Biology subjects

Bialy, D.

Publications and source records attributed to Bialy, D..

8 recordsLinked to original sources

bioRxiv2025

The G57 genotype of the BJ/94-like H9N2 lineage exhibits increased replication and virulence in chickens compared to the G1 Middle East Group B lineage

Avian influenza H9N2 viruses cause significant economic losses to the poultry industry and pose a public health risk due to their potential to reassort with other avian influenza viruses, generating strains with zoonotic and pandemic potential. Two major H9N2 lineages dominate globally: the G1 lineage (genotype G1-B), prevalent in the Middle East, Africa and the Indian subcontinent, and the BJ/94 lineage (predominantly genotype G57), dominant in China, Vietnam, South Korea, Indonesia, and the Far East. We investigated replication, transmission, and pathogenicity of representatives of these two lineages, linking genotype to phenotype. The G57 strain A/Ck/Vietnam/H7F-14-BN4-315/2014 (Vietnam/315) was more lethal to chicken embryos than the G1-B strain A/chicken/Pakistan/UDL-01/2008 (Pakistan/UDL-01). Vietnam/315 exhibited higher replication in both directly infected and contact chickens, with increased virus shedding from the oropharynx and cloaca. In contrast, Pakistan/UDL-01 virus was primarily shed from the oropharynx, highlighting differences in replication, tissue tropism and transmission. Gene analysis showed the M gene of Vietnam/315 enhanced replication in primary chicken kidney cells, whereas the PB2, HA, NA, and M genes promoted increased replication in Madin-Darby Canine Kidney cells. Both viruses showed preferential binding to avian-like receptors over human-like receptors. However, Vietnam/315, however, exhibited higher neuraminidase activity and a more acid-stable HA (pH fusion 5.2) than Pakistan/UDL-01 virus. These findings suggest G57 genotype viruses possess greater replication and transmission fitness than G1-B viruses in vivo, ex vivo and in vitro. Reassortment events involving G1-B strains acquiring G57 genes may enhance replication and virulence, potentially increasing the risk of animal and human infection. ImportanceH9N2 avian influenza viruses are widespread in poultry, resulting in significant economic losses and occasional human infections. Different genetic variants dominate in various regions, but their ability to cause disease and spread in poultry remains unclear. These viruses can exchange genes with other avian influenza strains, altering their infectivity and transmission. This study compared two major H9N2 genotypes: G1-B (common in the Indian subcontinent and the Middle East) and G57 (dominant in China and Vietnam). The G57 virus showed higher replication in laboratory tests and infected chickens, shedding more virus through the orofecal route. It also exhibited a stronger attachment to bird cells and had a more acid-stable HA, suggesting an increased potential for infection and spread. Our findings indicate that G57 genotype viruses are more infectious and adaptable in poultry than G1 viruses. Gene exchange with other avian influenza strains may generate more virulent viruses with increased transmission potential. This study supports the risk assessment of emerging strains and enhances disease mitigation strategies.

microbiology↗

bioRxiv2023

Alteration of the chicken upper respiratory microbiota following H9N2 avian influenza virus infection

Several studies have highlighted the importance of the gut microbiota in developing immunity against viral infections in chickens. We have previously shown that H9N2 avian influenza A virus (AIV) infection retards the diversity of the natural colon associated microbiota, which may further influence chicken health following recovery from infection. The effects of influenza infection on the upper respiratory tract (URT) microbiota are largely unknown. Here we showed that H9N2 AIV infection lowers alpha diversity indices in the acute phase of infection in URT, largely due to the family Lactobacillaceae being highly enriched during this time in the respiratory microbiota. Interestingly, microbiota diversity did not return to levels similar to control chickens in the recovery phase after viral shedding has ceased. Beta diversity followed similar trend following challenge. Lactobacillus associate statistically with the disturbed microbiota of infected chickens at acute and recovery phase of infection. Additionally, we study age-related changes in the respiratory microbiota during maturation in chickens. From 7 to 28 days of age, species richness and evenness were observed to advance over time as the microbial composition evolved. Maintaining microbiota homeostasis might be considered as a potential therapeutic target to prevent or aid recovery from H9N2 AIV infection.

microbiology↗

bioRxiv2021

A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus.

BackgroundNon-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. MethodsThe performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. ResultsThe SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of COVID that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. ConclusionsThe SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.

microbiology↗

bioRxiv2021

Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines

A commensal microbiome regulates and is in turn regulated by viruses during host infection which can influence virus infectivity. In this study, analysis of colon microbiome population changes following a low pathogenicity avian influenza virus (AIV) of the H9N2 subtype infection of two different chicken breeds was conducted. Using 16S rRNA sequencing and subsequent data analysis we found reduced microbiome alpha diversity in the acute period of AIV infection (day 2-3) in both Rhode Island Red and VALO chicken lines. From day 4 post infection a gradual increase in diversity of the colon microbiome was observed, but the diversity did not reach the same level as in uninfected chickens by day 10 post infection, suggesting that AIV infection retards the natural accumulation of colon microbiome diversity, which may further influence chicken health following recovery from infection. Beta diversity analysis indicated differences in diversity between the chicken lines during and following acute influenza infection suggesting the impact of host gut microflora dysbiosis following H9N2 influenza virus infection could differ for different breeds.

