Biology subjects

Resende, P. C.

Publications and source records attributed to Resende, P. C..

10 recordsLinked to original sources

bioRxiv2026

Discovery of two potential new species and two novel bat-coronavirus subgenera (Phyllacovirus and Phyllobecovirus) in the Neotropics

Bats are major natural reservoirs for coronaviruses, yet complete viral genomes from South America remain scarce, limiting evolutionary and taxonomic understanding. Here, we conducted metatranscriptomic sequencing of coronavirus-positive bat samples collected across two ecologically distinct Brazilian biomes: the Atlantic Forest and the semi-arid Caatinga. We recovered seven complete or near-complete genomes belonging to Alphacoronavirus and Betacoronavirus. Phylogenetic and comparative similarity analyses of conserved replicase domains (3CLpro, NiRAN, RdRp, ZBD, HEL1), following International Committee on Taxonomy of Viruses (ICTV) demarcation criteria, revealed significant viral diversity. Within Alphacoronavirus, two genomes from Atlantic Forest phyllostomid bats (Artibeus lituratus and Carollia perspicillata) formed a deeply divergent sister lineage to Amalacovirus, exhibiting a mean amino acid similarity of 76.7% with the reference genome. Within Betacoronavirus, one genome from a Caatinga phyllostomid bat (Artibeus planirostris) clustered within the recently described Ambecovirus clade, displaying 75.9% mean amino acid similarity with mormoopid-associated reference sequences. Based on these divergence levels and non-recombinant genomic architectures, we propose two novel candidate subgenera, Phyllacovirus and Phyllobecovirus, alongside potential novel viral species. Furthermore, our findings demonstrate strong host-associated structuring and biogeographical partitioning of viral lineages across Neotropical biomes. Overall, this study expands the genomic landscape of South American bat coronaviruses and underscores the importance of continuous genomic surveillance at human-wildlife interfaces.

genomics↗

bioRxiv2025

Genomics insights reveal multi-year maintenance of a new Deltacoronavirus infecting Seabirds from the Cagarras Island Archipelago Natural Monument, Brazil

Previous studies have identified various pathogens in seabirds, notably coronaviruses (CoVs) and influenza A viruses (IAVs), due to their potential to cause significant morbidity and mortality. The Cagarras Island Archipelago Natural Monument, located near Rio de Janeiro, Brazil, serves as nesting site for two species, the magnificent frigatebird (Fregata magnificens) and the brown booby (Sula leucogaster). Despite its ecological importance, no prior studies have investigated viral infections in these species, which share habitat interfaces with densely populated human areas. To address this gap, we sampled and tested seabirds for CoVs and IAVs from January 2022 to April 2024. Birds were captured and identified by species, age, and sex. Oropharyngeal and cloacal swabs, as well as blood samples, were collected. Viral RNA was extracted using the QIAamp Viral RNA Mini Kit, and the presence of IAVs was screened via real-time RT-PCR, while CoVs were screened using semi-nested RT-PCR. Sanger and metatranscriptomic sequencing were performed to identify viral strains and assess phylogenetic relationships. Of the 153 seabirds sampled, CoVs were detected in 6 individuals (9.1%) of F. magnificens and 16 individuals (18.4%) of S. leucogaster. No IAVs were found in either oropharyngeal or cloacal swabs, and all serum samples were negative for the presence of antibodies against the virus. We recovered two full deltacoronavirus genomes and eight additional draft genomes from S. leucogaster samples obtained from distinct sampling expeditions and additional enteroviruses, passeriviruses, and picornaviruses. Phylogenetic analysis revealed that the detected CoVs are closely related to avian deltacoronaviruses from environmental samples of S. leucogaster in the Sao Pedro and Sao Paulo Archipelago, indicating potential viral exchange between these seabird populations living at these distant islands. Moreover, multiple detections in different individuals at different time points are associated with specific Spike NTD deletions that have been shown to accumulate in immune escape lineages, supporting the long-term maintenance through new infections and reinfection of this virus in these bird populations. This is the first detection of CoVs in F. magnificens, highlighting their circulation in marine ecosystems. Further research is needed to understand the ecological and epidemiological implications, including potential cross-species transmission.

