Early-Stage Phenotyping of Sweet Potato Virus Disease Caused by Sweet Potato Chlorotic Stunt Virus and Sweet Potato Virus C to Support Breeding.

Sweet potato virus disease (SPVD) is a global constraint to sweetpotato (Ipomoea batatas) production, especially under intensive cultivation in the humid tropics such as East Africa. The objectives of this study were to develop a precision SPVD phenotyping protocol, to find new SPVD-resistant genotypes, and to standardize the first stages of screening for SPVD resistance. The first part of the protocol was based on enzyme-linked immunosorbent assay results for sweet potato chlorotic stunt virus (SPCSV) and sweet potato virus C (SPVC) with adjustments to a negative control (uninfected clone Tanzania) and was performed on a prebreeding population (VZ08) comprising 455 clones and 27 check clones graft inoculated under screenhouse conditions. The second part included field studies with 52 selected clones for SPCSV resistance from VZ08 and 8 checks. In screenhouse conditions, the resistant and susceptible check clones performed as expected; 63 clones from VZ08 exhibited lower relative absorbance values for SPCSV and SPVC than inoculated check Tanzania. Field experiments confirmed SPVD resistance of several clones selected by relative absorbance values (nine resistant clones in two locations; that is, 17.3% of the screenhouse selection), supporting the reliability of our method for SPVD-resistance selection. Two clones were promising, exhibiting high storage root yields of 28.7 to 34.9 t ha-1 and SPVD resistance, based on the proposed selection procedure. This modified serological analysis for SPVD-resistance phenotyping might lead to more efficient development of resistant varieties by reducing costs and time at early stages, and provide solid data for marker-assisted selection with a quantitative tool for classifying resistance.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Towards application of CRISPR-Cas12a in the design of modern viral DNA detection tools (Review).

Early detection of viral pathogens by DNA-sensors in clinical samples, contaminated foods, soil or water can dramatically improve clinical outcomes and reduce the socioeconomic impact of diseases such as COVID-19. Clustered regularly interspaced short palindromic repeat (CRISPR) and its associated protein Cas12a (previously known as CRISPR-Cpf1) technology is an innovative new-generation genomic engineering tool, also known as 'genetic scissors', that has demonstrated the accuracy and has recently been effectively applied as appropriate (E-CRISPR) DNA-sensor to detect the nucleic acid of interest. The CRISPR-Cas12a from Prevotella and Francisella 1 are guided by a short CRISPR RNA (gRNA). The unique simultaneous cis- and trans- DNA cleavage after target sequence recognition at the PAM site, sticky-end (5-7 bp) employment, and ssDNA/dsDNA hybrid cleavage strategies to manipulate the attractive nature of CRISPR-Cas12a are reviewed. DNA-sensors based on the CRISPR-Cas12a technology for rapid, robust, sensitive, inexpensive, and selective detection of virus DNA without additional sample purification, amplification, fluorescent-agent- and/or quencher-labeling are relevant and becoming increasingly important in industrial and medical applications. In addition, CRISPR-Cas12a system shows great potential in the field of E-CRISPR-based bioassay research technologies. Therefore, we are highlighting insights in this research direction.

Seasonal Dynamics of Mosquito-Borne Viruses in the Southwestern Florida Everglades, 2016, 2017.

Mosquitoes were collected for 12 consecutive months beginning June 2016, from 11 locations in the Florida Everglades, Collier County, and tested for viruses by isolation in Vero cells and subsequent identification. One species complex and 31 species of mosquitoes were identified from 668,809 specimens. Ochlerotatus taeniorhynchus comprised 72.2% of the collection. Other notable species were Anopheles crucians complex, Culex nigripalpus, Cx. erraticus, and Cx. cedecei. Seven species of virus were identified from 110 isolations: Everglades, Gumbo Limbo, Mahogany Hammock, Pahayokee, Shark River, Tensaw, and West Nile viruses. Everglades, West Nile, Tensaw, and Mahogany Hammock viruses were most frequently isolated. Largest numbers of viruses were identified from Cx. cedecei, Cx. nigripalpus, and An. crucians complex. Five species of virus were isolated from Cx. cedecei. Viruses were isolated from mangrove, cypress swamp, hardwood hammock, and sawgrass habitats. West Nile virus was isolated August through October when Cx. nigripalpus was most abundant. Everglades virus was the most frequently isolated virus from nine species of mosquitoes collected from June through August. Tensaw virus was isolated primarily from Anopheles species. Isolations were made in July, August, January, February, and April, suggesting that this virus may be present in host-seeking mosquitoes throughout the year. Mahogany Hammock, Shark River, Gumbo Limbo, and Pahayokee viruses were isolated primarily from Cx. cedecei from June through December. Shotgun metagenomic sequencing was used to document that seven pools of Cx. cedecei were infected with two arboviruses. As communities expand into the Everglades, more humans will become exposed to arboviruses.

