Doris Sobral Marques Souza

Since December 2019, the COVID-19 pandemic caused by SARS-CoV-2 has reached approximately 769 million people, leading to more than 7 million deaths worldwide. Faced with the possibility of other respiratory pathogens co-infecting patients and modifying their clinical response to SARS-CoV-2, some researchers have explored this line of investigation. The relationship between these co-infections remains unclear, underscoring the need to deepen our understanding of interactions among pathogens and between pathogens and the host. Thus, the present study employed RT-qPCR to assess the presence of Human Adenovirus (HAdV), Influenza A (Flu A), Influenza B (Flu B), Human Metapneumovirus (HMPV), Respiratory Syncytial Virus (RSV), Human Rhinovirus (HRV), and Parainfluenza Virus (PIV). Nasopharyngeal samples (187) from adult patients exhibiting respiratory symptoms were collected between February 2021 and November 2022 at the University Hospital Polydoro Ernani de São Thiago in Florianópolis, SC, Brazil. The present findings revealed that 25.16% of samples tested positive for non-SARS-CoV-2 respiratory viruses (29.8%—HRV; 5.3%—PIV; 4.3%—RSV; and 1.1%—HMPV). In the 74.84% of SARS-CoV-2-positive patients, co-infection was observed in 9.7% of patients, with 7.5% being HRV, 1.1% HAdV, and 1.1% Influenza A. Since co-infections can potentially alter patient prognoses and impact local epidemiological dynamics, this study highlights the significance of ongoing monitoring and epidemiological assessment through genomic surveillance of other clinically relevant respiratory pathogens.

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, one of the main diseases leading to economic losses in industrial poultry farming due to high morbidity and mortality and its role in the condemnation of chicken carcasses. This study aimed to isolate and characterize APEC obtained from necropsied chickens on Brazilian poultry farms. Samples from birds already necropsied by routine inspection were collected from 100 batches of broiler chickens from six Brazilian states between August and November 2021. Three femurs were collected per batch, and characteristic E. coli colonies were isolated on MacConkey agar and characterized by qualitative PCR for minimal predictive APEC genes, antimicrobial susceptibility testing, and whole genome sequencing to identify species, serogroups, virulence genes, and resistance genes. Phenotypic resistance indices revealed significant resistance to several antibiotics from different antimicrobial classes. The isolates harbored virulence genes linked to APEC pathogenicity, including adhesion, iron acquisition, serum resistance, and toxins. Aminoglycoside resistance genes were detected in 79.36% of isolates, 74.6% had sulfonamide resistance genes, 63.49% showed β-lactam resistance genes, and 49.2% possessed at least one tetracycline resistance gene. This study found a 58% prevalence of avian pathogenic E. coli in Brazilian poultry, with strains showing notable antimicrobial resistance to commonly used antibiotics.

Since December 2019, the COVID-19 pandemic caused by SARS-CoV-2 has reached approximately 769 million people, leading to more than 7 million deaths worldwide. Faced with the possible presence of other respiratory pathogens that could co-infect and modify the clinical response of patients detected for SARS-CoV-2, some researchers have explored this line of investigation. The relationship between these co-infections remains unclear, leading to a need to deepen our knowledge about interactions among pathogens, and between pathogens and the host. Thus, the present study employed RT-qPCR to assess the presence of Human Adenovirus (HAdV), Influenza A (Flu A), Influenza B (Flu B), Human Metapneumovirus (HMPV), Respiratory Syncytial Virus (RSV), Human Rhinovirus (HRV), and Parainfluenza Virus (PIV). A total of 187 nasopharyngeal samples from adult patients exhibiting respiratory symptoms were collected between February 2021 and November 2022 at the University Hospital Polydoro Ernani de Sao Thiago in Florianopolis, SC, Brazil. Our findings revealed that 25.16% of samples tested positive for non-SARS-CoV-2 respiratory viruses (29.8% - HRV, 5.3% - PIV, 4.3%-RSV, and 1.1% - HMPV). From the 74.84% of SARS-CoV-2 positive patients, the presence of co-infection was observed in 9,7% of patients, with 7.5% being HRV, 1.1% HAdV and 1.1% Flu A. Since co-infections can potentially alter patient prognoses and impact local epidemiological dynamics, this study highlights the significance of ongoing monitoring and epidemiological assessment through genomic surveillance of other clinically relevant respiratory pathogens.

SARS-CoV-2 genome surveillance is important for monitoring risk groups and health workers as well as data on new cases and mortality rate due to COVID-19. We characterized the circulation of SARS-CoV-2 variants from May 2021 to April 2022 in the state of Santa Catarina, southern Brazil, and evaluated the similarity between variants present in the population and healthcare workers (HCW). A total of 5291 sequenced genomes demonstrated the circulation of 55 strains and four variants of concern (Alpha, Delta, Gamma and Omicron—sublineages BA.1 and BA.2). The number of cases was relatively low in May 2021, but the number of deaths was higher with the Gamma variant. There was a significant increase in both numbers between December 2021 and February 2022, peaking in mid-January 2022, when the Omicron variant dominated. After May 2021, two distinct variant groups (Delta and Omicron) were observed, equally distributed among the five Santa Catarina mesoregions. Moreover, from November 2021 to February 2022, similar variant profiles between HCW and the general population were observed, and a quicker shift from Delta to Omicron in HCW than in the general population. This demonstrates the importance of HCW as a sentinel group for monitoring disease trends in the general population.