microbiology↗

bioRxiv2024

High Pathogenicity Avian Influenza Virus (HPAIV) H5N1 clade 2.3.4.4b recovered from a kelp gull (Larus dominicanus) in the South Shetland Islands, Antarctica

Whole-genome analysis of the earliest-detected High Pathogenicity Avian Influenza Virus (HPAIV) H5N1 clade 2.3.4.4b detected in Hannah Point, Antarctica (January 2024) reveals close relatedness to strains that circulated in pinnipeds and seabirds along the Atlantic coast of South America during the second half of 2023.

molecular biology↗

bioRxiv2024

Detection of Deltacoronavirus in Environmental Fecal Samples from Seabirds in the Saint Peter and Saint Paul Archipelago, central equatorial Atlantic Ocean

This study investigates the presence of avian coronaviruses (CoVs), influenza A viruses (IAVs), and Avian rotaviruses (RVs) group A in seabird populations inhabiting the Saint Peter and Saint Paul Archipelago (SPSPA), an isolated and remote oceanic island situated in the equatorial region of the Atlantic Ocean. In July 2022, 95 environmental fecal samples were collected from seabird colonies and screened for the viruses by quantitative one-step real-time RT-PCR (IAVs and RVs), by the conventional pancoronavirus RT-PCR protocols and metatranscriptomics of a positive sample. Four environmental feces samples tested positive for CoVs. Avian IAVs and RVs were not detected. Phylogenetic analysis revealed CoVs closely related to avian deltacoronaviruses previously identified in waterbirds from Asia and Australia. We could not recover the CoV by metatranscriptomics but we recovered a single viral contig of an avian enterovirus. The findings contribute valuable insights into virus dynamics among seabird populations, laying the groundwork for future investigations in this field.

molecular biology↗

bioRxiv2024

Detection and full genome sequencing of a Deltacoronavirus and other bird associated viruses from feces of the kelp gull (Larus dominicanus) sampled at the South Shetland Islands Antarctica.

Bird species are known to be the main reservoir of a range of respiratory viruses such as Influenza, Newcastle and Coronaviruses. Migratory birds are particularly important for the maintenance and long distance spread of the virus to wild bird and poultry species but eventually to mammal species as well. Antarcticas pristine environment and wildlife is of immense biological value, but the spread of such deadly viruses pose a substantial threat to the regions fragile ecosystems. To investigate the presence of respiratory viruses in the region we sampled feces of different wild migratory birds at various localities in the South Shetland Islands in the Antarctic summer of 2023 and screened them for coronaviruses (CoVs) and influenza A virus (IAV). Viral screening was performed by the conventional pancoronavirus RT-PCR protocol (CoVs), by quantitative one-step real-time RT-PCR (IAVs) followed by metatranscriptomic sequencing of positive samples. During January and February of 2023, we collected and examined a total of 243 fecal samples representing Stercorarius spp (N=5), Larus dominicanus (N=16), Phalacrocorax bransfieldensis (N=3), Pygoscelis adeliae (N=19), Pygoscelis antarcticus (N=38), Pygoscelis papua (N=139), Pygoscelis spp (N=23). All tested samples were negative for influenza A and one sample from the colony of L. dominicanus at Keller Peninsula, King George Island, tested positive for CoVs. Metatranscriptomic sequencing recovered a full deltaCoV genome. Nucleotide and amino acid distance analysis revealed that the deltacoronavirus detected belongs to subgenus Buldecovirus and to the novel wild bird deltaCoV clade previously identified infecting Antarctica penguins. The identified deltaCov is most closely related to a deltacoronavirus previously identified 2014 in P. papua penguin sampled at Isla Kopaitik, Base OHiggin suggesting a potential cross species transmission. The presence of CoVs in Antarctic migratory seabirds raises concerns about their impact on the wild bird population in Antarctica and their potential role in virus dispersion through intra and intercontinental migratory routes. These findings contribute valuable insights into virus dynamics among seabird populations, laying the groundwork for future investigations in this field and warning of the importance of viral surveillance on the Antarctic fauna. RepositoriesThe raw reads were submitted to NCBI Sequence Read Archive (SRA) database and are available under project number: PRJNA1160912 and Run Accessions: SRR30664529 and SRR30664530. Impact statementThis study provides insights into the presence of respiratory viruses, specifically coronaviruses (CoVs), in Antarctic seabirds. By detecting a novel wild bird deltacoronavirus in gulls population in the South Shetland Islands, our research contributes to the growing body of literature on viral transmission in remote ecosystems. The findings highlight the potential of migratory birds to act as reservoirs and vectors of viruses in the Antarctic region and underscores the urgent need for continued viral surveillance.

