Gene duplication as a major force driving the genome expansion in some giant viruses

IMPORTANCE

Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes.

Detection of human Mastadenovirus C in wild guinea pigs (Cavia aperea aperea) feces

The Adenoviridae family is composed by a high diversity of viruses that are extremely resistant in environment and are frequently excreted in animal reservoir feces for long periods. The knowledge of adenovirus (AdV) diversity among wild species may be important for the understanding of the epidemiology of putative emerging diseases. Cavia aperea aperea, commonly known as wild guinea pigs, wild cavies, or preas, are small herbivorous rodents widely distributed throughout South America and classified in Caviidae family, as well as domestic guinea pigs and capybaras. In order to investigate their potential role as reservoir of zoonotic agents, the present study aimed to verify the presence of AdV in fecal samples of 14 preas from Northeast Brazil. When submitted to nested PCR, two out of 14 samples (14.28%) were positive for AdV and classified as human Mastadenovirus C (HAdV-C) using DNA sequencing and phylogenetic analysis. Wild guinea pigs are synanthropic rodents that live in close contact with humans. The investigation of viral agents in rodents is important due to their potential role as reservoirs of human and animal pathogens. Moreover, the present work presents the first known evidence of HAdV in wild guinea pig stool samples, which may represent both the impact of anthropogenic pollution to wild animals and an important knowledge in terms of human health.

Cattle influenza D virus in Brazil is divergent from established lineages

Influenza D virus (IDV) is endemic in cattle on several continents and can also infect a wide range of hosts. IDV was first detected in a bovine respiratory disease outbreak associated with bovine alphaherpesvirus 1 in Brazil. Sequence analysis of partial segments showed that the virus is phylogenetically divergent from previously described IDVs from other continents. As the first molecular description of IDV in South America, this can be a first step toward investigating IDV infections in cattle in Brazil and surrounding countries in which the beef industry is economically important.

Proteinase K treatment in absence of RNA isolation classical procedures is a quick and cheaper alternative for SARS-CoV-2 molecular detection

The World Health Organization (WHO) has declared a pandemic of COVID-19, the disease caused by the recently described SARS-CoV-2. The relevance and importance of mass diagnosis in order to find the asymptomatic individuals is widely recognized as a mandatory tool to reinforce the control measures for monitoring virus circulation and reduce the spreading of SARS-CoV-2. Here, we described quickness and cheaper strategies of direct RT-qPCR (in the absence of RNA isolation) and compared the results to those obtained using standard RNA isolation procedure. The tests varied using pure, diluted samples, combined with Proteinase K (PK) or Lysis Buffer. Our findings showed consistently that PK pre-treated samples in the absence of RNA extraction procedures presents similar results to those obtained by standard RNA isolation procedures. On average, 16 samples extracted with the MagMAX™ CORE Kit, take around 2 h, costing an average of USD 5, the pre-treatment of samples using PK, on the other hand, would cut the value to less than USD 0.30 and reduce the time of procedure in more than 1 ½ hours. The present study suggests the use of PK treatment instead of RNA isolation in order to reduce costs and time in processing samples for molecular diagnosis of SARS-CoV-2.

Microbial risk assessment in recreational freshwaters from southern Brazil

In this study, total coliforms (TC), Escherichia coli, enterovirus (EV), rotavirus (RV), and human mastadenovirus species C and F (HAdV-C and HAdV-F) were evaluated in water samples from Belo Stream. For HAdV-C and F, the infectivity was assessed by integrated cell culture quantitative real-time polymerase chain reaction (ICC-qPCR). Samples were collected monthly (May/2015 to April/2016) at four sites. Viral analyses were performed for both ultracentrifuge-concentrated and unconcentrated samples. For site P4 (used for recreational purposes), QMRA was applied to estimate health risks associated with exposure to E. coli and HAdV-C and F. TC and E. coli were present throughout the collection period. EV and RV were not detected. HAdV-C were present in 8.51% (1.89E + 06 to 2.28E + 07 GC (Genomic Copies)/L) and 21.27% (2.36E + 05 to 1.29E + 07 GC/L) for unconcentrated and concentrated samples, respectively. For HAdV-F were 12.76% (2.77E + 07 to 3.31E + 08 GC/L) and 48.93% (1.10E + 05 to 4.50E + 08 GC/L) for unconcentrated and concentrated samples, respectively. For unconcentrated samples, infectivity for HAdV-C was detected in 37.20% (1st ICC-qPCR) and 25.58% (2nd ICC-qPCR). For HAdV-F, infectivity was detected in 6.97% (1st ICC-qPCR) and 6.97% (2nd ICC-qPCR). For concentrated samples, HAdV-C infectious was observed in 17.02% (1st ICC-qPCR) and in 8.51% (2nd ICC-qPCR). For HAdV-F, were present in 8.51% for both 1st and 2nd ICC-qPCR. Statistical analyzes showed significant difference between the collection sites when analyzed the molecular data of HAdV-F, data of TC and E. coli. Correlation tests showed direct correlation between HAdV-F with E. coli and TC. E. coli concentrations translated to the lowest estimates of infection risks (8.58E-05 to 2.17E-03). HAdV-F concentrations were associated with the highest infection risks at 9.99E-01 and for group C, 1.29E-01 to 9.99E-01. These results show that commonly used bacterial indicators for water quality may not infer health risks associated with viruses in recreational freshwaters.

Human adenovirus in tissues of freshwater snails living in contaminated waters

Human adenovirus (HAdV) is resistant to environment and can be used as a marker to detect fecal contamination. Considering the importance of freshwater snails in the aquatic environment, their use as concentrators for HAdV is a complementary tool for viral analysis of water. The goal of the study was to detect HAdV in snails and surface water collected from wetlands of the Sinos River (Rio Grande do Sul, Brazil) basin and to compare rates and viral loads found in both samples. HAdV was detected through real-time PCR. Total and fecal coliforms were detected by Colilert^® kit, and viral infectivity of positive samples of the DNA genome was performed in A549 human cell line. All wetlands presented bacterial and viral contamination, but no viral particle was considered viable. The wetland that showed lower fecal coliform mean was Campo Bom, and São Leopoldo (both cities in Rio Grande do Sul) was representative of the highest mean. HAdV was detected in water samples (53%), gastropods' hemolymph (31%) and tissues (16%). Wetlands proved to be environments already altered by human action. Water samples exhibited a higher frequency of HAdV detection; however, in some instances, the target viral genomes were only found in gastropod biological samples. This was a pioneer study in the use of freshwater snails for human enteric viral assessment thus demonstrating that the human organism can retain fecal contamination, complementing and assisting in microbiological water analyzes.

Hepatitis E Virus in Surface Water, Sediments, and Pork Products Marketed in Southern Brazil

Hepatitis E virus (HEV) is an emerging causative agent of food and waterborne hepatitis in human beings. HEV circulates among human populations and swine herds, and may be found in water contaminated by swine feces, as well as in pork. In the present study, 68 sediment samples and 250 water samples collected from the Sinos River tributaries, as well as 50 samples of pork products (pâté and blood sausage) marketed in the Sinos River watershed region, Brazil, were tested for the presence of HEV genome. Reverse-transcriptase polymerase chain reaction followed by nucleotide sequencing was used for detection and characterization of HEV genomes. Overall, 36 % of food samples tested positive for HEV (genotype 3). No sediment or water samples were positive. These results suggest that contaminated pork products may be a source of HEV infection within this region and indicate a need for better monitoring of food safety and swine herds.