molecular assays had 100% specificity. Maximum concordance values of 86.9% were recorded among CDC DENV-1-4 rRT-PCR assay and trioplex assay with kappa value of 0.74, suggestive of substantial agreement. CDC DENV-1-4 rRT-PCR assay can be used as a reliable and accurate test for diagnosis of DENV during acute phase of illness.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"365-372"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transforming clinical virology with AI, machine learning and deep learning: a comprehensive review and outlook.","authors":"Abhishek Padhi, Ashwini Agarwal, Shailendra K Saxena, C D S Katoch","doi":"10.1007/s13337-023-00841-y","DOIUrl":"10.1007/s13337-023-00841-y","url":null,"abstract":"<p><p>In the rapidly evolving field of clinical virology, technological advancements have always played a pivotal role in driving transformative changes. This comprehensive review delves into the burgeoning integration of artificial intelligence (AI), machine learning, and deep learning into virological research and practice. As we elucidate, these computational tools have significantly enhanced diagnostic precision, therapeutic interventions, and epidemiological monitoring. Through in-depth analyses of notable case studies, we showcase how algorithms can optimize viral genome sequencing, accelerate drug discovery, and offer predictive insights into viral outbreaks. However, with these advancements come inherent challenges, particularly in data security, algorithmic biases, and ethical considerations. Addressing these challenges head-on, we discuss potential remedial measures and underscore the significance of interdisciplinary collaboration between virologists, data scientists, and ethicists. Conclusively, this review posits an outlook that anticipates a symbiotic relationship between AI-driven tools and virology, heralding a new era of proactive and personalized patient care.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"345-355"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41103604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First report of carnation cryptic virus 3 infecting <i>Dianthus caryophyllus</i> in Iran.","authors":"Hajar Hosseini, Mohsen Mehrvar, Mohammad Zakiaghl","doi":"10.1007/s13337-023-00828-9","DOIUrl":"10.1007/s13337-023-00828-9","url":null,"abstract":"","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"446-447"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41136734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotypic characterization of HPV serotypes in cervical samples from Indian women: a multi centric study.","authors":"Ganesh Kumar Sarvesan, Krupakar Parthasarathy, Chirayu Padhiar, HariBalaji V","doi":"10.1007/s13337-023-00838-7","DOIUrl":"10.1007/s13337-023-00838-7","url":null,"abstract":"<p><p>Human papilloma virus (HPV infection) plays a important role in causing cervical cancer. Out of 184 different HPV genotypes, 40 diverse types only can cause anogenital infection. HPV present in >99% of cervical cancers with high risk types (16, 18) associated with cancer and Low risk types (6, 11) are associated with genital warts. Aim of the study is to determine the epidemiology of HPV infection in Indian women's population. Three hundred and thirty four liquid based cytology (LBC) samples were collected across India from the different age groups of Indian women. Pap smear, PCR and gene sequencing tests were performed for the collected LBC samples. Low risk serotype 6 (16.7%) were detected compared to other high risk serotypes. Majority of positive cases were observed in the age group between 19 and 39 groups. Northern part of India contributes high (7.1%) in HPV infection compared to other regions of India. Reports from these studies covered few regions of India showing a wide range in the prevalence of HPV infection and serotype distribution due to diversified socio economic and geo climatic conditions. This study aims to identify the epidemiology of HPV in the Indian population and concludes that early and periodic screening of women for HPV can avoid the risk of cervical cancer at the early stage of infection.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"395-401"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41154832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Geographical distribution of tomato-infecting begomoviruses in major cucurbits in India: a diagnostic analysis using begomovirus species specific PCR.","authors":"S Naveen Nayaka, Oinam Washington Singh, Pradeep Kumar, Anirban Roy, Bikash Mandal","doi":"10.1007/s13337-023-00837-8","DOIUrl":"10.1007/s13337-023-00837-8","url":null,"abstract":"<p><p>Cucurbits are an essential summer-season vegetable crops, but they are highly vulnerable from a range of abiotic and biotic factors. One of the significant biotic factors posing a growing menace to the production of major cucurbits in India is the emergence of tomato-infecting begomoviruses. In this study, we utilized PCR-based species-specific primers, developed earlier in our laboratory for the detection of begomoviruses infecting tomato and chilli plants, to identify begomoviruses in cucurbits across various regions of India. Leaf samples from major cucurbits were collected from different regions of Haryana, Delhi, Uttar Pradesh, Chhattisgarh, Maharashtra, Telangana and Karnataka, during the year 2020-2021. Total nucleic acid (TNA) was extracted from the samples and subjected to PCR using a generic primer specific to begomoviruses. The samples that exhibited positive amplification were further tested using six different species-specific primers targeting specific begomovirus species, namely <i>Tomato leaf curl New Delhi virus</i> (ToLCNDV), <i>Tomato leaf curl Palampur virus</i> (ToLCPalV), <i>Tomato leaf curl Bangalore virus</i> (ToLCBV), <i>Tomato leaf curl Joydebpur virus</i> (ToLCJoV), <i>Tomato leaf curl Gujarat virus</i> (ToLCGuV), and <i>Chilli leaf curl virus</i> (ChiLCV). The PCR analysis revealed that among the 551 plant samples tested, a total of 124 samples exhibited positive amplification using the universal begomovirus PCR. Specifically, 47 samples tested positive for ToLCNDV, 73 samples were positive for ToLCPalV and only one sample showed positive amplification for ChiLCV. However, none of the samples tested positive for ToLCJoV, ToLCGuV and ToLCBV. These findings from our study indicate the prevalence of ToLCNDV and ToLCPalV in major cucurbits across India. Furthermore, the study highlights the varied distribution of begomoviruses in major cucurbits between northern and southern regions of India.</p>","PeriodicalId":23708,"journal":{"name":"VirusDisease","volume":"34 3","pages":"421-430"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41140985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}