Circular agriculture increases food production and can reduce N fertilizer use of commercial farms for tropical environments.

World food production must increase in the coming years with minimal environmental impact for food and nutrition security. Circular Agriculture has emerged as an approach to minimize non-renewable resource depletion and encourage by-product reuse. The goal of this study was to evaluate Circular Agriculture as a tool to increase food production and N recovery. The assessment was conducted for two Brazilian farms (Farm 1; Farm 2) with Oxisols under no-till and a diversified cropping system, including five species of grain, three cover crop species, and sweet potato. Both farms implemented an annual two-crop rotation and an integrated crop-livestock system with beef cattle confined for 2-years. Grain and forage from the fields, leftovers from silos, and crop residues were used as cattle feed. Grain yield was 4.8 and 4.5 t ha-1 for soybean, 12.5 and 12.1 t ha-1 for maize, and 2.6 and 2.4 t ha-1 for common bean, for Farm 1 and Farm 2, respectively, which is higher than the national average. The animals gained 1.2 kg day-1 of live weight. Farm 1 exported 246 kg ha-1 year-1 of N in grains, tubers, and animals, while 216 kg ha-1 year-1 was added as fertilizer and N to cattle. Farm 2 exported 224 kg ha-1 year-1 in grain and animals, while 215 kg ha-1 year-1 was added as fertilizer and N to cattle. Circular practices, i.e., no-till, crop rotation, year-round soil covered, maize intercropped with brachiaria ruziziensis, biological N fixation, and crop-livestock integration, increased crop yield and decreased N application by 14.7 % (Farm 1) and 4.3 % (Farm 2). 85 % of the N consumed by the confined animals was excreted and converted into organic compost. Overall, circular practices associated with adequate crop management allowed recovering high rate of applied N, reducing environmental impacts, and increasing food production with lower production costs.

Nitrate losses and nitrous oxide emissions under contrasting tillage and cover crop management.

Agroecosystems in the upper Mississippi River Basin are highly productive but often contribute to deterioration of water quality and greenhouse gas emissions. Cover cropping and no-till are conservation strategies implemented to reduce the environmental impact of these agroecosystems. However, using multiple strategies can lead to systemwide interactions that are not fully understood. These interactions can affect not only environmental quality metrics, such as subsurface drainage nitrate losses or nitrous oxide (N2 O) emissions, but also may influence crop production potential. A field trial was initiated comparing nitrate losses, N2 O emissions, and crop production under systems with fall chisel plow tillage, fall chisel plow tillage with an oat (Avena sativa L.) cover crop (CP-oat), no-till (NT), no-till with a rye (Secale cereale L.) cover crop (NT-rye), and NT with zero N fertilizer. Pathways for nitrate losses and N2 O emissions did not appear linked and were not tied to cover crop or tillage practices. Nitrate losses were linked with drainage volumes, and cover crops and tillage had limited effect on cumulative drainage volumes. Notably, NT-rye altered the relationship between drainage volume and nitrate losses by reducing nitrate concentrations, lowering nitrate losses by 59 ±9% compared with CP-oat and 67 ± 9% compared with NT. Neither cover crop nor tillage consistently affected N2 O emissions or crop yield. Rather, N2 O emissions were closely tied with fertilizer N application and seasonal weather patterns. These findings indicate that nitrate leaching and N2 O emissions are regulated by separate mechanisms, so conservation management may require stacking multiple practices to be effective.

Both subsurface nitrate losses and nitrous oxide emissions were linked with weather. Subsurface nitrate losses were linked with cumulative annual drainage. Nitrous oxide emissions were linked with fertilizer N applications. Rye cover crop with no-till reduced nitrate losses with no yield declines.

Near-complete genome of cosavirus A from a child hospitalized with acute gastroenteritis, Brazil.

Acute gastroenteritis (AG) is responsible for 525,000 deaths worldwide in children under-5-years and is caused by the Human Cosavirus (HCoSV; family Picornaviridae, Genus Cosavirus). Although its health importance, a significant percentage of diarrhea cases (≈ 40 %) still of unknown etiology. In Brazil, few studies have reported HCoSV-A sequences analyzing partial 5' UTR. This study characterized the first near-complete genome of a Cosavirus A (strain AM326) from a child hospitalized with AG in Amazonas state, Northern Brazil. High throughput sequencing (HTS) was performed using the HiSeq™ 2500 platform (Illumina) in one fecal specimen collected from the Surveillance of Rotavirus Network of the Evandro Chagas Institute collected in 2017. Sequence reads were assembled by the De Novo approach using three distinct algorithmic (IDBA-UD, Spades, and MegaHit). The final contig was recovered from the HCoSV-AM326 sample revealing 7,735 nt in length (SRA number SRR12535029; GenBank MT023104) and the genetic characterization, as well as phylogenetic analysis demonstrated a new variant strain from Brazil, highlighting the association of HCoSV-A as a possible causative agent of AG. This finding demonstrates the importance of the metagenomic approach to elucidate cases of diarrhea without a defined etiology, as well as providing a better understanding about the virus genetics, evolution and epidemiology.

