VirusDisease最新文献

Although nasopharyngeal swabs (NPSs) are superior to saliva specimens, saliva can be used as an alternative specimen for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. Moreover, studies have reported contradicting findings on whether SARS-CoV-2 can be detected in urine or not. Thus, we aimed to evaluate the diagnostic utility of NPSs, saliva and urine specimens in suspected COVID-19 patients. We conducted a cross-sectional study among a total of 604 specimens collected from 219 individuals suspected for COVID-19 from February to July 2022. We recruited participants from two COVID-19 isolation and treatment centers in Addis Ababa. We analyzed the specimens by real-time reverse transcriptase polymerase chain reaction (RT-PCR) with a Cobas 8800 automated system. The presence of SARS-CoV-2 in NPS, saliva, and urine samples was measured by cycle threshold (Ct) values. Descriptive statistics such as frequency, percent, and mean with standard deviation were used to summarize participants characteristics. We conducted chi-square test to compare RT‒PCR results of NPS, saliva and urine specimens. All data was analyzed by SPSS version 27, and the level of significance was set at a p value ≤ 0.05. Of the 219 participants, 126 (57.5%) were positive for SARS-CoV-2 either from NPS, saliva, urine or all specimens. The rate of SARS-CoV-2 detection was significantly higher in NPS (53.9%) than in saliva (35.2%; p = 0.001) and urine (9.0%; p = 0.001) specimens. The percentage of positive agreement between NPS and saliva was 92.2%, while negative agreement was 66.9%. The overall agreement between NPS and saliva was 75.8% (K = 0.53, p < 0.001). In addition, there was a significant correlation in Ct values of both ORF1ab and E genes between the paired NPS and saliva specimens. There was significant positive correlation between NPS and saliva specimens Ct values of both ORF1ab and E genes and days from onset of symptoms to specimen collection. SARS-CoV-2 was significantly detected in NPS than in saliva and urine specimens. Although NPS is better for SARS-CoV-2 detection, saliva specimen can be used as an alternative clinical specimen in resource-limited settings where access to swabs is limited. Both saliva and urine could be sources of viral transmission.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00892-9.

Acute gastroenteritis is common in infants and children of Sri Lanka. There is limited information on the burden of rotavirus gastroenteritis in infants and children in Sri Lanka but none in adults. Adenovirus gastroenteritis is not previously reported in Sri Lanka. This study is aimed to determine the viral etiology of acute gastroenteritis in hospitalized infants, children and adults of two geo-climatically different provinces of Sri Lanka. Diarrhoeic specimens from patients hospitalized with acute gastroenteritis in Western (n = 300) and Central (n = 271) provinces of Sri Lanka were tested for rotavirus and enteric adenovirus antigens by Enzyme Linked Immunosorbent Assay. In Western and Central provinces, overall positivity was 25.3 and 44.7% for rotavirus, 1.7 and 3.3% for enteric adenoviruses and, 0.7 and 1.5% for co-infections with rotavirus and adenovirus respectively. In children of Western and Central provinces, the positivity was 32.1 and 52.9% for rotavirus, and 2.2 and 3.4% for enteric adenoviruses respectively, whereas among adults, the positivity was 13.9 and 15.6% for rotavirus, and 0.9 and 0% for enteric adenoviruses respectively. Occurrence of rotavirus gastroenteritis in hospitalized children is significantly higher compared to adults in both Western and Central provinces. Adenovirus gastroenteritis in Sri Lanka occurs at a very low frequency with no significant difference between children and adults in both provinces. Rotavirus and adenovirus co-infection also occurs at a very low frequency.

Plant-infecting alphaflexiviruses cause moderate to severe diseases in economically important crops worldwide. In the present study, we identified nine putative novel alphaflexiviruses in nine plant species by exploring the publicly available plant transcriptome data in Sequence Read Archive (SRA) database. Coding-complete genomes of all the identified viruses were recovered and contained five to six open reading frames (ORFs). ORFs 1-5 encode replicase (Rep), triple gene block (TGB) proteins 1-3 and coat protein (CP), respectively. The additional ORF6, identified in two viruses, encoded the nucleic acid-binding (NB) protein or a protein with no significant similarity to known viral sequences. Genome organization of the first alphaflexivirus identified in a gymnospermic host (black pine potex-like virus 1-BlpPV1) slightly differed from that of known alphaflexiviruses and formed a distinct sub-clade in phylogenetic analysis. Thus, BlpPV1 can represent a novel taxon within the family Alphaflexiviridae. Based on phylogeny, sequence similarity to known members and sequence-based species demarcation criteria, six other identified viruses were tentatively assigned to the genera Potexvirus (4), Lolavirus (1) and Mandarivirus (1), while the two lola-like viruses may potentially represent a new genus. Further studies are needed to understand the biology and geographical spread of identified novel viruses.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00898-3.