microbiology↗

bioRxiv2020

A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses

There is dire need for an effective and affordable vaccine against SARS-CoV-2 to tackle the ongoing pandemic. In this study, we describe a modular virus-like particle vaccine candidate displaying the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) using SpyTag/SpyCatcher technology (RBD-SpyVLP). Low doses of RBD-SpyVLP in a prime-boost regimen induced a strong neutralising antibody response in mice and pigs that was superior to convalescent human sera. We evaluated antibody quality using ACE2 blocking and neutralisation of cell infection by pseudovirus or wild-type SARS-CoV-2. Using competition assays with a monoclonal antibody panel, we showed that RBD-SpyVLP induced a polyclonal antibody response that recognised all key epitopes on the RBD, reducing the likelihood of selecting neutralisation-escape mutants. The induction of potent and polyclonal antibody responses by RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic. Moreover, RBD-SpyVLP is highly resilient, thermostable and can be lyophilised without losing immunogenicity, to facilitate global distribution and reduce cold-chain dependence.

immunology↗

bioRxiv2020

Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19

Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Here, we compared the immunogenicity of one or two doses of ChAdOx1 nCoV-19 in both mice and pigs. Whilst a single dose induced antigen-specific antibody and T cells responses, a booster immunisation enhanced antibody responses, particularly in pigs, with a significant increase in SARS-CoV-2 neutralising titres.

immunology↗

bioRxiv2020

The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins

SARS-CoV-2 emerged in late 2019, leading to the COVID-19 pandemic that continues to cause significant global mortality in human populations. Given its sequence similarity to SARS-CoV, as well as related coronaviruses circulating in bats, SARS-CoV-2 is thought to have originated in Chiroptera species in China. However, whether the virus spread directly to humans or through an intermediate host is currently unclear, as is the potential for this virus to infect companion animals, livestock and wildlife that could act as viral reservoirs. Using a combination of surrogate entry assays and live virus we demonstrate that, in addition to human ACE2, the Spike glycoprotein of SARS-CoV-2 has a broad host tropism for mammalian ACE2 receptors, despite divergence in the amino acids at the Spike receptor binding site on these proteins. Of the twenty-two different hosts we investigated, ACE2 proteins from dog, cat and rabbit were the most permissive to SARS-CoV-2, while bat and bird ACE2 proteins were the least efficiently used receptors. The absence of a significant tropism for any of the three genetically distinct bat ACE2 proteins we examined indicates that SARS-CoV-2 receptor usage likely shifted during zoonotic transmission from bats into people, possibly in an intermediate reservoir. Interestingly, while SARS-CoV-2 pseudoparticle entry was inefficient in cells bearing the ACE2 receptor from bats or birds the live virus was still able to enter these cells, albeit with markedly lower efficiency. The apparently broad tropism of SARS-CoV-2 at the point of viral entry confirms the potential risk of infection to a wide range of companion animals, livestock and wildlife.

microbiology↗

bioRxiv2019

Defining functional neuraminidase inhibitor drug resistance motifs in avian influenza viruses and the consequential impact on virus fitness in chicken cells.

Neuraminidase inhibitors (NAIs) are antiviral agents recommended worldwide to treat or prevent influenza virus infections in humans. Mapping of functional resistance to currently licensed NAIs has been limited to human influenza viruses with only sporadic reports investigating avian influenza viruses (AIV). However past pandemics as well as the increasing number of humans infected with AIV have shown the importance of having information about avian NAs that could cross the species barrier. In this study we introduced four NAI resistance-associated mutations previously found in human strains into the NA of six prevalent AIV subtypes that threaten the poultry industry and human health: H7N9, H6N1, H4N6 and highly pathogenic H5N8, H5N6 and H5N2. Using the established MUNANA assay we show that R292K substitution significantly impaired NA activity in all strains, whereas E119V, H274Y and N294S have more variable effects on NA activity. The impact of these mutations on NAI susceptibility was drug- and strain-specific. We have shown that despite compromised NA activity drug-resistant H5N6 and H6N1 viruses replicated to comparable or significantly higher titres in primary chicken cells as compared to wild type. The replicative fitness of NAI-resistant H5N6 was also confirmed in ovo. Two drug resistant H5N6 viruses had single amino acid substitutions in their haemagglutinin (HA) which reduced receptor binding properties. Our results demonstrate that there are no universal NAI resistance determinants for all strains and although some are clearly deleterious for the virus, others can be rapidly compensated by acquiring concurrent changes in other gene segments.\n\nIMPORTANCEThe number of human infections caused by avian influenza viruses (AIV) keeps increasing. This together with the rapid emergence of influenza strains resistant to neuraminidase inhibitor drugs (NAIs) observed in the past raises a significant concern to public health. We studied the NAI resistance-associated molecular changes, previously reported in neuraminidase (NA) of human influenza, in AIV background. We found that single amino acid substitution can confer a multidrug resistance, or lead to a single-drug resistance across multiple virus subtypes. We also found that the drug-resistant viruses retained or showed enhanced fitness properties as compared to the corresponding wild-type, and this could be achieved by quick acquisition of concurrent mutations in haemagglutinin. Our study highlights the need for constant monitoring of NAI-resistance in AIV and understanding the molecular basis of antiviral resistance, as such information would be invaluable for pandemic preparedness and may facilitate the development of novel therapeutics.

microbiology↗