Decline of Influenza and Respiratory Viruses With COVID-19 Public Health Measures: Alberta, Canada.

OBJECTIVE: To determine the incidence of influenza and noninfluenza respiratory viruses (NIRVs) pre-/post-implementation of public health measures aimed to decrease coronavirus disease 2019 (COVID-19) transmission using population-based surveillance data. We hypothesized that such measures could reduce the burden of respiratory viruses (RVs) transmitting via the same routes. PATIENTS AND METHODS: An interrupted time-series analysis of RV surveillance data in Alberta, Canada, from May 2017 to July 2020 was conducted. The burden of influenza and NIRVs before and after intervention initiation at week 11 was compared. The analysis was adjusted for seasonality, overdispersion, and autocorrelation. RESULTS: During the study period, an average of 708 and 4056 weekly respiratory multiplex molecular panels were conducted pre-/post-intervention, respectively. We found significant reductions in test positivity rates in the postintervention period for influenza (-94.3%; 95% CI, -93.8 to 97.4%; P<.001) and all NIRVs (-76.5%; 95% CI, -77.3 to -75.8%; P<.001) in the crude model, and -86.2% (95% CI, -91.5 to -77.4%: P<.001) and -75% (95% CI, -79.7 to -69.3%; P<.001), respectively, in the adjusted models. Subanalyses for individual viruses showed significant decreases in respiratory syncytial virus, human metapneumovirus, enterovirus/rhinovirus, and parainfluenza. For non-severe acute respiratory coronavirus 2 human coronaviruses, the decline was not statistically significant after adjustment (-22.3%; 95% CI, -49.3 to +19%, P=.246). CONCLUSION: The implementation of COVID-19 public health measures likely resulted in reduced transmission of common RVs. Although drastic lockdowns are unlikely to be required given widespread COVID-19 vaccination, targeted implementation of such measures can lower RV disease burden. Studies to evaluate relative contributions of individual interventions are warranted.

The Link between Cannabis Use, Immune System, and Viral Infections.

Cannabis continues to be the most used drug in the world today. Research shows that cannabis use is associated with a wide range of adverse health consequences that may involve almost every physiological and biochemical system including respiratory/pulmonary complications such as chronic cough and emphysema, impairment of immune function, and increased risk of acquiring or transmitting viral infections such as HIV, HCV, and others. The review of published research shows that cannabis use may impair immune function in many instances and thereby exerts an impact on viral infections including human immune deficiency virus (HIV), hepatitis C infection (HCV), and human T-cell lymphotropic type I and II virus (HTLV-I/II). The need for more research is also highlighted in the areas of long-term effects of cannabis use on pulmonary/respiratory diseases, immune dysfunction and the risk of infection transmission, and the molecular/genetic basis of immune dysfunction in chronic cannabis users.

Kawasaki Disease Patient Stratification and Pathway Analysis Based on Host Transcriptomic and Proteomic Profiles.

The aetiology of Kawasaki disease (KD), an acute inflammatory disorder of childhood, remains unknown despite various triggers of KD having been proposed. Host 'omic profiles offer insights into the host response to infection and inflammation, with the interrogation of multiple 'omic levels in parallel providing a more comprehensive picture. We used differential abundance analysis, pathway analysis, clustering, and classification techniques to explore whether the host response in KD is more similar to the response to bacterial or viral infections at the transcriptomic and proteomic levels through comparison of 'omic profiles from children with KD to those with bacterial and viral infections. Pathways activated in patients with KD included those involved in anti-viral and anti-bacterial responses. Unsupervised clustering showed that the majority of KD patients clustered with bacterial patients on both 'omic levels, whilst application of diagnostic signatures specific for bacterial and viral infections revealed that many transcriptomic KD samples had low probabilities of having bacterial or viral infections, suggesting that KD may be triggered by a different process not typical of either common bacterial or viral infections. Clustering based on the transcriptomic and proteomic responses during KD revealed three clusters of KD patients on both 'omic levels, suggesting heterogeneity within the inflammatory response during KD. The observed heterogeneity may reflect differences in the host response to a common trigger, or variation dependent on different triggers of the condition.

Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection?

