An annotated list of plant viruses described in Paraguay (1920-2023) / Una lista comentada de virus de plantas descritos en Paraguay (1920-2023)

Abstract Despite an economy based mostly on agriculture, literature on viral diseases of plants is scarce in Paraguay. Only recently, researches on plant viruses took an impulse resulting in a precise identification of many of them affecting plants either cultivated or not. To provide reliable information regarding plant viruses present in Paraguay, an annotated list of them was prepared, covering descriptions from 1920 to present day. There have been some important outbreaks with severe yield losses in crops as cucurbits, citrus, sesame, bean, maize, peanuts and tomato. Many of older descriptions are included for their historical significance, but most identifications made require confirmation. On the other hand, recent descriptions have been completed, based on several assays, especially molecular characterization. This list is organized alphabetically following scientific names of the plant species found naturally infected by viruses, with comments about symptoms, geographical distribution, incidence, identification procedures, and other information, with due literature references. It is based on a compilation of publications made on plant virus diseases in Paraguay. Described virus species, in a total of 38 recognized by ICTV, belonging to 17 different genera (Alphaendornavirus, Ampelovirus, Begomovirus, Benyvirus, Carlavirus, Cilevirus, Closterovirus, Comovirus, Cucumovirus, Dichorhavirus, Fabavirus, Luteovirus, Ophiovirus, Orthotospovirus, Potexvirus, Potyvirus and Tobamovirus), besides two unclassified, and four unidentified. There is also a case of viroid described in Citrus spp. Infections caused by potyviruses are the most numerous. These viruses were described in more than 40 plant species, belonging to 18 botanical families. Because of crop diversity and richness in native flora, many more viruses must be present in Paraguay, which future works will certainly reveal, especially with the increase in manpower involving researches, especially cooperative with foreign centers, on plant viruses, which has been very limited until now. Also, knowledge on existing viruses may have relevance in understanding their epidemiology and provide the basis for their control strategies and quarantine measures, to avoid new variants of existing viruses or new viruses being introduced.

Resumo A pesar de una economía basada principalmente en la agricultura, la literatura sobre enfermedades virales de las plantas es escasa en Paraguay. Sólo recientemente se han impulsado las investigaciones sobre los virus de plantas, lo que ha permitido identificar con precisión muchos de ellos que afectan a plantas cultivadas o no. Para brindar información confiable sobre los virus de plantas presentes en el Paraguay, se elaboró una lista comentada de los mismos, abarcando descripciones desde 1920 hasta la actualidad. Se han producido algunos focos importantes con severas pérdidas de rendimiento en cultivos de cucurbitáceas, cítricos, sésamo, frijol, maíz, maní y tomate. Muchas de las descripciones más antiguas se incluyen por su importancia histórica, pero la mayoría de las identificaciones realizadas requieren confirmación. Por otro lado, las descripciones recientes han sido completadas, basadas en varios ensayos, especialmente de caracterización molecular. Esta lista está organizada alfabéticamente siguiendo los nombres científicos de las especies de plantas que se encontraron naturalmente infectadas por virus, con comentarios sobre síntomas, distribución geográfica, incidencia, procedimientos de identificación y otras informaciones, con las debidas referencias bibliográficas. Se basa en una recopilación de publicaciones realizadas sobre enfermedades virales de plantas en Paraguay. Especies de virus descritas, en un total de 38 reconocidas por el ICTV, pertenecientes a 17 géneros diferentes (Alphaendornavirus, Ampelovirus, Begomovirus, Benyvirus, Carlavirus, Cilevirus, Closterovirus, Comovirus, Cucumovirus, Dichorhavirus, Fabavirus, Luteovirus, Ophiovirus, Orthotospovirus, Potexvirus, Potyvirus y Tobamovirus), además de dos sin clasificar y cuatro sin identificar. También existe un caso de un viroide descrito en Citrus spp. Las infecciones causadas por potyvirus son las más numerosas. Estos virus fueron descritos en más de 40 especies de plantas, pertenecientes a 18 familias botánicas. Debido a la diversidad de cultivos y la riqueza de la flora nativa, muchos más virus deben estar presentes en Paraguay, lo que seguramente revelarán trabajos futuros, especialmente con el aumento de la mano de obra involucrada en investigaciones, en cooperación con centros extranjeros, sobre virus de plantas, que ha sido muy limitada hasta el momento. Además, el conocimiento sobre los virus existentes puede ser relevante para comprender su epidemiología y proporcionar una base para sus estrategias de control y medidas de cuarentena, para evitar la introducción de nuevas variantes de virus existentes o nuevos virus.

