Cryptococcus neoformans and Other Opportunistic Cryptococcus Species in Pigeon Dropping in Saudi Arabia: Identification and Characterization by DNA Sequencing

The prevalent variants of Cryptococcus neoformans, and other Cryptococcus species in pigeon excreta in Western Region of Saudi Arabia were studied. Ninety pigeon dropping samples were plated directly on Niger seed agar, and suspected colonies were sequenced using Illumina MiSeq. Species identification was determined using sequence read mapping to reference genomes of the two C. neoformans variants. In addition, sequence reads were identified using the KmerFinder tool. internal transcribed spacer 2 in the rDNA was also used for fungal barcoding of none of the C. neoformans species using two fungal identification databases. Phylogeny was studied using CSI Phylogeny (Center for Genomic Epidemiology, Denmark). The C. neoformans var. grubii mitochondrion and chromosome 1 reference sequences (accession numbers NC_004336.1 and CP022321.1, respectively) were used for sequence comparison and variant calling. Fifteen Cryptococcus isolates were isolated, 11 were identified as C. neoformans var. grubii, and 4 were found to be other opportunistic Cryptococcus species. Phylogeny analysis of C. neoformans var. grubii isolates showed a high degree of similarity between the C. neoformans isolates especially at the mitochondrial genome level. This study supports the fact that pathogenic and opportunistic Cryptococcus species are prevalent in domestic bird excreta which is an easy source of infection in the susceptible population.

Detection of a novel enterotropic Mycoplasma gallisepticum-like in European Starling (Sturnus vulgaris) around poultry farms in France

Recent outbreaks of highly pathogenic avian influenza in southwest France have raised questions regarding the role of commensal wild birds in the introduction and dissemination of pathogens between poultry farms. To assess possible infectious contacts at the wild-domestic bird interface, the presence of Mycoplasma gallisepticum (MG) was studied in the two sympatric compartments in southwest France. Among various peridomestic wild birds (n=385), standard PCR primers targeting the 16S rRNA of MG showed a high apparent prevalence (up to 45%) in cloacal swabs of European starlings (Sturnus vulgaris, n=108), while the MG-specific mgc2 gene was not detected. No tracheal swab of these birds tested positive, and no clinical sign was observed in positive birds, suggesting commensalism in the digestive tract of starlings. A mycoplasma strain was then isolated from a starling swab and its whole genome was sequenced using both Illumina and Nanopore technologies. Phylogenetic analysis showed that it was closely related to MG and M. tullyi, although it was a distinct species. A pair of specific PCR primers targeting the mgc2-like gene of this MG-like strain was designed and used to screen again the same avian populations and a wintering urban population of starlings (n=50). Previous PCR results obtained in starlings were confirmed to be mostly due to this strain (20/22 positive pools). In contrast, the strain was not detected in fresh faeces of urban starlings. Furthermore, it was detected in one tracheal pool of cattle egrets and one cloacal pool of white wagtails, suggesting infectious transmissions between synanthropic birds with similar feeding behaviour. As the new starling mycoplasma was not detected in free-range ducks (n=80) in close contact with positive starlings, nor in backyard (n=320) and free-range commercial (n=720) chickens of the area, it might not infect poultry. However, it could be involved in mycoplasma gene transfer in such multi-species contexts.

Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology

Avian influenza is one of the largest known threats to domestic poultry. Influenza outbreaks on poultry farms typically lead to the complete slaughter of the entire domestic bird population, causing severe economic losses worldwide. Moreover, there are highly pathogenic avian influenza (HPAI) strains that are able to infect the swine or human population in addition to their primary avian host and, as such, have the potential of being a global zoonotic and pandemic threat. Migratory birds, especially waterfowl, are a natural reservoir of the avian influenza virus; they carry and exchange different virus strains along their migration routes, leading to antigenic drift and antigenic shift, which results in the emergence of novel HPAI viruses. This requires monitoring over time and in different locations to allow for the upkeep of relevant knowledge on avian influenza virus evolution and the prevention of novel epizootic and epidemic outbreaks. In this review, we assess the role of migratory birds in the spread and introduction of influenza strains on a global level, based on recent data. Our analysis sheds light on the details of viral dissemination linked to avian migration, the viral exchange between migratory waterfowl and domestic poultry, virus ecology in general, and viral evolution as a process tightly linked to bird migration. We also provide insight into methods used to detect and quantify avian influenza in the wild. This review may be beneficial for the influenza research community and may pave the way to novel strategies of avian influenza and HPAI zoonosis outbreak monitoring and prevention.

Highly Pathogenic Avian Influenza Viruses at the Wild–Domestic Bird Interface in Europe: Future Directions for Research and Surveillance

Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks—in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996—have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.

