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ABSTRACT

Objectives: To identify and characterize respiratory viruses that infect children from daycare centers with symptoms of respiratory infection and to evaluate the association of clinical and epidemiological disease data with the identified virus. Methods:We conducted a study between 2003 and 2005 in 176 children with respiratory infection symptoms attending a municipal daycare center. Samples from nasopharyngeal secretion were tested by reverse transcriptase polymerase chain reaction and positive samples for picornavirus were sequenced.Results: All 782 collected samples were analyzed and 31.8% were positive for at least one of the studied respiratory viruses. Respiratory infections were characterized by the presence of mild symptoms of the upper respiratory tract, the most common of which were runny nose and cough. In the 2 years of study, most cases of infection occurred in autumn and winter, but respiratory viruses were detected throughout all the study period. Conclusions:Respiratory viruses and respiratory infections caused by them are part of the daily life of children attending daycare centers. Our results show the great impact that respiratory infections have on these children and suggest that more attention must be paid to viral pathogens. Resultados: Todas as 782 amostras coletadas foram analisadas, e 31,8% foram positivas para algum dos vírus respiratórios estudados. As infecções respiratórias foram caracterizadas pela presença de sintomas moderados do trato respiratório superior, sendo os mais comuns coriza e tosse. Em 2 anos de estudo, a maioria dos casos de infecção ocorreram no outono e no inverno, mas vírus respiratórios foram detectados ao longo de todo o período de estudo. J Pediatr (Rio J) Conclusões:Vírus respiratórios e as infecções respiratórias causadas por eles fazem parte do cotidiano de crianças que frequentam creches. Nossos resultados mostram o grande impacto gerado pelas infecções respiratórias nessas crianças e sugere que uma maior atenção deve ser dispensada aos patógenos virais.J Pediatr (Rio J). 2011;87(5):439-44: Vírus respiratórios, infecção respiratória aguda, crianças de creche.

The evolution and population dynamics of avian coronaviruses (AvCoVs) remain underexplored. In the present study, in-depth phylogenetic and Bayesian phylogeographic studies were conducted to investigate the evolutionary dynamics of AvCoVs detected in wild and synanthropic birds. A total of 500 samples, including tracheal and cloacal swabs collected from 312 wild birds belonging to 42 species, were analysed using molecular assays. A total of 65 samples (13%) from 22 bird species were positive for AvCoV. Molecular evolution analyses revealed that the sequences from samples collected in Brazil did not cluster with any of the AvCoV S1 gene sequences deposited in the GenBank database. Bayesian framework analysis estimated an AvCoV strain from Sweden (1999) as the most recent common ancestor of the AvCoVs detected in this study. Furthermore, the analysis inferred an increase in the AvCoV dynamic demographic population in different wild and synanthropic bird species, suggesting that birds may be potential new hosts responsible for spreading this virus.

One of the biggest challenges during the pandemic has been obtaining and maintaining critical material to conduct the increasing demand for molecular tests. Sometimes, the lack of suppliers and the global shortage of these reagents, a consequence of the high demand, make it difficult to detect and diagnose patients with suspected SARS-CoV-2 infection, negatively impacting the control of virus spread. Many alternatives have enabled the continuous processing of samples and have presented a decrease in time and cost. These measures thus allow broad testing of the population and should be ideal for controlling the disease. In this sense, we compared the SARS-CoV-2 molecular detection effectiveness by Real time RT-PCR using two different protocols for RNA extraction. The experiments were conducted in the National Institute of Health (INS) from Peru. We compared Ct values average (experimental triplicate) results from two different targets, a viral and internal control. All samples were extracted in parallel using a commercial kit and our alternative protocol–samples submitted to proteinase K treatment (3 μg/μL, 56°C for 10 minutes) followed by thermal shock (98°C for 5 minutes followed by 4°C for 2 minutes); the agreement between results was 100% in the samples tested. In addition, we compared the COVID-19 positivity between six epidemiological weeks: the initial two in that the Real time RT-PCR reactions were conducted using RNA extracted by commercial kit, followed by two other using RNA obtained by our kit-free method, and the last two using kit once again; they did not differ significantly. We concluded that our in-house method is an easy, fast, and cost-effective alternative method for extracting RNA and conducing molecular diagnosis of COVID-19.

HRSV is one of the most important pathogens causing acute respiratory tract diseases as bronchiolitis and pneumonia among infants. HRSV was isolated from two distinct communities, a public day care center and a public hospital in São José do Rio Preto – SP, Brazil. We obtained partial sequences from G gene that were used on phylogenetic and selection pressure analysis. HRSV accounted for 29% of respiratory infections in hospitalized children and 7.7% in day care center children. On phylogenetic analysis of 60 HRSV strains, 48 (80%) clustered within or adjacent to the GA1 genotype; GA5, NA1, NA2, BA-IV and SAB1 were also observed. SJRP GA1 strains presented variations among deduced amino acids composition and lost the potential O-glycosilation site at amino acid position 295, nevertheless this resulted in an insertion of two potential O-glycosilation sites at positions 296 and 297. Furthermore, a potential O-glycosilation site insertion, at position 293, was only observed for hospital strains. Using SLAC and MEME methods, only amino acid 274 was identified to be under positive selection. This is the first report on HRSV circulation and genotypes classification derived from a day care center community in Brazil.

Cattle babesiosis is a tick-borne disease responsible for significant losses for the livestock industries in tropical areas of the world. These piroplasms are under constant control of the host immune system, which lead to a strong selective pressure for arising more virulent or attenuated phenotypes. Aiming to better understand the most critical genetic modifications in Babesia bovis genome, related to virulence, an in silico analysis was performed using DNA sequences from GenBank. Fourteen genes trap, 18S rRNA, p0, related to parasite infection and immunogenicity and ITS region were selected for alignment and comparison of several isolates of Babesia bovis from different geographic regions around the world. Among the 15 genes selected for the study of diversity, only 7 genes trap, Bv80) and the ITS region presented sufficient genetic variation for the studies of phylogeny. Despite this genetic diversity observed into groups, there was not sufficient information available to associate molecular markers with virulence of isolates. However, some genetic groups no were correlated with geographic region what could indicate some typical evolutionary characteristics in the relation between parasitehost. Further studies using these genes in herds presenting diverse clinical conditions are required. The better understanding of evolutionary mechanisms of the parasite may contribute to improve prophylactic and therapeutic measures. In this way, we suggest that genes used in our study are potential markers of virulence and attenuation and have to be analyzed with the use of sequences from animals that present clinical signs of babesiosis and asymptomatic carriers.

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