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Article ; Online: Respiratory disease complex due to mixed viral infections in chicken in Jordan.

Al-Natour, Mohammad Q / Rohaim, Mohammed A / El Naggar, Rania F / Abdelsabour, Mohammed A / Afify, Ahmed F / Madbouly, Yahia M / Munir, Muhammad

Poultry science

2024 Volume 103, Issue 4, Page(s) 103565

Abstract: The global distribution of avian respiratory viruses highlights the need for effective surveillance programs and international collaboration to monitor viral circulation and implement timely control measures. In the current study, we aim to provide a ... ...

Abstract	The global distribution of avian respiratory viruses highlights the need for effective surveillance programs and international collaboration to monitor viral circulation and implement timely control measures. In the current study, we aim to provide a comprehensive overview of avian respiratory viral infections in the poultry flocks in Jordan, focusing on the major viruses involved, their epidemiology, clinical manifestations, and evolution based on viroinformatics that will be helpful to improve the diagnostic methods, and control strategies including vaccines in the region. In this research, various poultry broiler groups in Jordan experiencing respiratory symptoms were tested for respiratory viral pathogens from January 2021 to February 2022. The mortality rates observed in the examined groups varied between 6% and 40%. The identified strains were authenticated using the RT-qPCR assay. Furthermore, they underwent in-depth characterisation through the sequencing of the complete spike (S1) gene for infectious bronchitis virus (IBV) and the haemagglutinin (HA) gene for avian influenza virus (AIV) subtype H9N2. Co-infection of IBV and AIV H9N2 viruses was detected through molecular analysis. The IBV strains showed affiliation with the variant groups GI-16 (3 strains) and GI-23 (9 strains) and exhibited numerous mutations. Meanwhile, H9N2 avian influenza viruses displayed various changes in amino acids within the HA gene, suggesting the influence of antibody-driven selection pressure. The phylogenetic analysis revealed that the H9N2 viruses identified in this investigation shared close genetic ties with EG3 (3 strains) and the Middle East group (ME1; 8 strains). These strains have been recently found in Jordan and nearby countries in the Middle East. Moreover, their HA genes exhibited similarities to viruses belonging to the G1-like lineage. In conclusion, avian respiratory viral infections remain a significant concern for the poultry industry, requiring constant vigilance and proactive measures to minimise their impact. Continued surveillance, robust diagnostic methods, effective vaccines, and international cooperation are essential components of a comprehensive approach to combat avian respiratory viral infections (AI, IBV, ND and ILT 'viruses) and safeguard avian health and global poultry production.
MeSH term(s)	Animals ; Chickens ; Influenza A Virus, H9N2 Subtype/genetics ; Jordan/epidemiology ; Coinfection/veterinary ; Phylogeny ; Poultry Diseases/epidemiology ; Influenza in Birds/epidemiology ; Poultry ; Vaccines
Chemical Substances	Vaccines
Language	English
Publishing date	2024-02-16
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2024.103565
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Zs.B 853: Show issues

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Article: Avian Orthoavulavirus Type-1 as Vaccine Vector against Respiratory Viral Pathogens in Animal and Human.

Vilela, Julianne / Rohaim, Mohammed A / Munir, Muhammad

Vaccines

2022 Volume 10, Issue 2

Abstract: Avian orthoavulaviruses type-1 (AOaV-1) have recently transitioned from animal vaccine vector to a bona fide vaccine delivery vehicle in human. Owing to induction of robust innate and adaptive immune responses in mucus membranes in both birds and mammals, ...

Abstract	Avian orthoavulaviruses type-1 (AOaV-1) have recently transitioned from animal vaccine vector to a bona fide vaccine delivery vehicle in human. Owing to induction of robust innate and adaptive immune responses in mucus membranes in both birds and mammals, AOaVs offer an attractive vaccine against respiratory pathogens. The unique features of AOaVs include over 50 years of safety profile, stable expression of foreign genes, high infectivity rates in avian and mammalian hosts, broad host spectrum, limited possibility of recombination and lack of pre-existing immunity in humans. Additionally, AOaVs vectors allow the production of economical and high quantities of vaccine antigen in chicken embryonated eggs and several GMP-grade mammalian cell lines. In this review, we describe the biology of AOaVs and define protocols to manipulate AOaVs genomes in effectively designing vaccine vectors. We highlighted the potential and established portfolio of AOaV-based vaccines for multiple respiratory and non-respiratory viruses of veterinary and medical importance. We comment on the limitations of AOaV-based vaccines and propose mitigations strategies. The exploitation of AOaVs vectors is expanding at an exciting pace; thus, we have limited the scope to their use as vaccines against viral pathogens in both animals and humans.
Language	English
Publishing date	2022-02-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10020259
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Article ; Online: Structural topological analysis of spike proteins of SARS-CoV-2 variants of concern highlight distinctive amino acid substitution patterns.