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.

Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.

ICTV Virus Taxonomy Profile: Peribunyaviridae.

Peribunyaviruses are enveloped and possess three distinct, single-stranded, negative-sense RNA segments comprising 11.2-12.5 kb in total. The family includes globally distributed viruses in the genera Orthobunyavirus, Herbevirus, Pacuvirus and Shangavirus. Most viruses are maintained in geographically-restricted vertebrate-arthropod transmission cycles that can include transovarial transmission from arthropod dam to offspring. Others are arthropod-specific. Arthropods can be persistently infected. Human infection occurs through blood feeding by an infected vector arthropod. Infections can result in a diversity of human and veterinary clinical outcomes in a strain-specific manner. Segment reassortment is evident between some peribunyaviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the family Peribunyaviridae, which is available at ictv.global/report/peribunyaviridae.

Evolutionary Dynamics of Oropouche Virus in South America.

The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribunyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach.IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.

Characterization of Three Novel Viruses from the Families Nyamiviridae, Orthomyxoviridae, and Peribunyaviridae, Isolated from Dead Birds Collected during West Nile Virus Surveillance in Harris County, Texas.

This report describes and characterizes three novel RNA viruses isolated from dead birds collected during West Nile virus surveillance in Harris County, TX, USA (the Houston metropolitan area). The novel viruses are identified as members of the families Nyamaviridae, Orthomyxoviridae, and Peribunyaviridae and have been designated as San Jacinto virus, Mason Creek virus, and Buffalo Bayou virus, respectively. Their potential public health and/or veterinary importance are still unknown.

Transcriptomic Analysis of Mucor irregularis Containing a Negative Single-Stranded RNA Mycovirus.

The fungus Mucor irregularis is a causative agent of mucormycosis. The transcriptome analysis of the isolated M. irregularis strain C3B revealed the presence of an RNA polymerase domain of a negative-polarity RNA virus. In this work, we describe the gene ontology-based annotation of the Mucor irregularis transcriptome, which includes a putative RNA mycovirus.

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.

In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.org.za/tools.php.

Genome Sequence of Chiqui Virus, a Novel Reovirus Isolated from Mosquitoes Collected in Colombia.

We report here the complete genome sequence of a novel reovirus, designated Chiqui virus (CHQV) strain CoB38d, that was isolated from a pool of unidentified mosquitoes collected in northern Colombia in 2013. CHQV has nine double-stranded DNA (dsRNA) genome segments and has similarity to viruses belonging to the family Reoviridae, subfamily Spinareovirinae.

Zika Virus Epidemic in Brazil. II. Post-Mortem Analyses of Neonates with Microcephaly, Stillbirths, and Miscarriage.

INTRODUCTION: The recent Zika virus(ZIKV) epidemic in Brazil was characterized by a range of different clinical presentations, particularly microcephaly, Guillain-Barré syndrome, and death. In this context, we determined the causal relationship between fatal microcephaly cases and ZIKV infection. METHODS: Twelve fatal cases of neonates, whose mothers were infected with ZIKV during pregnancy, were examined; cases included nine neonatal deaths due to microcephaly, one miscarriage, and two stillbirths. Tissue samples were obtained from all cases at necropsy and were submitted for virological investigation (RT-qPCR and virus isolation) and/or histopathology (hematoxylin and eosin staining) and immunohistochemical assay for the detection of ZIKV antigens. RESULTS: ZIKV antigens and/or ZIKV RNA were detected in tissue samples of all 12 cases examined. ZIKV was recovered in one case. Results of the virological and immunohistochemical analyses, as well as the anatomic abnormalities and histopathologic changes observed at necropsy on the 12 fatal cases, are presented. CONCLUSIONS: Data from these 12 cases provide strong evidence of the causal relationship between ZIKV and congenital disease in fetuses of women who were infected with the virus during pregnancy.

Characterization of Three New Insect-Specific Flaviviruses: Their Relationship to the Mosquito-Borne Flavivirus Pathogens.

Three novel insect-specific flaviviruses, isolated from mosquitoes collected in Peru, Malaysia (Sarawak), and the United States, are characterized. The new viruses, designated La Tina, Kampung Karu, and Long Pine Key, respectively, are antigenically and phylogenetically more similar to the mosquito-borne flavivirus pathogens, than to the classical insect-specific viruses like cell fusing agent and Culex flavivirus. The potential implications of this relationship and the possible uses of these and other arbovirus-related insect-specific flaviviruses are reviewed.

