Recovery of complete genomes of canine parvovirus from clinical samples.

Canine parvovirus (CPV) is a highly pathogenic virus that affects dogs, especially puppies. CPV is believed to have evolved from feline panleukopenia virus (FPV), eventually giving rise to three antigenic types, CPV-2a, 2b, and 2c. CPV-2 is recognized for its resilience in contaminated environments, ease of transmission among dogs, and pathogenicity for puppies. Despite the relevance of the virus, complete genome sequences of CPV available at GenBank, to date, are scarce. In the current study, we have developed a methodology to allow the recovery of complete CPV-2 genomes directly from clinical samples. For this, seven fecal samples from Gurupi, Tocantins, North Brazil, were collected from puppies with clinical signals of viral enteritis, and submitted to viral DNA isolation and amplification. Two multiplex PCR strategies were designed including primers targeting fragments of 400 base pairs (bp) and 1,000 bp along the complete genome. Sequencing was performed with the Nanopore® technology and results obtained with the two approaches were compared. Genome assembly revealed that the 400 bp amplicons generated larger numbers of reads, allowing a more reliable coverage of the whole genome than those attained with primers targeting the larger (1000 bp) amplicons. Nevertheless, both enrichment methodologies were efficient in amplification and sequencing. Viral genome sequences were of high quality and allowed more precise typing and subtyping of viral genomes compared to the commonly employed strategy relying solely on the analysis of the VP2 region, which is limited in scope. The CPV-2 genomes recovered in this study belong to the CPV2a and CPV-2c subtypes, closely related to isolates from the neighboring Amazonian region. In conclusion, the technique reported here may contribute to increase the number of full CPV genomes available, which is essential for understanding the genetic mechanisms underlying the evolution and spread of CPV-2.

Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil.

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins; (ii) analyze them phylogenetically against global SARS-CoV-2 sequences; and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.

The impact of COVID-19 on the indigenous peoples related to air and road networks and habitat loss.

The vegetation loss in the Brazil's Legal Amazon (BLA) in 2020 corresponds to the highest loss observed in a decade, caused by the intensification of fires, mineral extraction activities, and other pressures. The possibility of earning from illegal activities such as deforestation and mining attracts the population to indigenous territories, while fires aggravate respiratory problems and enhance the current COVID-19 crisis. Furthermore, the BLA's road network is usually related to increased deforestation and fires in its areas of influence, and airports are known to contribute to spreading COVID-19 infections worldwide. Therefore, we decided to evaluate the effect of characteristics of Special Indigenous Health Districts (DSEIs) (including population, number of airports, and extent of the road network) and vegetation loss rates (deforestation, and area of vegetation lost by fires and mining) on the number of COVID-19 cases and deaths among the indigenous population in DSEIs in the BLA. We observed a positive correlation between the number of cases and deaths and the number of Indigenous Primary Healthcare Units, suggesting that many of these units did not increase appropriate activities for prevention and protection from COVID-19 in the DSEIs. The DSEIs with larger air transport and road networks were more affected by COVID-19. These networks constituted critical mechanisms for facilitating the spread of SARS-CoV-2 in the BLA. Additionally, we noted that changes that impact the landscape of DSEIs, such as fires and mining, also impact legal indigenous areas (IAs). Thus, IAs are not spared from exploratory processes in the district's landscape. Models that associate the air transport and road networks with the transformation of the landscape in IAs from burning or mining can explain the number of indigenous people who died due to COVID-19. These results are particularly important given the current disruptive scenario imposed by the Brazilian government on critical institutions that detect and fight fires in indigenous lands and the policies enacted to combat COVID-19 in Brazil, which are based on denying isolation measures and delaying vaccinations.

High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021.

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5' and two in 3' UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough "space" for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the "hotspots" in the generation of new variants.

The complete chloroplast genome of Artocarpus altilis (Moraceae) and phylogenetic relationships.

The chloroplast (cp) is an essential organelle in higher plants. The genes of the plastome are well suited to infer phylogenetic relationships among taxa. In this study, we report the assembly of the cp genome of Artocarpus altilis and its phylogeny among species from Moraceae family. The cp genome of A. altilis was 160,822 base pair (bp) in length, comprising one large single-copy region of 88,692 bp, one small single-copy region of 19,290 bp, and a pair of inverted repeat regions (IRs) of 26,420 bp. A total of 113 different genes were predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis of 19 species belonging to the Moraceae family confirmed the phylogenetic proximity of the genus Artocarpus and Morus and the genetic similarity of A. camansi and A. altilis.

Development and characterization of microsatellite markers in Stryphnodendron adstringens (Leguminosae).

In this study, we report the development and characterization of 15 new microsatellite markers for Stryphnodendron adstringens (Leguminosae) in order to support future analyses of genetic diversity in populations of this species. In screening with 48 individuals from three different populations of S. adstringens, we tested the amplification of 20 microsatellite loci, of which five are not useful for population genetic studies due to the lack of polymorphisms or amplification failures. For the final set of 15 loci, the number of alleles ranged from 2 to 15, with a total of 116 alleles. The expected heterozygosity ranged from 0.1219 to 0.8965, with an average of 0.6694 per locus. The combined probability of genetic identity (PI = 8.12 × 10-15) and paternity exclusion (Q = 0.99999) estimations showed that the loci may be useful to discriminate between individuals of S. adstringens. Initial cross-amplification tests were satisfactory in three species of the genus Stryphnodendron: S. rotundifolium, S. coriaceum and S. polyphyllum. This new set of markers will be a useful tool for population genetic studies, contributing to the knowledge about the evolutionary history of S. adstringens and, additionally, correlated species.