Biology subjects

Selim, A.

Publications and source records attributed to Selim, A..

3 recordsLinked to original sources

bioRxiv2023

Emergence of the Novel Infectious bursal disease viruse Variant in Vaccinated Poultry Flocks in Egypt

Infectious bursal disease viruses (IBDVs) have a profound impact on poultry production worldwide, directly causing mortality rates of up to 100%, and indirectly through their immunosuppressive effects. Since the emergence of the antigenically modified very virulent IBDV (vvIBDV) in Egypt in late 1999, the country has experienced recurrent outbreaks with high mortality rates and typical vvIBDV gross lesions. However, a notable shift occurred in 2023, characterized by a substantial increase in reported subclinical IBDV cases exhibiting atrophied bursa and associated immunosuppression. To assess the field situation, we examined samples from 21 farms in 2023 and 18 farms from 2021 and 2022, all of which experienced IBD outbreaks based on clinical diagnosis. These samples were submitted to our laboratory for confirmatory testing and subsequently subjected to VP2-HVR sequencing. Phylogenetic analysis revealed that all samples collected in 2021 and 2022 clustered with classical virulent strains and very virulent IBDV. In 2023, one sample clustered with the Egyptian vvIBDV, while one sample clustered with classic virulent IBDV, and the remaining 2023 samples clustered with the Chinese novel variant IBDV (nVarIBDV). The alignment of deduced amino acid sequences for VP2 revealed that all Egyptian classic virulent strains were similar to the Winterfield or Leukert strains. In contrast, vvIBDV strains exhibited two out of the three typical residues found in Egyptian antigenically atypical vvIBDV, namely Y220F and G254S, but not A321T, and one sample was identical to the European vvIBDV (emerged in 1989). Meanwhile, all variant strains recognized in the present study exhibited typical residues found in variant IBDV, in addition to the three conserved amino acid residues found only in Chinese variant IBDVs. However, all Egyptian variant strains showed a mutation at position 321 (321V), which represents the most exposed part of the capsid and is known to have a massive impact on IBDV antigenicity, with the exception of one sample that had 318G instead. This report highlights the emergence of a new variant IBDV clustered with the Chinese new variant in Egypt, causing bursa atrophy and spreading subclinically in broiler farms over a wide geographic distance, resulting in massive economic losses due to immunosuppression.

microbiology↗

bioRxiv2023

Statistical prediction of microbial metabolic traits from genomes

The metabolic activity of microbial communities is central to their role in biogeochemical cycles, human health, and biotechnology. Despite the abundance of sequencing data characterizing these consortia, it remains a serious challenge to predict microbial metabolic traits from sequencing data alone. Here we culture 96 bacterial isolates individually and assay their ability to grow on 10 distinct compounds as a sole carbon source. Using these data as well as two existing datasets, we show that statistical approaches can accurately predict bacterial carbon utilization traits from genomes. First, we show that classifiers trained on gene content can accurately predict bacterial carbon utilization phenotypes by encoding phylogenetic information. These models substantially outperform predictions made by constraint-based metabolic models automatically constructed from genomes. However, phylogeny-based predictions fail to predict traits for taxa that are phyloge-netically distant from any strains in the training set. To overcome this we train improved models on gene presence/absence to predict carbon utilization traits from gene content. We show that models that predict carbon utilization traits from gene presence/absence can generalize to taxa that are phylogenetically distant from the training set either by exploiting biochemical information for feature selection or by having sufficiently large datasets. In the latter case, we provide evidence that a statistical approach can identify putatively mechanistic genes involved in metabolic traits. Our study demonstrates the potential power for predicting microbial phenotypes from genotypes using statistical approaches.

ecology↗

bioRxiv2022

Pre-existing immunity to influenza viruses through infection and/or vaccination leads to viral mutational signatures associated with unique immune responses during a subsequent infection

Our biggest challenge to reducing the burden of seasonal influenza is the constant antigen drift of circulating influenza viruses which then evades the protection of pre-existing immunity. Continual viral infection and influenza vaccination creates a layered immune history in people, however, how host preimmunity interacts with an antigenically divergent virus exposure is poorly understood. Here we investigated the influence of host immune histories on influenza viral mutations. Immune backgrounds were devised in mice similar to what is experienced in people: naive; previously infected (A/FM/1/1947); previously vaccinated (Sanofi quadrivalent vaccine); and previously infected and then vaccinated. Mice were challenged with the heterologous H1N1 strain A/Mexico/4108/2009 to assess protection, viral mutation, and host responses in respect to each immune background by RNAseq. Viral sequences were analyzed for antigenic changes using DiscoTope 2.0 and Immune Epitope Database (IEDB) Analysis Resource NetMHCpan EL 4.1 servers. The mock infected-vaccinated group consistently had the greatest number of viral mutations seen across several viral proteins, HA, NA, NP, and PB1 which was associated with strong antiviral responses and moderate T cell and B cell responses. In contrast, the preimmune-vaccinated mice were not associated with variant emergence and the host profiles were characterized by minimal antiviral immunity but strong T cell, B cell, and NK cell responses. This work suggests that the infection and vaccination history of the host dictates the capacity for viral mutation at infection through immune pressure. These results are important for developing next generation vaccination strategies. ImportanceInfluenza is a continual public health problem. Due to constant virus circulation and vaccination efforts, people have complex influenza immune histories which may impact the outcome of future infections and vaccinations. How immune histories influence the emergence of new variants and the immune pressure stimulated at exposure is poorly understood. Our study addressed this knowledge gap by utilizing mice that are preimmune to influenza viruses and analyzing host responses as well as viral mutations associated with changes in antigenicity. Importantly, we found previous vaccination induced immune responses with moderate adaptive immunity and strong antiviral immunity which was associated with increased mutations in the influenza virus. Interestingly, animals that were previously infected with a heterologous virus and also vaccinated had robust adaptive responses with little to no antiviral induction which was associated with no emergence of viral variants. These results are important for the design of next generation influenza vaccines.

microbiology↗