The emergence of the Zika virus (ZIKV) mirrors its evolutionary nature and, thus, its ability to grow in diversity or complexity (i.e., related to genome, host response, environment changes, tropism, and pathogenicity), leading to it recently joining the circle of closed congenital pathogens. The causal relation of ZIKV to microcephaly is still a much-debated issue. The identification of outbreak foci being in certain endemic urban areas characterized by a high-density population emphasizes that mixed infections might spearhead the recent appearance of a wide range of diseases that were initially attributed to ZIKV. Globally, such coinfections may have both positive and negative effects on viral replication, tropism, host response, and the viral genome. In other words, the possibility of coinfection may necessitate revisiting what is considered to be known regarding the pathogenesis and epidemiology of ZIKV diseases. ZIKV viral coinfections are already being reported with other arboviruses (e.g., chikungunya virus (CHIKV) and dengue virus (DENV)) as well as congenital pathogens (e.g., human immunodeficiency virus (HIV) and cytomegalovirus (HCMV)). However, descriptions of human latent viruses and their impacts on ZIKV disease outcomes in hosts are currently lacking. This review proposes to select some interesting human latent viruses (i.e., herpes simplex virus 2 (HSV-2), Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), human parvovirus B19 (B19V), and human papillomavirus (HPV)), whose virological features and co-exposition with ZIKV may provide evidence of the syndemism process, shedding some light on the emergence of the ZIKV-induced global congenital syndrome in South America.

Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses.

Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.

Bacillus Calmette-Guerin Vaccine and Nonspecific Immunity.

Bacillus Calmette-Guerin (BCG) vaccine is one of the most widely used vaccines in the world. It protects against many non-mycobacterial infections secondary to its nonspecific immune effects. The mechanism for these effects includes modification of innate and adaptive immunity. The alteration in innate immunity is through histone modifications and epigenetic reprogramming of monocytes to develop an inflammatory phenotype, a process called "trained immunity." The memory T cells of adaptive immunity are also responsible for resistance against secondary infections after administration of BCG vaccine, a process called "heterologous immunity." Bacillus Calmette-Guerin vaccine is known to not only boosts immune responses to many vaccines when they are co-administered but also decrease severity of these infections when used alone. The BCG vaccine by itself induces a TH1 type response, and its use as a vector has also shown promising results. This review article summarizes the studies showing effects of BCG vaccines on various viral infections, its role in enhancing vaccine responses, the mechanisms for this protective effect, and information on its effect on COVID-19.

Predominance of ON1 and BA9 genotypes of respiratory syncytial virus (RSV) in Bulgaria, 2016-2018.

The objectives of this study were to investigate the prevalence of respiratory syncytial virus (RSV) infections in Bulgaria, to characterize the genetic diversity of the RSV strains, and to perform amino acid sequence analysis of the RSV G protein. Clinical, epidemiological data and nasopharyngeal swabs were prospectively collected from children aged less than 5 years presenting with acute respiratory infections from October 2016 to September 2018. Real-time polymerase chain reaction for 12 respiratory viruses, and sequencing, phylogenetic, and amino acid analyses of the RSV G gene/protein were performed. Of the 875 children examined, 645 (73.7%) were positive for at least one viral respiratory pathogen. RSV was the most commonly detected virus (26.2%), followed by rhinoviruses (15%), influenza A (H3N2) (9.7%), adenoviruses (9%), bocaviruses (7.2%), human metapneumovirus (6.1%), parainfluenza viruses 1/2/3 (5.8%), influenza type B (5.5%), and A(H1N1)pdm09 (3.4%). The detection rate for RSV varied across two winter seasons (36.7% vs 20.3%). RSV-B cases outnumbered those of the RSV-A throughout the study period. RSV was the most common virus detected in patients with bronchiolitis (45.1%) and pneumonia (24%). Phylogenetic analysis indicated that all the sequenced RSV-A strains belonged to the ON1 genotype and the RSV-B strains were classified as BA9 genotype. Amino acid substitutions at 15 and 22 positions of the HVR-2 were identified compared with the ON1 and BA prototype strains, respectively. This study revealed the leading role of RSV as a causative agent of serious respiratory illnesses in early childhood, year-on-year fluctuations in RSV incidence, the dominance of RSV-B, and relatively low genetic diversity in the circulating RSV strains.

Advances in the development of entry inhibitors for sialic-acid-targeting viruses.

Over the past decades, several antiviral drugs have been developed to treat a range of infections. Yet the number of treatable viral infections is still limited, and resistance to current drug regimens is an ever-growing problem. Therefore, additional strategies are needed to provide a rapid cure for infected individuals. An interesting target for antiviral drugs is the process of viral attachment and entry into the cell. Although most viruses use distinct host receptors for attachment to the target cell, some viruses share receptors, of which sialic acids are a common example. This review aims to give an update on entry inhibitors for a range of sialic-acid-targeting viruses and provides insight into the prospects for those with broad-spectrum potential.