Peisahovics, Filips / Rohaim, Mohammed A / Munir, Muhammad

European journal of cell biology

2022 Volume 101, Issue 4, Page(s) 151275

Abstract: Since the onset of pandemic in 2019, SARS-CoV-2 has diverged into numerous variants driven by antigenic and infectivity-oriented selection. Some variants have accumulated fitness-enhancing mutations, evaded immunity and spread despite global vaccination ... ...

Abstract	Since the onset of pandemic in 2019, SARS-CoV-2 has diverged into numerous variants driven by antigenic and infectivity-oriented selection. Some variants have accumulated fitness-enhancing mutations, evaded immunity and spread despite global vaccination campaigns. The spike (S) glycoprotein of SARS-CoV-2 demonstrated the greatest immunogenicity and amino acid substitution diversity owing to its importance in the interaction with human angiotensin receptor 2 (hACE2). The S protein consistently emerges as an amino acid substitution (AAS) hotspot in all six lineages, however, in Omicron this enrichment is significantly higher. This study attempts to design and validate a method of mapping S-protein substitution profile across variants to identify the conserved and AAS regions. A substitution matrix was created based on publicly available databases, and the substitution localization was illustrated on a cryo-electron microscopy generated S-protein model. Our analyses indicated that the diversity of N-terminal (NTD) and receptor-binding (RBD) domains exceeded that of any other regions but still contained extended low substitution density regions particularly considering significantly broader substitution profiles of Omicron BA.2 and BA.4/5. Finally, the substitution matrix was compared to a random sample alignment of variant sequences, revealing discrepancies. Therefore, it was suggested to improve matrix accuracy by processing a large number of S-protein sequences using an automated algorithm. Several critical immunogenic and receptor-interacting residues were identified in the conserved regions within NTD and RBD. In conclusion, the structural and topological analysis of S proteins of SARS-CoV-2 variants highlight distinctive amino acid substitution patterns which may be foundational in predicting future variants.
Language	English
Publishing date	2022-09-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	391967-5
ISSN	1618-1298 ; 0070-2463 ; 0171-9335
ISSN (online)	1618-1298
ISSN	0070-2463 ; 0171-9335
DOI	10.1016/j.ejcb.2022.151275
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Article ; Online: Mapping molecular gene signatures mediated by SARS-COV-2 and large-scale and genome-wide transcriptomics comparative analysis among respiratory viruses of medical importance.

Smith, Thomas / Rohaim, Mohammed A / Munir, Muhammad

Molecular and cellular probes

2022 Volume 64, Page(s) 101820

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging RNA virus causing COVID-19 disease, across the globe. SARS-CoV-2 infected patients may exhibit acute respiratory distress syndrome which can be compounded by endemic respiratory ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging RNA virus causing COVID-19 disease, across the globe. SARS-CoV-2 infected patients may exhibit acute respiratory distress syndrome which can be compounded by endemic respiratory viruses and thus highlighting the need to understand the genetic bases of clinical outcome under multiple respiratory infections. In this study, 42 individual datasets and a multi-parametric based selected list of over 12,000 genes against five medically important respiratory viruses (SARS-CoV-2, SARS-CoV-1, influenza A, respiratory syncytial virus (RSV) and rhinovirus were collected and analysed in an attempt to understand differentially regulated gene patterns and to cast genetic markers of individual and multiple co-infections. While a certain cohort of virus-specific genes were regulated (negatively and positively), notably results revealed a greatest correlation among genes regulation by SARS-CoV-2 and RSV. Furthermore, out of analysed genes, the MAP2K5 and NFKBIL1 were specifically and highly upregulated in SARS-CoV-2 infection both in vivo or in vitro. The most conserved genetic signature was JAK2 gene as well as the constitutively downregulated ZNF219 gene. In contrast, several genes including GPBAR1 and SC5DL were specifically downregulated in SARS-CoV-2 datasets. Finally, we catalogued a set of genes that were conserved or differentially regulated across studied respiratory viruses. These finding provide foundational and genome-wide data to gauge the markers of respiratory viral infections individually and under co-infection. This work compares the virogenomic signatures among human respiratory viruses and provides valid targets for potential antiviral therapy.
MeSH term(s)	COVID-19/genetics ; Coinfection ; Humans ; Influenza, Human ; Receptors, G-Protein-Coupled ; SARS-CoV-2/genetics ; Transcriptome
Chemical Substances	GPBAR1 protein, human ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2022-04-30
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	639082-1
ISSN	1096-1194 ; 0890-8508
ISSN (online)	1096-1194
ISSN	0890-8508
DOI	10.1016/j.mcp.2022.101820
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Zs.A 2230: Show issues

