Guilherme Pereira Scagion

Avian infectious bronchitis (IB) is a highly contagious viral disease that affects domestic chickens (Gallus gallus domesticus), causing respiratory, renal, and reproductive disorders that result i...

Pigeon paramyxovirus 1 (PPMV-1) comprises pigeon-associated variants of Newcastle disease virus (NDV), predominantly belonging to genotypes VI, XX, and XXI. These viruses have been detected in feral pigeons in Brazil since at least 2014, and an NDV outbreak associated with a pigeon-origin genotype VI virus was reported in commercial broilers in 2024. Here, we characterized two PPMV-1 strains detected in pigeons samples from geographically distinct regions of Brazil. Virus BR/105/21 was detected in Midwestern Brazil, whereas BR/34/22 was detected in Southeastern Brazil. Genome sequencing yielded a complete genome sequence for BR/105/21 (15,192 nt; 100% reference-genome coverage; mean depth, 3334×) and a near-complete genome sequence for BR/34/22 (15,133 nt; 99.5% reference-genome coverage; mean depth, 20.8×). Both viruses possessed the F-protein cleavage-site motif ^113RQKR↓F^117, which is consistent with the molecular criterion for virulent NDV. Phylogenetic analysis based on the complete F-gene coding sequence grouped both viruses with PPMV-1 previously detected in Brazil between 2014 and 2019. Analysis of VI.2.1.2 sequences identified three well-supported phylogenetic groups with between-group nucleotide distances of 6.1–8.0%. Based on established NDV classification criteria, two groups are proposed as VI.2.1.2.1, comprising viruses from Nigeria detected between 2007 and 2015, and VI.2.1.2.2, comprising Brazilian viruses detected between 2014 and 2022 and one virus detected in Argentina in 1997. These findings expand the available genetic data for pigeon-associated NDV in South America and reveal substantial genetic heterogeneity and phylogenetic structure within VI.2.1.2, reinforcing the importance of genomic surveillance of NDV in pigeons.

The SARS-CoV-2 Omicron variant caused a global surge in COVID-19 cases following its emergence in November 2021, rapidly diversifying in the subsequent months. Although many studies have documented Omicron’s diversification, few have explored its impact on pediatric populations or the seasonality of other respiratory viruses in children. This study aims to investigate the diversity and circulation patterns of SARS-CoV-2 Omicron sublineages in pediatric patients in São Paulo, Brazil, and assess their co-circulation with other respiratory pathogens. Respiratory samples collected from patients under 18 years old across five hospitals between January 2022 and April 2023 were tested for different respiratory viruses using real-time RT-PCR. Whole-genome sequencing was performed on SARS-CoV-2-positive samples. Among the 7868 pediatric respiratory samples tested, 3902 were positive for viral pathogens. Respiratory Syncytial Virus accounted for the highest number of positive cases (n = 1248), exhibiting an atypical off-season peak in November 2022. SARS-CoV-2 was detected in 297 samples, of which 103 were sequenced. BA.1 and BA.5 sublineages had predominant genomic diversity and circulation time. These findings highlight the Omicron variant’s significant impact on the epidemiology and seasonal distribution of respiratory viruses in children, emphasizing the ongoing need for vaccination and robust surveillance efforts in pediatric populations.

Background: Chronic cytomegalovirus (CMV) infection may favor the development of immunosenescence and inflammation that impair vaccine responses, including COVID-19. In addition, the polymorphism of the interferon-lambda gene (IFNλ) affects COVID-19 immune responses in older adults. Objective: We aimed to investigate the impact of IFNλ polymorphism (IL28B gene-rs12979860) on the immune/inflammatory response to vaccination with CoronaVac for COVID-19 in older adults who were CMV-seropositive. Methods: Blood samples from 42 CMV-seropositive older adults (73.7 ± 4.5 years) were collected before and 30 days after immunization with a second dose of the CoronaVac vaccine to evaluate the immune/inflammatory response. Results: At genotyping, 20 subjects were homozygous for the C/C alleles (Allele-1 group), 5 were homozygous for the T/T Alleles (Allele-2 group), and 17 were heterozygous (C/T, Alleles-1/2 group). The Allele-1 group showed higher IgG levels for COVID-19 (p = 0.0269) and intermediate monocyte percentage (p = 0.017), in contrast to a lower non-classical monocyte percentage (p = 0.0141) post-vaccination than pre-vaccination. Also, this group showed that IgG levels for CMV were positively associated with a systemic pro-inflammatory state and senescent T cells (CD4+ and CD8+). The Allele-2 group presented higher IFN-β levels at pre- (p = 0.0248) and post-vaccination (p = 0.0206) than the values in the Allele-1 and Alleles-1/2 groups, respectively. In addition, the Allele-2 and Alleles-1/2 groups showed that IgG levels for COVID-19 were positively associated with a balanced systemic inflammatory state. Conclusion: CMV-seropositivity in older adults who had Allele-1 could lead to an unbalanced systemic inflammatory state, which may impair their antibody response to COVID-19 vaccination compared to other volunteer groups.