An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To provide a feasible and cost-effective next-generation sequencing (NGS) method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples.</p><p><b>METHODS</b>Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure: reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide (random hexamer or non-ribosomal hexanucleotide) primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline.</p><p><b>RESULTS</b>NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease (HFMD) and identified other potential viruses or differentiated misdiagnosis events.</p><p><b>CONCLUSION</b>The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.</p>

Study of Human Cytomegalovirus mRNA Transcription Profile at Different Infection Stages in Infants / 天津医药

Objective Human cytomegalovirus (HCMV) can induce infection in multiple organs, including genitouri-nary system, central nervous system and liver. It can even lead to serious defects and death. China, as a high-incidence area of HCMV, need employ early treatment. However, the sensitivity of present HCMV diagnosis is not satisfied. Methods In the present study, we focused on transcription level of HCMV IE and pp67 mRNA using real-time quantitative PCR. Results IE mRNA was positive even in a portion of patients who were regarded as negative by traditional DNA diagnosis method. On the other hand, pp67 mRNA that were normally expressed at the late stage of HCMV infection was 100%posi-tive in the first-visit patients who were regarded as positive using traditional DNA diagnosis method. Conclusion The pres-ent study indicated that mRNA detection based on PCR method was more sensitive compared with DNA detection for assess-ing HCMV virus infection. Finally, different treatment should be performed upon mRNA transcription profile at different in-fection stages.

Prognostic Indicators for Infants Infected HCMV Virus after Ganciclovir Treatment / 天津医药

Objective To study the IE and pp67 mRNA expressions in infants infected human cytomegalovirus (HCMV) after ganciclovir treatment. Methods The values of total bilirubin (TBIL), direct bilirubin (DBIL), alanine amino-transferase (ALT) and alkaline phosphatase (ALP) were detected in patients with HCMV before treatment, 2 weeks and 4 weeks after treatment. The HCMV-DNA was detected by quantitative PCR. The expression levels of IE mRNA and pp 67 mRNA were detected by real-time fluorescent quantitative PCR. Results HCMV DNA stopped copying and the infected in-fants were cured following the traditional criterion, however, RNA expression was still tested in part of these infants. Conclusion It should be identified for mRNA expression when HCMV-DNA copies were hardly identified in these infants to prevent from relapse.

Study on Detection, Isolation and Identifications of Infectious Viruses in Various Water Samples

Various factors using cell lines can effect kinds and frequencies of infectious viruses obtained in the detection tests on various water samples. We tried to find out technical problems for the maximum virus isolations from water samples and characterize the virus isolates from waters in nature and in various purification stages. Fourteen viruses were isolated from 169 water samples by virus monitoring protocol for the information collection requirements rule, US EPA. The morphological changes caused by viruses and mycoplasma infections were compared with for increasing the specificity of tests employed. Cytopathic effects of slow growing viruses were found very similar with those by toxic effects in water samples and mycoplasma infections. Five of 6 stream water samples tested (83.33%) showed virus contaminations with the range of 1.03 to 5.75 MPNs/100 liter. Eight of 24 source water samples (33.35%) showed viral contaminations. One water sample of 24 water samples during precipitation stages was shown to include infectious viruses. It was confirmed that infectious viruses were significantly decreased by purification stages from streams. The titers (TCID50) of virus isolates were ranged as 10(-6.8) ~ 10(-6.925)/ml. The virus isolates were identified by immune fluorescent antibody (IFA) method using virus specific immune sera and serotyped using serotype specific reference sera. Of 14 virus isolates, 7 samples were identified as poliovirus and the other 7 were identified as coxsakie virus. Of 7 polioviruses, one was serotyped as type I, 3 viruses as type II and another 3 as type III. Conclusively, BGM cell lines must be free of mycoplasma for the strict examination of infectious viruses in water and highly sensitive for mainly enteroviruses. In addition, most of infectious viruses showing typical cytopathic effect from water samples were confirmed as coxsackie B and live attenuated vaccine strains of 3 polio types when BGM cells were used for virus isolations.