Antivirals such as nucleotide analogs (NAs) are potent inhibitors of hepatitis B virus (HBV) replication. However, NAs fail to diminish the signaling and mitogenic activities of the transactivator HBx protein. Earlier we have shown that thiourea derivative IR-415 (DSA-00) targeted HBx to down-regulate its target viral and host genes. However, the molecular mechanism of its antiviral action is poorly understood. Here we investigated the anti-HBV properties of DSA-00 and its new derivatives in cell culture models. DSA-00 and its derivatives DSA-02 and DSA-09 not only suppressed HBV DNA levels similar to well-known antiviral Entecavir but also diminished the expression of pgRNA and secretion of HBsAg and HBeAg. Apparently, the three DSA derivatives inhibited the viral pregenomic RNA expression by stabilizing the episomal DNA silencing protein SMC5, suppressed transcription from viral and host gene promoters, and normalized intracellular CDK2 activity. As none the compounds are reportedly cytotoxic, thiourea derivatives could be good candidates for developing future antivirals for a functional cure of hepatitis B infection.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00895-6.

Chandipura vesiculovirus (CHPV) is an emerging neurotropic virus primarily affecting children and causing acute encephalitis syndrome (AES) in India. The virus, transmitted mainly by sand flies, has led to multiple outbreaks with high mortality rates, particularly in rural and resource-limited settings. CHPV infection is characterized by rapid disease progression, with symptoms ranging from fever and seizures to coma and death, often within 24 to 48 h of onset. The current management of CHPV is limited to supportive care due to the lack of specific antiviral therapies. Diagnosis relies on laboratory methods such as RT-PCR, serology, and immunofluorescence, though these face challenges due to the rapid progression of the disease and the need for timely sample collection and analysis. Prevention strategies are focused on vector control through insecticide use and public health interventions, including community education and early detection programs. Despite some progress in understanding CHPV, significant research gaps remain, particularly in developing effective antiviral treatments and vaccines, understanding transmission dynamics, and improving diagnostic capabilities. The potential for the virus to spread globally due to factors like climate change and increased human movement underscores the need for international collaboration in surveillance and response efforts. Strengthening public health infrastructure, enhancing vector control measures, and fostering global partnerships are crucial steps toward mitigating the impact of CHPV and preventing future outbreaks. Continued research and proactive public health strategies are essential to protect vulnerable populations and control the spread of this potentially deadly virus.

Patients with chronic kidney disorders, such as hemodialysis, are at a higher risk of infection with hepatitis viruses than the other population due to high nosocomial transmission by the dialysis units. The incidence of occult HCV infection (OCI) among chronic hemodialysis (CHD) remains controversial and the real burden of HCV in this population may be affected by the rate of OCI. This study aimed to evaluate the prevalence of OCI among patients with CHD from Lorestan province, Western Iran. In this cross-sectional study, whole blood samples were collected from 122 patients with CHD. Subsequently, anti-HCV antibody and HCV-RNA were assessed in serum/peripheral blood mononuclear cells (PBMCs) using Enzyme-Linked Immunosorbent Assay and Real-Time PCR technique, respectively. Out of the 122 patients, 61.15% were male and 38.8% were female. Regarding HCV results, out of the 122 studied patients, 4 cases (3.3%) were positive for anti-HCV IgM Ab and 3 patients (2.47%) for anti-HCV IgG Ab in their serum. Moreover, none of the 122 patients were positive for HCV-RNA in serum samples, while in PBMC samples, two patients (1.6%) tested positive for HCV-RNA, of which one patient was anti-HCV IgG Ab positive. Furthermore, the prevalence of OCI was correlated with the history of blood transfusion and serum level of transaminases (P = 0.012). The results of the current study suggest that there is a potential risk of occult HCV infection among patients undergoing hemodialysis. Therefore, it is necessary to use appropriate molecular techniques for early diagnosis and treatment of these patients.