Influenza A viruses of the H2 subtype represent a zoonotic and pandemic threat to humans due to a lack of widespread specific immunity. Although A(H2) viruses that circulate in wild bird reservoirs are distinct from the 1957 pandemic A(H2N2) viruses, there is concern that they could impact animal and public health. There is limited information on AIVs in Latin America, and next to nothing about H2 subtypes in Brazil. In the present study, we report the occurrence and genomic sequences of two influenza A viruses isolated from wild-caught white-rumped sandpipers (Calidris fuscicollis). One virus, identified as A(H2N1), was isolated from a bird captured in Restinga de Jurubatiba National Park (PNRJ, Rio de Janeiro), while the other, identified as A(H2N2), was isolated from a bird captured in Lagoa do Peixe National Park (PNLP, Rio Grande do Sul). DNA sequencing and phylogenetic analysis of the obtained sequences revealed that each virus belonged to distinct subtypes. Furthermore, the phylogenetic analysis indicated that the genomic sequence of the A(H2N1) virus isolated from PNRJ was most closely related to other A(H2N1) viruses isolated from North American birds. On the other hand, the A(H2N2) virus genome recovered from the PNLP-captured bird exhibited a more diverse origin, with some sequences closely related to viruses from Iceland and North America, and others showing similarity to virus sequences recovered from birds in South America. Viral genes of diverse origins were identified in one of the viruses, indicating local reassortment. This suggests that the extreme South of Brazil may serve as an environment conducive to reassortment between avian influenza virus lineages from North and South America, potentially contributing to an increase in overall viral diversity.

Background: Here, we investigated the impact of IFN-lambda-3 polymorphism on specific IgG responses for COVID-19 in older adults seropositive for CMV. Methods: Blood samples of 25 older adults of both sexes were obtained at three different times: during a micro-outbreak (MO) of SARS-CoV-2 in 2020; eight months after (CURE); and 30 days after the administration of the second dose of ChadOx-1 vaccine (VAC). The specific IgG for both SARS-CoV-2 and CMV antigens, neutralizing antibodies against SARS-CoV-2, and also the polymorphism profile for IFN-lambda-3 (rs12979860 C > T) were assessed. Results: Higher levels of specific IgG for SARS-CoV-2 antigens were found in the MO and VAC than in the CURE time-point. Volunteers with specific neutralizing antibodies against SARS-CoV-2 showed better specific IgG responses for SARS-CoV-2 and lower specific IgG levels for CMV than volunteers without specific neutralizing antibodies. Significant negative correlations between the specific IgG levels for SARS-CoV-2 and CMV were found at the MO time-point, as well as in the group of individuals homozygous for allele 1 (C/C) in the MO time-point and heterozygotes (C/T) in the CURE time-point. Conclusion: Our results suggested that both CMV seropositivity and the homozygosis for allele 1 (C/C) in IFN-lambda-3 gene can negatively impact the antibody response to COVID-19 infection and vaccination in older adults.

Bat coronaviruses (Bat-CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat-CoV surveillance programmes were carried out in the country. Thus, our aim was to jevaluate the Bat-CoV diversity in the Atlantic Forest, the second biome with the highest number of bat species in Brazil. We analysed 456 oral and rectal swabs and 22 tissue samples from Atlantic Forest bats, detecting Alphacoronavirus in 44 swab samples (9.6%) targeting the RdRp gene from seven different bat species, three of which have never been described as Bat-CoV hosts. Phylogenetic analysis of the amino acid (aa) sequences coding the RdRp gene grouped the sequences obtained in our study with Bat-CoV previously detected in identical or congeneric bat species, belonging to four subgenera, with high aa identity (over 90%). The RdRp gene was also detected in three tissue samples from Diphylla ecaudata and Sturnira lilium, and the partial S gene was successfully sequenced in five tissues and swab samples of D. ecaudata. The phylogenetic analysis based on the partial S gene obtained here grouped the sequence of D. ecaudata with CoV from Desmodus rotundus previously detected in Peru and Brazil, belonging to the Amalacovirus subgenus, with aa identity ranging from 73.6% to 88.8%. Our data reinforce the wide distribution of Coronaviruses in bats from Brazil and the novelty of three bats species as Bat-CoV hosts and the co-circulation of four Alphacoronavirus subgenera in Brazil.

Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and hemorrhages were observed in different tissues. Histopathology changes with infiltration of mononuclear inflammatory cells were also found in the brain, kidney, proventriculus, heart, and spleen. NDV staining was detected by immunohistochemistry. Twenty-seven out of thirty-four tested samples (swabs and tissues) were positive for Newcastle disease virus by RT-qPCR test, targeting the M gene. One isolate, obtained from a pool of positive swab samples, was characterized by the intracerebral pathogenicity index (ICPI) and the hemagglutination inhibition (HI) tests. This isolate had an ICPI of 0.99, confirming a virulent NDV strain. The monoclonal antibody 617/161, which recognizes a distinct epitope in pigeon NDV strains, inhibited the isolate with an HI titer of 512. A complete genome of NDV was obtained using next-generation sequencing. Phylogenetic analysis based on the complete CDS F gene grouped the detected isolate with other viruses from subgenotype VI.2.1.2, class II, including one previously reported in Southern Brazil in 2014. This study reports a comprehensive characterization of the subgenotype VI.2.1.2, which seems to have been circulating in Brazilian urban areas since 2014. Due to the zoonotic risk of NDV, virus surveillance in feral pigeons should also be systematically performed in urban areas.

Background CoronaVac is an inactivated SARS-CoV-2 vaccine that has been rolled out in several low and middle-income countries including Brazil, where it was the mainstay of the first wave of immunization of health care workers and the elderly population. We aimed to assess the T cell and antibody responses of vaccinees as compared to convalescent subjects. Methods We detected IgG against SARS-CoV-2 antigens, neutralizing antibodies against the original SARS-CoV-2 strain, and used SARS-CoV-2 peptides to detect IFN-g and IL-2 specific T cell responses in a cohort of CoronaVac vaccinees (N=101) and convalescent (N=72) individuals. Findings Among vaccinees, 95% displayed T cell or antibody responses to SARS-CoV-2 as compared to 99% convalescent individuals. However, we observed that among vaccinees, males and individuals 55 years or older developed significantly lower anti-RBD, anti-NP and neutralizing antibody responses as well as antigen-induced IL-2 production by T cells. Interpretation Even though some studies indicated Coronavac helped reduce mortality among elderly people, considering the current dominance of the gamma variant of concern (VOC) and potential increase of the delta VOC, in Brazil, our data support that Coronavac vaccinees above 55 years old Coronavac vaccinees above 55 years old could benefit from a heterologous third dose/booster vaccine to improve immune response and protection. Funding Brazilian Ministry for Science, Technology and Innovation, Sao Paulo State Foundation for Scientific research (FAPESP), JBS S.A.

Canine mammary carcinoma (CMC) is one of the major health threats in dogs. The oncolytic virotherapy is a promising strategy to treat canine as well as human cancer patients with non‐pathogenic replicating viruses. Here, we evaluated the antitumor activity of one lentogenic, non‐lytic Newcastle disease virus (NDV) LaSota strain expressing GFP (NDV‐GFP) on five different CMCs and one non‐tumorigenic cell line, regarding cell viability, cell death, selectivity index, morphology, global and target gene expression analysis. As evidenced by the selectivity index, all CMC cell lines were more susceptible to NDV‐GFP in comparison with the non‐tumorigenic cells (~3.1× to ~78.7×). In addition, the oncolytic effect of NDV‐GFP was more evident in more malignant CMC cells. Also, we observed an inverse association of the IFN pathway expression and the susceptibility to NDV. The downregulated genes in NDV‐GFP‐sensitive cells were functionally enriched for antiviral mechanisms by interferon and immune system pathways, demonstrating that these mechanisms are the most prominent for oncolysis by NDV. To our knowledge, this is the first description of oncolysis by an NDV strain in canine mammary cancer cells. We also demonstrated specific molecular pathways related to NDV susceptibility in these cancer cells, opening the possibility to use NDV as a therapeutic‐targeted option for more malignant CMCs. Therefore, these results urge for more studies using oncolytic NDVs, especially considering genetic editing to improve efficacy in dogs.