New Virus Genome Sequences of the Guama Serogroup (Genus Orthobunyavirus, Family Bunyaviridae), Isolated in the Brazilian Amazon Region.

This is the first announcement of two nearly complete viral genome sequences belonging to the Guama serogroup (genus Orthobunyavirus, family Bunyaviridae) isolated in the Brazilian Amazon region: Mirim virus (MIRV; BEAN7722) and Ananindeua virus (ANUV; BEAN109303).

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses.

Sinu virus, a novel and divergent orthomyxovirus related to members of the genus Thogotovirus isolated from mosquitoes in Colombia.

The genome and structural organization of a novel insect-specific orthomyxovirus, designated Sinu virus, is described. Sinu virus (SINUV) was isolated in cultures of C6/36 cells from a pool of mosquitoes collected in northwestern Colombia. The virus has six negative-sense ssRNA segments. Genetic analysis of each segment demonstrated the presence of six distinct ORFs encoding the following genes: PB2 (Segment 1), PB1, (Segment 2), PA protein (Segment 3), envelope GP gene (Segment 4), the NP (Segment 5), and M-like gene (Segment 6). Phylogenetically, SINUV appears to be most closed related to viruses in the genus Thogotovirus.

Zika virus epidemic in Brazil. I. Fatal disease in adults: Clinical and laboratorial aspects.

BACKGROUND: Zika virus (ZIKV) was first detected in Brazil in May 2015 and the country experienced an explosive epidemic. However, recent studies indicate that the introduction of ZIKV occurred in late 2013. Cases of microcephaly and deaths associated with ZIKV infection were identified in Brazil in November, 2015. OBJECTIVES: To determine the etiology of three fatal adult cases. STUDY DESIGN: Here we report three fatal adult cases of ZIKV disease. ZIKV infection in these patients was confirmed by cells culture and/or real-time reverse transcriptase polymerase chain reaction (RT-qPCR) and by antigen detection using immunohistochemical assay. Samples of brain and other selected organs taken at autopsy from three patients were also analyzed by histopathological and immunohistological examination. RESULTS: The first patient, a 36-year-old man with lupus and receiving prednisone therapy, developed a fulminant ZIKV infection. At autopsy, RT-qPCR of blood and tissues was positive for ZIKV RNA, and the virus was cultured from an organ homogenate. The second patient, a previously healthy female, 16 years of age, presented classic symptoms of Zika fever, but later developed severe thrombocytopenia, anemia and hemorrhagic manifestations and died. A blood sample taken on the seventh day of her illness was positive RT-PCR for ZIKV RNA and research in the serum was positive for antinuclear factor fine speckled (1/640), suggesting Evans syndrome (hemolytic anemia an autoimmune disorder with immune thrombocytopenic purpura) secondary to ZIKV infection. The third patient was a 20-year-old woman hospitalized with fever, pneumonia and hemorrhages, who died on 13days after admission. Histopathological changes were observed in all viscera examined. ZIKV antigens were detected by immunohistochemistry in viscera specimens of patients 1 and 3. These three cases demonstrate other potential complications of ZIKV infection, in addition to microcephaly and Guillain-Barre syndrome (GBS), and they suggest that individuals with immune suppression and/or autoimmune disorders may be at higher risk of developing severe disease, if infected with ZIKV.

Mobile real-time surveillance of Zika virus in Brazil.

The World Health Organization has declared Zika virus an international public health emergency. Knowledge of Zika virus genomic epidemiology is currently limited due to challenges in obtaining and processing samples for sequencing. The ZiBRA project is a United Kingdom-Brazil collaboration that aims to improve this situation using new sequencing technologies.

Isolation of Madre de Dios Virus (Orthobunyavirus; Bunyaviridae), an Oropouche Virus Species Reassortant, from a Monkey in Venezuela.

Oropouche virus (OROV), genus Orthobunyavirus, family Bunyaviridae, is an important cause of human illness in tropical South America. Herein, we report the isolation, complete genome sequence, genetic characterization, and phylogenetic analysis of an OROV species reassortant, Madre de Dios virus (MDDV), obtained from a sick monkey (Cebus olivaceus Schomburgk) collected in a forest near Atapirire, a small rural village located in Anzoategui State, Venezuela. MDDV is one of a growing number of naturally occurring OROV species reassortants isolated in South America and was known previously only from southern Peru.

Inhangapi Virus: Genome Sequencing of a Brazilian Ungrouped Rhabdovirus Isolated in the Amazon Region.

We report here nearly complete genome sequence of Inhangapi virus (INHV) strain BEAR177325, which was isolated from a pool of sandflies (Lutzomyia flaviscutellata) in the Utinga neighborhood, Belém (01º28´S 48°27'W), State of Pará, Brazil, in 1969. The genome of this virus showed similarity with members belonging to the family Rhabdoviridae.