Local-scale virome depiction supports significant differences between Aedes aegypti and Aedes albopictus

Aedes spp. comprise the primary group of mosquitoes that transmit arboviruses such as dengue, Zika, and chikungunya viruses to humans, and thus these insects pose a significant burden on public health worldwide. Advancements in next-generation sequencing and metagenomics have expanded our knowledge on the richness of RNA viruses harbored by arthropods such as Ae. aegypti and Ae. albopictus ; increasing evidence suggests that vectorial competence can be modified by the microbiome (comprising both bacteriome and virome) of mosquitoes present in endemic zones. Using an RNA-seq-based metataxonomic approach, this study determined the virome structure of field-caught Ae. aegypti and Ae. albopictus mosquitoes in Medellín, Colombia, a municipality with a high incidence of mosquito-transmitted arboviruses. The two species are sympatric, but their core viromes differed considerably in richness, diversity, and abundance; the viromes were dominated by a few viruses. BLAST searches of assembled contigs suggested that at least 17 virus species (16 of which are insect-specific viruses [ISVs]) infect the Ae. aegypti population. Dengue virus 3 was detected in one sample. In Ae. albopictus , up to 11 ISVs and one plant virus were detected. Therefore, the virome composition was species-specific. The bacterial endosymbiont Wolbachia was identified in all Ae. albopictus samples and in some Ae. aegypti samples collected after 2017. The presence of Wolbachi a sp. in Ae. aegypti was not related to significant changes in the richness, diversity, or abundance of this mosquito’s virome, although it was related to an increase in the abundance of Aedes aegypti To virus 2 (unclassified). The mitochondrial diversity of these mosquitoes suggested that the Ae. aegypti population underwent a change that started in the second half of 2017, which coincides with the release of Wolbachia -infected mosquitoes in Medellín, indicating that the population of w Mel-infected mosquitoes has expanded. However, additional studies are required on the dispersal speed and intergenerational stability of w Mel in Medellín and nearby areas as well as on the introgression of genetic variants in the native mosquito population.

Human land-use impacts viral diversity and abundance in a New Zealand river

Although water borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral diversity and evolution in water systems such as rivers. We used metagenomic next generation sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land use impact, ranging from pristine to urban. From this we identified 504 putative virus species, of which 97% were novel. Many of the novel viruses were highly divergent, and likely included a new subfamily within the Parvoviridae. We identified at least 63 virus species that may infect vertebrates, most likely fish and water birds, from the Astroviridae, Birnaviridae, Parvoviridae and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n=150) and pristine sites (n=119), and more viruses were shared between the urban and farming sites (n=76) than between the pristine and farming or urban sites (n=24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Overall, our study shows that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanization on water systems.

A case report on Severe Acute Respiratory Infection

Introduction: Severe Acute Respiratory Syndrome is a zootoxic viral respiratory illness caused by the severe acute respiratory syndrome corona virus (SARS-CoV or SARS-The syndrome was the cause of the Severe Acute Respiratory Syndrome outbreak in 2002–2004. The virus was traced back to cave-dwelling horseshoe bats via Asian palm civets in late 2017 by Chinese scientists in Xizang Yi Ethnic Township, Yunnan. SARS was a rare illness; there were 8,422 cases at the end of the pandemic in June 2003, with an 11 percent case fatality rate (CFR) (CoV-1), the initial strain of the SARS corona virus species (SARSr-CoV). Clinical Finding: Swelling over Right. Half of face, Breathlessness. Diagnostic Evaluation: Blood test: Hb – 9.2gm%, Total RBC count- 3.22 millions/cu.mm, HCT- 26.6%, Total WBC count – 6600/cu.mm, Monocytes-02%, granulocytes-85%, lymphocytes-10000 /mcl. HRCT Scan OF Thorax: Multiple ill defined patchy ground glass opacities with consolidation and sepal thickening in bilateral lungs filled s/o infective etiology possibility of atypical viral pneumonia. View of covid positive PCR test; imagine grading corad-6 with CT severity score – 03\25 (Mild). Therapeutic Intervention: Inj.Amphotericin-B 500mg IV, Inj.Piptaz 4.4gm IV x TDS, Inj.levoflox 500 mg x OD, Inj.Clindamycin 300mg x BD, Inj.pantaprazol 40 mg x OD, Inj.Emset 4mg x TDS, Tab. limcee 500 mg x BD. Outcome: After Treatment, the patient shows improvement. His swelling over face decrease, and breathlessness decrease. Conclusion: My patient was admitted in SARI-HDU, AVBRH with complaint of swelling over face Right side, and breathlessness. After getting appropriate treatment his condition was improved.

Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover, is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, co-circulating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semi-independent epidemiological niches that are not regionally or seasonally defined. Typically, intra-lineage mutational signatures are similar to inter-lineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage-defining. The persistence of virus lineages appears to stem from limited outbreaks within small communities so that only a minor fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.SignificanceNumerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential of causing new pandemics? We show that most human pathogenic RNA viruses form multiple, co-circulating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that a minor fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics.