O surgimento de patógenos ao longo da história evolutiva que utilizam vias ambientais de infecção/contaminação denotou a necessidade das ferramentas de monitoramento. Em meio a pandemia de COVID-19, causada pelo vírus SARS-CoV-2, a detecção do RNA viral no esgoto bruto tornou-se possível e útil como uma ferramenta epidemiológica, já que o vírus é excretado pelas fezes humanas. Métodos focados na detecção do RNA viral (técnicas baseadas em biologia molecular) e de partículas virais infecciosas (por cultura celular) foram utilizados para a detecção do SARS-CoV-2 em amostras de secreção de pacientes infectados. O monitoramento se mostra eficaz para compreender a circulação de vírus que utilizam rota fecal-oral, podendo antecipar futuros surtos em regiões específicas. Além disso, possibilita a observação das mutações e variantes em circulação num dado momento, através do sequenciamento. Este capítulo é um reporte das bases da ferramenta epidemiológica para o monitoramento viral em esgoto sanitário implementada pelo Laboratório de Virologia Aplicada da Universidade Federal de Santa Catarina, denominado “VigEAI” - Vigilância Epidemiológica Ambiental Integrativa.

Oysters are filter-feeders and retain sewage-derived pathogens in their organs or tissues. Since most enteric viruses involved in outbreaks cannot grow in cell culture, studies using viral surrogate models are essential. Some species are proposed as surrogates for enteric viruses in environmental samples, including in bivalve mollusk samples, such as murine norovirus type 1 (MNV-1) and somatic (as φX) or F-specific coliphages (as MS2) bacteriophages. This study evaluated the tissue distribution of viral surrogates for enteric virus contamination after their bioaccumulation by Crassostrea gigas. Oyster tissues were analyzed for the distribution of viral surrogates (MNV-1, φX-174, and MS2) in digestive tissue (DT), gills (GL), and mantle (MT) after 4, 6, and 24 h of experimental bioaccumulation. MNV-1 had higher counts at 6 h in DT (1.2 × 10³ PFU/g), followed by GL and MT (9.5 × 10² and 3.8 × 10² PFU/g, respectively). The bacteriophage φX-174 had a higher concentration in the MT at 4 and 6 h (3.0 × 10² PFU/g, in both) and MS2 in the GL after 24 h (2.2 × 10² PFU/g). The bioaccumulation pattern of MNV-1 by oysters was similar to the other enteric viruses (more in DT), while that of phages followed distinct patterns from these. Since the MNV-1 is bioaccumulated by C. gigas and is adapted to grow in cell culture, it is an important tool for bioaccumulation and viral inactivation tests in oysters. Although bacteriophage bioaccumulation was not similar to enteric viruses, they can be indicated for viral bioaccumulation analysis, analyzing MT and GL, since they do not bioaccumulate in DT.

Esta revisão resume os achados de estudos realizados em Santa Catarina (SC) sobre redução de patógenos em moluscos por meio de tratamentos pós-colheita. Estudos indicam que os níveis de Salmonella e Vibrio spp. de ocorrência natural podem ser eficientemente reduzidos em ostras por meio de ciclos de depuração de 48h, enquanto vírus (hepatite A e norovírus murino) requerem mais de 48 horas para serem completamente inativados. Protozoários (Cryptosporidium e Giardia) não foram eliminados pelos protocolos de depuração testados. O protocolo de tratamento térmico adotado nas indústrias locais (cozimento a vapor durante 6 min a 100ºC) é capaz de eliminar Vibrio spp. de mexilhões e norovírus murino de ostras. Apesar de algumas limitações, a adoção desses tratamentos pós-colheita é uma estratégia importante para melhorar a segurança dos moluscos em SC.

Os vírus entéricos são vírus não envelopados que se replicam no trato gastrointestinal e apresentam transmissão fecal-oral. Estão, portanto, associados às más condições de saneamento básico e controles sanitários. As infecções por vírus entéricos podem causar enfermidades em indivíduos susceptíveis, principalmente crianças com idade inferior aos dez anos. Estas enfermidades estão associadas ao consumo de água e alimentos contaminados devido ao descarte inadequado de esgotos e águas residuais. A legislação brasileira não inclui a análise de vírus entéricos para determinar a qualidade da água, apenas padrões bacterianos, recomendando a análise de vírus apenas em caso de surtos de veiculação hídrica. Os vírus entéricos, por terem característica proteica e serem não-envelopados permanecem com capacidade infecciosa no ambiente, mesmo em contato com cloro, salinidade e aumentos de temperatura. Neste sentido, o presente capítulo apresenta uma introdução aos vírus entéricos, destacando sua presença em águas, alimentos e em efluentes de humanos e animais, considerando a necessidade do seu monitoramento para fins de segurança sanitária.

The western mesoregion of the state of Santa Catarina (SC), Southern Brazil, was heavily affected as a whole by the COVID-19 pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state from March 2020 to April 2021 using genomic surveillance. During this period, there were 23 distinct variants, including Beta and Gamma, among which the Gamma and related lineages were predominant in the second pandemic wave within SC. A regionalization of P.1-like-II in the Western SC region was observed, concomitant to the increase in cases, mortality, and the case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 transmission in SC and it highlights the importance of tracking the variants, dispersion, and impact of SARS-CoV-2 on the public health systems.

The Western mesoregion, the State of Santa Catarina (SC), Southern Brazil, was heavily affected as a whole by the COVID-19 pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state through March 2020 to April 2021 using genomic surveillance. During this period, 23 distinct variants, including Beta and Gamma, among which, the Gamma and related lineages were predominant in the second pandemic wave within SC. A regionalization of P.1-like-II in the Western-SC region was observed, concomitant to the increase in cases, mortality, and case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 in SC transmission and highlights the importance of tracking variants, dispersion, and impact of SARS-CoV-2 on the public health systems.