Scavengers as Prospective Sentinels of Viral Diversity: the Snowy Sheathbill Virome as a Potential Tool for Monitoring Virus Circulation, Lessons from Two Antarctic Expeditions

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Until recent events, the Antarctic was the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) had never previously been detected. Here we report on the detection of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands, respectively. We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8th October 2023. Since this detection, mortalities were observed in several avian and mammalian species at multiple sites across South Georgia. Subsequent testing confirmed H5N1 HPAIV across several sampling locations in multiple avian species and two seal species. Simultaneously, we also confirmed H5N1 HPAIV in southern fulmar and black-browed albatross in the Falkland Islands. Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Critically, genetic assessment of sequences from mammalian species demonstrates no increased risk to human populations above that observed in other instances of mammalian infections globally. Here we describe the detection, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region. We also speculate on the threat to specific populations following recent reports in the area.

An innovative approach for low input forensic DNA sample analysis using the GlobalFiler™ IQC PCR amplification Kit on the Magelia® platform

Short Tandem Repeat (STR) markers have been the gold standard for human identification testing in the forensic field for the last few decades. The GlobalFiler™ IQC PCR amplification Kit has shown sensitivity, high power of discrimination and is therefore widely used. Samples with limited DNA quantities remain a significant hurdle for streamlined human forensic identification. Reaction volume reduction in a closed system paired with automation can provide solutions to secure DNA profiles when routine methods fall short. We automated and optimized the GlobalFilerTM IQC PCR Amplification Kit on the Magelia®, a closed molecular biology platform, to test whether reaction volume reduction in a confined automated system would improve signal and sensitivity. We evaluated the platform's performance using reference and real casework samples (blood, cigarette butt, saliva and touch DNA) in the context of a 5-fold volume reduction when compared to the routine protocol. This strategy showed distinct advantages over standard treatment, notably increased signal for lower DNA inputs. Importantly, negative casework samples through routine treatment yielded "usable" DNA profiles after amplification using this strategy. This novel approach represents a first proof of concept for a method enabling users to treat limited samples, or to partition routine samples for multiple analyses.

Metagenomic comparison of gut communities between wild and captive Himalayan griffons

Introduction

Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited.

Methods

In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions.

Results

Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs).

Discussion

In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.

Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife

Before December 2020, Antarctica had remained free of COVID-19 cases. The main concern during the pandemic was the limited health facilities available at Antarctic stations to deal with the disease as well as the potential impact of SARS-CoV-2 on Antarctic wildlife through reverse zoonosis. In December 2020, 60 cases emerged in Chilean Antarctic stations, disrupting the summer campaign with ongoing isolation needs. The SARS-CoV-2 RNA was detected in the wastewater of several scientific stations. In Antarctica, treated wastewater is discharged directly into the seawater. No studies currently address the recovery of infectious virus particles from treated wastewater, but their presence raises the risk of infecting wildlife and initiating new replication cycles. This study highlights the initial virus detection in wastewater from Antarctic stations, identifying viral RNA via RT-qPCR targeting various genomic regions. The virus's RNA was found in effluent from two wastewater plants at Maxwell Bay and O'Higgins Station on King George Island and the Antarctic Peninsula, respectively. This study explores the potential for the reverse zoonotic transmission of SARS-CoV-2 from humans to Antarctic wildlife due to the direct release of viral particles into seawater. The implications of such transmission underscore the need for continued vigilance and research.

Active surveillance for influenza virus and coronavirus infection in Antarctic birds and mammals in environmental fecal samples, South Shetland Islands

Numerous Antarctic species are recognized as reservoirs for various pathogens, and their migratory behavior allows them to reach the Brazilian coast, potentially contributing to the emergence and circulation of new infectious diseases. To address the potential zoonotic risks, we conducted surveillance of influenza A virus (IAV) and coronaviruses (CoVs) in the Antarctic Peninsula, specifically focusing on different bird and mammal species in the region. During the summer of 2021/2022, as part of the Brazilian Antarctic Expedition, we collected and examined a total of 315 fecal samples to target these respiratory viruses. Although we did not detect the viruses of interest during this particular expedition, previous research conducted by our team has shown the presence of the H11N2 subtype of influenza A virus in penguin fecal samples from the same region. Given the continuous emergence of new viral strains worldwide, it is crucial to maintain active surveillance in the area, contributing to strengthening integrated One Health surveillance efforts.