Phenotypic and molecular screening of dry bean (Phaseolus vulgaris L.) breeding lines for resistance to bean common mosaic virus and bean common mosaic necrosis virus

Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) are among the most economically important virus species infecting common bean. The use of resistant plant cultivars is the most effective way to control these viruses. National dry bean breeding studies have been conducted by seven different governmental agricultural research institutes in Turkey, and advanced breeding lines have been developed by using the selected local dry bean populations and crossing studies. In this study, 204 breeding lines were tested for resistance levels to BCMV and BCMNV. Initially, BCMNV NL-3 and BCMV NL-4 strains were individually sap-inoculated onto the leaves of bean plants belonging to each breeding lines with 10 replications, and the reactions of plants were evaluated for symptomatic appearance of virus infection 21 days after inoculation. Additionally, phenotypic evaluation was confirmed by molecular markers linked to resistance genes. As a result of the study, 153 breeding lines were found to involve the dominant I gene whereas four and five of the tested lines had the recessive genes bc-1² and bc-2², respectively. In conclusion, it was emphasized that these breeding lines could be registered after evaluating them in terms of yield and quality. Also, the use of seeds of the resistant lines to supply the source of virus-resistance in breeding studies and maintaining their seeds at the national genebank were recommended.

Metatranscriptomic Sequencing Suggests the Presence of Novel RNA Viruses in Rice Transmitted by Brown Planthopper

Viral pathogens are a major threat to stable crop production. Using a backcross strategy, we find that integrating a dominant brown planthopper (BPH) resistance gene Bph3 into a high-yield and BPH-susceptible indica rice variety significantly enhances BPH resistance. However, when Bph3-carrying backcross lines are infested with BPH, these BPH-resistant lines exhibit sterile characteristics, displaying panicle enclosure and failure of seed production at their mature stage. As we suspected, BPH-mediated viral infections could cause the observed sterile symptoms, and we characterized rice-infecting viruses using deep metatranscriptomic sequencing. Our analyses revealed eight novel virus species and five known viruses, including a highly divergent virus clustered within a currently unclassified family. Additionally, we characterized rice plant antiviral responses using small RNA sequencing. The results revealed abundant virus-derived small interfering RNAs in sterile rice plants, providing evidence for Dicer-like and Argonaute-mediated immune responses in rice plants. Together, our results provide insights into the diversity of viruses in rice plants, and our findings suggest that multiple virus infections occur in rice plants.

Polerovirus Genomic Variation

The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single, positive strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3) and a read-through domain (ORF5) that is fused to the CP to form a CP-RT protein. The genus Polerovirus contains 26 virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and VPg contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. Results described here suggest that using contrasting mechanisms, P0, VPg and CP-RT mediate adaptation to host plants, to vectors, and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, identification of susceptibility genes, and contributes to our understanding of virus interactions with their host, vectors, and environment.

Cucurbit aphid-borne yellows virus (CABYV) infecting melon and bitter gourd in Java, Indonesia

Recently, Cucurbit aphid-borne yellows polerovirus (CABYV) had been reported firstly to infect cucumber in Java. The typical symptoms of CABYV infection are leaf yellowing with green veins and the thickening of older leaves. This study aimed to detect and identify the occurrence of CABYV infection on other cucurbit hosts in Java. A total of 600 Polerovirus-like symptomatic leaves were taken from open-fields cultivated plants in West Java, Central Java, and East Java. The virus incidence was determined serologically, RT-PCR and DNA sequencing confirmed the identity of CABYV. Based on serological test revealed six virus species in single or multiple infections with varying incidence. Among tested plants, the CABYV DNA with size ± 489 bp was successfully amplified from melon in Kediri, Tulungagung, Nganjuk (East Java), Kulonprogo, and bitter gourd in Bogor. The sequencing result confirmed the identity of melon isolates from Nganjuk showed the highest similarity with the CABYV cucumber isolate from Nganjuk and Tulungagung. In contrast, bitter gourd isolates with melon isolates from France and squash isolates from Spain. These are the first reports of CABYV infection on melon and bitter gourd in Java, indicating its rapid host expansion on Cucurbitaceae.

Virus Yellows in sugar beet – possibilities to achieve virus resistance

Virus yellows in sugar beet is caused by different virus species. Monitoring has shown that Beet yellows virus (BYV), Beet mild yellowing virus (BMYV), Beet chlorosis virus (BChV) are common and widespread, while Beet mosaic virus (BtMV) is less prevalent. The green peach aphid (Myzus persicae) is considered the main vector of these viruses. Sugar beet varieties with resistance or tolerance traits are currently not available to practical growers, therefore it is imperative to support breeding efforts with improved strategies to achieve virus resistance. For this purpose, a field test was established in which yield differences between susceptible and tolerant varieties can be generated by a 3% inoculation with BMYV-carrying aphids. A greenhouse bioassay has also been developed to distinguish susceptible and tolerant genotypes following BYV infection. Both assays pave the way for future use of natural resources such as wild forms and other breeding material to screen for virus resistance. In addition, molecular biology approaches are used to identify plant susceptibility factors of the plant-virus interaction, which will be knocked out via modern precision breeding methods to generate recessive virus resistance. Consequently, genotypes with naturally occurring mutations in the appropriate factors can be used for crossbreeding processes into elite breeding material.

A Systematic Review on Viruses in Mass-Reared Edible Insect Species

Edible insects are expected to become an important nutrient source for animals and humans in the Western world in the near future. Only a few studies on viruses in edible insects with potential for industrial rearing have been published and concern only some edible insect species. Viral pathogens that can infect insects could be non-pathogenic, or pathogenic to the insects themselves, or to humans and animals. The objective of this systematic review is to provide an overview of the viruses detected in edible insects currently considered for use in food and/or feed in the European Union or appropriate for mass rearing, and to collect information on clinical symptoms in insects and on the vector role of insects themselves. Many different virus species have been detected in edible insect species showing promise for mass production systems. These viruses could be a risk for mass insect rearing systems causing acute high mortality, a drastic decline in growth in juvenile stages and in the reproductive performance of adults. Furthermore, some viruses could pose a risk to human and animal health where insects are used for food and feed.