Lower respiratory tract infection in the community: associations between viral aetiology and illness course.

OBJECTIVES: This study determined associations between respiratory viruses and subsequent illness course in primary care adult patients presenting with acute cough and/or suspected lower respiratory tract infection. METHODS: A prospective European primary care study recruited adults with symptoms of lower respiratory tract infection between November 2007 and April 2010. Real-time in-house polymerase chain reaction (PCR) was performed to test for six common respiratory viruses. In this secondary analysis, symptom severity (scored 1 = no problem, 2 = mild, 3 = moderate, 4 = severe) and symptom duration were compared between groups with different viral aetiologies using regression and Cox proportional hazard models, respectively. Additionally, associations between baseline viral load (cycle threshold (Ct) value) and illness course were assessed. RESULTS: The PCR tested positive for a common respiratory virus in 1354 of the 2957 (45.8%) included patients. The overall mean symptom score at presentation was 2.09 (95% confidence interval (CI) 2.07-2.11) and the median duration until resolution of moderately bad or severe symptoms was 8.70 days (interquartile range 4.50-11.00). Patients with influenza virus, human metapneumovirus (hMPV), respiratory syncytial virus (RSV), coronavirus (CoV) or rhinovirus had a significantly higher symptom score than patients with no virus isolated (0.07-0.25 points or 2.3-8.3% higher symptom score). Time to symptom resolution was longer in RSV infections (adjusted hazard ratio (AHR) 0.80, 95% CI 0.65-0.96) and hMPV infections (AHR 0.77, 95% CI 0.62-0.94) than in infections with no virus isolated. Overall, baseline viral load was associated with symptom severity (difference 0.11, 95% CI 0.06-0.16 per 10 cycles decrease in Ct value), but not with symptom duration. CONCLUSIONS: In healthy, working adults from the general community presenting at the general practitioner with acute cough and/or suspected lower respiratory tract infection other than influenza impose an illness burden comparable to influenza. Hence, the public health focus for viral respiratory tract infections should be broadened.

TCRD and Pharos 2021: mining the human proteome for disease biology.

In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.

Multi-assay investigation of viral etiology in pediatric central nervous system infections.

INTRODUCTION: In an attempt to identify a wide spectrum of viral infections, cerebrospinal fluid (CSF) specimens were collected from pediatric cases with the preliminary diagnosis of viral encephalitis/meningoencephalitis in two reference hospitals, from October 2011 to December 2015. METHODOLOGY: A combination of nucleic acid-based assays, including in house generic polymerase chain reaction (PCR) assays for enteroviruses, flaviviruses and phleboviruses, a commercial real-time PCR assay for herpesviruses and a commercial real time multiplex PCR, enabling detection of frequently-observed viral, bacterial and fungal agents were employed for screening. RESULTS: The microbial agent could be characterized in 10 (10%) of the 100 specimens. Viral etiology could be demonstrated in 7 (70%) specimens, which comprises Human Herpesvirus 6 (4/7), Herpes Simplex virus type1 (2/7) and Enteroviruses (1/7). In 3 specimens (30%), Streptococcus pneumoniae, Listeria monocytogenes and Staphylococcus aureus were detected via the multiplex PCR, which were also isolated in bacteriological media. All specimens with detectable viral nucleic acids, as well as unreactive specimens via nucleic acid testing remained negative in bacteriological cultures. CONCLUSIONS: Herpes and enteroviruses were identified as the primary causative agents of central nervous system infections in children. Enterovirus testing must be included in the diagnostic work-up of relevant cases.

Causes of swine polyserositis in a high-density breeding area in Italy.

We assessed the causes of polyserositis in pigs, categorized by causative agents and ages of animals affected. In a 3-y study, 246 pigs from 80 different farms with recurrent problems of polyserositis, in a high-density breeding area, were submitted for autopsy; 154 pigs with typical fibrinous serosal lesions were sampled for further bacterial and viral investigation. The most common gross lesions were pleuritis and pericarditis (141 of 154; 92%). The animals most affected were weaned pigs (139 of 154; 90%). Haemophilus parasuis and Mycoplasma hyorhinis were the most common bacteria detected and were present at the same rate (85 of 154; 55%). Other bacteria isolated were Streptococcus sp. (44 of 154; 29%), Pasteurella multocida (21 of 154; 14%), Escherichia coli (19 of 154; 12%), Actinobacillus pleuropneumoniae (7 of 154; 5%), and Trueperella pyogenes (4 of 154; 3%). Porcine reproductive and respiratory syndrome virus (PRRSV; 119 of 154; 77%) predominated among the viruses detected, followed, with lesser prevalence, by porcine circovirus 2 (40 of 154; 26%) and swine influenza A virus (19 of 154; 12%). Bacterial coinfection and coinfection of bacteria and viruses were common (128 of 154; 83%). A strong positive correlation was found between coinfection by H. parasuis and M. hyorhinis and also by H. parasuis with PRRSV.

