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

Abstract

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

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.06.19.660416v1

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#Neuroinvasive #Oropouche virus in a patient with #HIV from extra-Amazonian #Brazil

{Excerpt} A novel reassortant Oropouche virus (OROV) lineage (with medium [M], large [L], and small [S] RNA segments : M1L2S2) has driven Brazil's largest and most geographically widespread OROV epidemic , expanding beyond the endemic Amazon basin to establish local transmission across multiple Brazilian states and other previously unaffected Latin American countries . The rapid spread of this lineage underscores its evolutionary potential and reinforces its significance as a public health threat .1 Similar to chikungunya and Zika viruses, expanding arboviruses can exhibit unexpected clinical and epidemiological shifts , including vertical transmissions , neuroinvasive effects, and potentially fatal outcomes.2–4 Although OROV typically causes self-limited febrile illness, accumulating clinical and experimental evidence suggests neurotropic potential .5 This Correspondence describes the first confirmed case of neuroinvasive OROV infection caused by the emergent M1L2S2 lineage in ext...

Stability of #influenza viruses in the #milk of #cows and #sheep

Abstract In late 2023, H5N1 high pathogenicity avian influenza (HPAIV) started circulating in dairy cattle in the USA . High viral titres were detected in milk from infected cows , raising concerns about onwards human infections . Although pasteurisation was shown to effectively inactivate influenza viruses in milk, unpasteurised milk still poses a risk of infection, both from occupational exposure in dairies and from the consumption of raw milk. We therefore assessed how long influenza viruses could remain infectious for in milk without heat inactivation. We examined the stability of a panel of influenza viruses in milk , including a contemporary H5N1 HPAIV and a variety of other influenza A and D viruses. We incubated viruses in cows' milk under laboratory conditions : at room temperature to simulate exposure in dairies and at 4°C to simulate exposure to refrigerated raw milk. Following an isolated report of H5N1 viral RNA being detected in milk from a sheep in the UK , we also c...

#Evidence of #Viremia in Dairy #Cows Naturally Infected with #Influenza A {#H5N1} Virus, #California, #USA

Abstract We confirmed influenza A virus (IAV) by PCR in serum from 18 cows on 3 affected dairy farms in California, USA . Our findings indicate the presence of viremia and might help explain IAV transmission dynamics and shedding patterns in cows. An understanding of those dynamics could enable development of IAV mitigation strategies. Source: US Centers for Disease Control and Prevention, https://wwwnc.cdc.gov/eid/article/31/7/25-0134_article ____

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