Adaptive evolution of interferon induced protein with tetratricopeptide repeats 5(IFIT5) in birds

Background : Previous studies have revealed that wild birds are reservoirs and mobile vectors of viruses, many of which cause illness and mortality in domestic bird and humans. In birds, the invasion of viruses will quickly trigger the innate immune mechanism induced by interferon (IFN). As IFN-stimulated genes (ISGs), the IFIT gene family plays an important role in innate immunity. However, only IFIT5 of the IFIT gene family exists in birds, and the direction and strength of selection acting on IFIT5 are largely unknown. Results : Here, we studied the selection on IFIT5 based on the coding sequence (CDS) data of 20 birds. We identified 12 persistent positive selection sites (PSS), other sites suffered purifying selection and neutral selection; probably due to functional constraints. We also found humans have only 3PSS (189,197and 295), likely due to having more IFIT gene family member that can cooperate to resist virus invasion. The 12 PSS located in the closed clamp structure of the IFIT5 protein, except for position 45. In particular, 3 PSS (335, 342 and 367) were located in the TPR domain, which implied their important roles in virus recognition. We only found 2 episodic PSS (30,332) in Passeriformes, indicating episodic selection pressure in Passeriformes lineage. The positive selection of IFIT5 might provide a theoretical basis for the pathogen-host interaction in birds. Conclusions : We found that the diversity of IFIT5 domains in birds, and that the PSS of IFIT5 is the joint influence of functional domain conservation and the pressure of virus evolution.We speculated that persistent PSS may affect the antiviral function of IFIT5, especially in the region of closed clamp structure. These results lay a theoretical foundation for the further study of the antiviral immune mechanism of IFIT5 in birds.

Determinants of Livelihood Diversification Under Environmental Change in Coastal Community of Bangladesh

The life and livelihood of coastal farming communities in Bangladesh are highly vulnerable to climate and environmental change. Diversification of farmers’ income sources beyond agriculture can be an effective way to cope with the adverse impacts of environmental change. The purpose of this study is to analyse the options and determinants of livelihood diversification (LD) strategies adopted by farmers in the coastal region of Bangladesh. Multiple linear regression technique along with Simpson index, Herfindahl index and priority index have been used for the analysis. Simple random sampling and multistage sampling have been used to select the sample and the study area, respectively. The magnitude of farming household diversification is at medium level. A significant share of annual income comes primarily from fish and rice production, domestic bird rearing and working as agricultural labour. The adoption of diversified activities is strongly influenced by age and education of household head, number of earning family members, social network and government donation. The frequent occurrence of natural disasters, inadequate infrastructure and lack of financial capacity are the critical constraints to LD.

First serological evidence of West Nile virus among equines and birds in Kosovo, 2018-2019

Background: This study was conducted to survey the presence of West Nile virus (WNV) in Kosovo by serological testing of apparently healthy local horses and attempts to detect viral nucleic acid in birds and mosquitoes. Methods: Between January 2018 and June 2019, 260 equine serum samples were collected, additionally 580 adult mosquitoes (53 pools) grouped in for genera, including Culex spp. (226 individuals; 26 pools), Aedes spp. (136 individuals; 16 pools), Anopheles spp . (184 individuals; 7 pools), Culiseta spp . (34 individuals; 4 pools). 50 domestic birds and 51 wild birds were collected from different regions of Kosovo. Equine and domestic bird serum samples were tested by flavivirus IgG ELISA while mosquitoes and bird viscera were tested for WNV RNA by RT-qPCR. All ELISA-positive results were confirmed by plaque reduction neutralization test (PRNT) and by virus neutralization test (VNT). Results: This is the first report providing evidence of WNV antibodies among animals in Kosovo. WNV antibodies were present in 27 out of 260 equine sera (10.38%) and one out of 50 samples in domestic birds by ELISA and PRNT. Eight of 27 positive equine serum samples with high titer neutralized WNV, but not USUV. No WNV RNA was detected in birds or mosquitoes. Conclusions: The occurrence of WNV antibodies in local equines from all regions of Kosovo indicates that the virus is circulating within the country. Public health authorities should therefore plan a risk assessment and disease control program. Keywords: West Nile virus, Kosovo, Equines, Birds, Mosquitoes.

First serological evidence of West Nile virus among equines and birds in Kosovo, 2018-2019

Background: This study was conducted to survey the presence of the West Nile virus (WNV) in Kosovo by serological testing of the healthy autochthonous equine population and virus detection in birds and mosquitoes. Between January 2018 and June 2019, 260 equine serum samples, 626 mosquitoes (60 pools), 50 domestic birds and 51 wild birds were collected from different regions of Kosovo. Equine and domestic bird serum samples were tested by IgG ELISA while mosquitoes and bird viscera were tested for WNV RNA by RT-PCR. Positive ELISA samples were confirmed by Plaque Reduction Neutralization Test (PRNT) and eight by Virus Neutralization Test (VNT). Results: This is the first report providing evidence of WNV antibodies among animals in Kosovo. WNV antibodies were present in 27 out of 260 equine sera (10.38%) and one out of 50 samples in domestic birds by ELISA and PRNT. Eight of 27 positive equine serum samples were confirmed by VNT. No WNV RNA was detected in birds or mosquitoes.Conclusions: The occurrence of WNV antibodies in autochthonous equines from all regions of Kosovo indicates that the virus is circulating within the country. Public health authorities should therefore plan a risk assessment and disease control program.