An in silico integrative protocol for identifying key genes and pathways useful to understand emerging virus disease pathogenesis.

The pathogenesis of an emerging virus disease is a difficult task due to lack of scientific data about the emerging virus during outbreak threats. Several biological aspects should be studied faster, such as virus replication and dissemination, immune responses to this emerging virus on susceptible host and specially the virus pathogenesis. Integrative in silico transcriptome analysis is a promising approach for understanding biological events in complex diseases. In this study, we propose an in silico protocol for identifying key genes and pathways useful to understand emerging virus disease pathogenesis. To validate our protocol, the emerging arbovirus Zika virus (ZIKV) was chosen as a target micro-organism. First, an integrative transcriptome data from neural cells infected with ZIKV was used to identify shared differentially expressed genes (DEGs). The DEGs were used to identify the potential candidate genes and pathways in ZIKV pathogenesis through gene enrichment analysis and protein­protein interaction network construction. Thirty DEGs (24 upregulated and 6 downregulated) were identified in all ZIKV-infected cells, primarily associated with endoplasmic reticulum stress and DNA replication pathways. Some of these genes and pathways had biological functions linked to neurogenesis and/or apoptosis, confirming the potential of this protocol to find key genes and pathways involved on disease pathogenesis. Moreover, the proposed in silico protocol performed anintegrated analysis that is able to predict and identify putative biomarkers from different transcriptome data. These biomarkers could be useful to understand virus disease pathogenesis and also help the identification of candidate antiviral drugs.

Vaccines in adults.

The proportion of adult population has increased globally and the current projections indicate that, by 2050, the group of 60 years and older will represent 21.1%. There are now vaccines exclusively designed for adults and others that are applied in early life but need to be updated later in life. Vaccines for adults are not only based on their respective age group but are also linked to risk factors like occupation, life style, health situation, among others. At the same time, longevity brings with it a weakening of the immune response to vaccines, a process known as immunosenescence representing an increasing challenge to adequately protect this age group. For some time, WHO has been promoting the term "Vaccination through the life course" allowing for an extension of the vaccination vision and taking adults as an integral part into the national vaccination programs and calendars. There are several vaccine preventable diseases affecting adults, but those associated with influenza virus and pneumococcus are the ones that affect the largest age group. Several recommendations include, additionally, others to prevent diphtheria, tetanus, whooping cough, hepatitis A and B, meningococcus, chickenpox, measles, rubella, mumps, herpes zoster, human papilloma virus and others. There are still many challenges to overcome in order to fully include adults, particularly health personnel, and to make vaccines extensively valued as a prevention tool in order to achieve a healthy life.

La proporción de población de adultos se ha incrementado globalmente y las proyecciones muestran que para el año 2050 los mayores de 60 años representarán el 21.1%. Actualmente se dispone de vacunas dirigidas exclusivamente a adultos y otras que se aplican en niños pero que se deben actualizar a lo largo de la vida. Las vacunas en adultos se administran, no solo por el grupo de edad al que pertenecen, sino también por factores como ocupación, estilos de vida o estado de salud. Al mismo tiempo, la longevidad disminuye la respuesta inmune a las vacunas por el fenómeno de inmunosenescencia, lo cual representa un desafío para proteger adecuadamente a este grupo. Desde hace varios años la OMS, ha propiciado la utilización del término "Vacunación en el curso de la vida" lo cual permite extender la visión de la vacunación y considerar al adulto como una parte integral de los planes y calendarios de inmunización. Existen varias enfermedades prevenibles por vacunas en adultos, pero aquellas asociadas al virus de influenza y al neumococo, son las que comprenden el grupo más extenso. Diversas recomendaciones incluyen, además de estas vacunas, otras dirigidas a prevenir difteria, tétanos, tos convulsa, hepatitis A y B, meningococo, varicela, sarampión, rubéola, parotiditis, herpes zóster, virus del papiloma humano y otras enfermedades. Se reconocen muchos desafíos a superar para poder incorporar plenamente al adulto, incluyendo al personal de salud, y lograr que la vacunación sea una herramienta de prevención valorada ampliamente para el desarrollo de una vida saludable.