Peste des petits ruminants (PPR), an acute febrile viral disease impacting goats and sheep flocks, manifests with pyrexia, mucopurulent nasal and ocular discharges, necrotizing and erosive stomatitis, pneumonia, and enteritis. The disease-instigating agent, PPR virus, pertains to the Morbillivirus caprinae genus in the Paramyxoviridae family. The endemic presence of PPR in India results in notable economic losses due to heightened mortality and morbidity in infected animals. Understanding viral pathogen evolution is pivotal for delineating their emergence in diverse environments. This study explores the molecular evolutionary patterns of PPRV, concentrating on the N and F structural genes isolated from Indian sheep and goats. Analyzing evolutionary rate, phylogenetics, selection pressure, and codon usage bias, we determined the time to the most recent common ancestor (tMRCA) as 1984, 1973, 2000, and 2004 for goat and sheep's N and F genes, respectively, with evolutionary rates ranging from 2.859 x 10³ to 4.995 x 10⁴. The F-gene is found to exhibit a faster evolution than the N-gene, indicating apparent virus transmission across the regions of India, as supported by phylogenetic analysis. Codon usage bias examination, incorporating nucleotide composition and various plots (effective number of codon plot, parity plot, neutrality plot), suggests the evolution in India influenced by both natural selection and mutational pressure, resulting in alterations in the virus's codon bias. The integrated analysis underscores the significant role of selection pressures, implying PPRV's co-evolution and adaptations influenced by various genes. Insights from this study can guide effective disease control and vaccine development, aiding in managing PPR outbreaks in India and beyond.

Bovine herpesvirus 4 (BoHV-4) is responsible for reproductive disorders and abortions in cattle. The aim of this study was to investigate the potential role of BoHV-4 in abortions in dairy cows when the possible aetiological cause could not be determined in Türkiye. The study also provided the molecular characterization of BoHV-4 strains based on the gB gene. In this study, foetuses (n = 188) and serum (n = 50) were retrospectively used for PCR and indirect ELISA assays, respectively. In addition, foetuses with BoHV-4 were tested for the isolation of the BoHV-4 strain in MDBK cell culture. The BoHV-4 gB gene was detected in the brain, liver, lung, kidney, and spleen tissues of three foetuses out of 188 aborted foetuses. The BoHV-4 strain was isolated from the kidney of one foetus in MDBK cell culture. The three aborted foetuses were from different cows in the same herd in 2021. On this dairy farm, the BoHV-4 seroprevalence rate in cattle with a history of abortion was 96% (48/50). Phylogenetic analysis revealed that the detected strains belong to genotype II. The present study shows that the impact of BoHV-4 on abortions in cattle should not be ignored. It can therefore be informative to focus on BoHV-4 in routine laboratory diagnostics for abortions without a proven aetiology or in cattle herds that have previously been infected with BoHV-4.

Begomoviruses, member of the Geminiviridae family, are responsible for significant economic losses in crops worldwide. Chilli leaf curl India virus (ChiLCINV) is a well-known begomovirus that causes leaf curl disease, primarily affecting plants in the Solanaceae family. In this study, sample from a Jamaica cherry (Muntingia calabura) tree showing typical begomovirus symptoms of mosaic and leaf curling was collected from Nagavara village in the Bengaluru Rural district of Karnataka State, India. The collected sample was designated as the MUT-1 isolate. The association of the begomovirus (DNA-A) and betasatellites with the sample was confirmed by PCR using begomovirus-specific primers, resulting in the expected amplicons of approximately 1.2 kb and 1.3 kb, respectively. No amplification was obtained for DNA-B and alphasatellite specific primers. The complete genome sequence of DNA-A of begomovirus isolate MUT-1 was obtained through rolling circle amplification and compared with other begomoviruses using Sequence Demarcation Tool which revealed that, DNA-A of MUT-1 isolate, (Acc.No. PP475538) showed maximum nucleotide (nt) identity of 98.7-99.4% with chilli leaf curl India virus. Further, sequence of betasattelite (Acc.No. PP493212) of this isolate shared maximum nt identity of 86.5-100% with tomato leaf curl Bangladesh betasatellite (ToLCBDB). Recombination and GC plot analysis showed that the presence of two and three intraspecific recombination event in DNA-A and betasatellite genomic regions, respectively and are derived from the previously reported begomoviruses. This study presents one more evidence of expanding host range for begomoviruses and first record of begomovirus associated with mosaic and leaf curl disease of Jamaica cherry (M. calabura) from India.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00891-w.

The impact of plant diseases coupled with climate change on agriculture worldwide cannot be overemphasized from negative effects on crop yield as well as economy to food insecurity. The model plants are essential for understanding the intricacies of plant-pathogen interactions. One of such plants is the tomato (Solanum lycopersicum L.). Researchers hope to increase tomato productivity and boost its resilience to pathogen attacks by utilizing OMICS and biotechnological methods. With an emphasis on tomato viral infections, this review summarizes significant discoveries and developments from earlier research. The analysis elucidates ongoing efforts to advance plant pathology by exploring the implications for sustainability and tomato production.