genomics↗

bioRxiv2024

Unique RNA replication characteristics and nucleocapsid protein expression may explain differences in the replication capacity of SARS-COV-2 lineages.

COVID-19 pandemic in Brazil was characterized by the sequential circulation of the SARS-CoV-2 lineages B.1.1.33, and variants Zeta (P.2), Gamma (P.1/P.1.*), Delta (B.1.617.2/AY.*), and Omicron (BA.*). Our research aimed to compare the biological traits of these lineages and variants by analyzing aspects of viral replication including binding, entry, RNA replication, and viral protein production. We demonstrated that the replication capacity of these variants varies depending on the cell type, with Omicron BA.1 exhibiting the lowest replication in the human pulmonary cells. Additionally, the nucleocapsid proteoforms generated during infection exhibit distinct patterns across variants. Our findings suggest that factors beyond the initial stages of virus entry influence the efficiency of viral replication among different SARS-CoV-2 variants. Thus, our study underscores the significance of RNA replication and the role of nucleocapsid proteins in shaping the replicative characteristics of SARS-CoV-2 variants. Author summaryThe COVID-19 pandemic was characterized by the emergence of different viral variants that presents specific properties such as response to antibodies, pathogenicity and detection by diagnostic tests. The circulation of these variants presented a particular pattern depending on the global geographic regions. Despite the cessation of the pandemic, as officially declared by the World Health Organization in 2023, new viral variants continue to emerge while aspects of the virus-cell interaction that contribute to the replication of these variants have not yet been completely understood. In our study, we compared the biological characteristics of SARS-CoV-2 variants that circulated in Brazil during the pandemic, verifying aspects of entry, viral replication and production of viral RNA and proteins. Our results indicate that Omicron BA.1 variant has reduced replication and protein production in human lung cells. We also observed that the viral nucleocapsid protein presents proteoforms that vary according to the variant. These differences could help to explain the differences observed in viral replication in human pulmonary cells.

microbiology↗

bioRxiv2022

Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. This could result in the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of Spike gene (S). The 5' genome portion (circa 22 kb) resembles the AY.101 lineage (VOC Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 lineage (VOC Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, named AYBA-RS, is one out of almost 30 recombinants described this year. The submission of only four sequences in the GISAID database suggests that this Brazilian lineage had a minor epidemiological impact. On the other hand, the recent emergence of this and various other Deltacron recombinant lineages (i.e., XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that support this assertion, and we conclude that this stresses the need for continued genomic and epidemiological surveillance. This is particularly important for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.

evolutionary biology↗

bioRxiv2021

A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil

The SARS-CoV-2 epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. Two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved within lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North and Northeast regions.

microbiology↗

bioRxiv2020

Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil

Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil.

evolutionary biology↗

bioRxiv2020

SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms

Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger.

molecular biology↗