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Article: A Scalable Topical Vectored Vaccine Candidate against SARS-CoV-2.

Rohaim, Mohammed A / Munir, Muhammad

Vaccines

2020 Volume 8, Issue 3

Abstract: The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) caused an ongoing unprecedented global public health crises of coronavirus disease in 2019 (CoVID-19). The precipitously increased death rates, its impact on livelihood and trembling ... ...

Abstract	The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) caused an ongoing unprecedented global public health crises of coronavirus disease in 2019 (CoVID-19). The precipitously increased death rates, its impact on livelihood and trembling economies warrant the urgent development of a SARS-CoV-2 vaccine which would be safe, efficacious and scalable. Owing to unavailability of the vaccine, we propose a de novo synthesized avian orthoavulavirus 1 (AOaV-1)-based topical respiratory vaccine candidate against CoVID-19. Avirulent strain of AOaV-1 was engineered to express full length spike (S) glycoprotein which is highly neutralizing and a major protective antigen of the SARS-CoV-2. Broad-scale in vitro characterization of a recombinant vaccine candidate demonstrated efficient co-expression of the hemagglutinin-neuraminidase (HN) of AOaV-1 and S protein of SARS-CoV-2, and comparable replication kinetics were observed in a cell culture model. The recombinant vaccine candidate virus actively replicated and spread within cells independently of exogenous trypsin. Interestingly, incorporation of S protein of SARS-CoV-2 into the recombinant AOaV-1 particles attributed the sensitivity to anti-SARS-CoV-2 antiserum and more prominently to anti-AOaV-1 antiserum. Finally, our results demonstrated that the recombinant vaccine vector stably expressed S protein after multiple propagations in chicken embryonated eggs, and this expression did not significantly impact the in vitro growth characteristics of the recombinant. Taken together, the presented respiratory vaccine candidate is highly attenuated in primates per se, safe and lacking pre-existing immunity in human, and carries the potential for accelerated vaccine development against CoVID-19 for clinical studies.
Keywords	covid19
Language	English
Publishing date	2020-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines8030472
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Article ; Online: Correction to: Potential reverse spillover of infectious bursal disease virus at the interface of commercial poultry and wild birds.

Naggar, Rania F El / Rohaim, Mohammed A / Munir, Muhammad

Virus genes

2021 Volume 57, Issue 2, Page(s) 242–244

Language	English
Publishing date	2021-01-30
Publishing country	United States
Document type	Published Erratum
ZDB-ID	639496-6
ISSN	1572-994X ; 0920-8569
ISSN (online)	1572-994X
ISSN	0920-8569
DOI	10.1007/s11262-021-01824-1
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Zs.A 2397: Show issues

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Article ; Online: Interferon-induced protein with tetratricopeptide repeats 5 of black fruit bat (

Clayton, Emily / Atasoy, Mustafa O / Naggar, Rania F El / Franco, Ana Cláudia / Rohaim, Mohammed A / Munir, Muhammad

Frontiers in immunology

2024 Volume 15, Page(s) 1284056

Abstract: Bats are natural host reservoirs and have adapted a unique innate immune system that permits them to host many viruses without exhibiting symptoms. Notably, bat interferon stimulated genes (ISGs) have been shown to play antiviral roles. Interferon ... ...

Abstract	Bats are natural host reservoirs and have adapted a unique innate immune system that permits them to host many viruses without exhibiting symptoms. Notably, bat interferon stimulated genes (ISGs) have been shown to play antiviral roles. Interferon induced protein with tetratricopeptide repeats 5 (IFIT5) is a well-characterised ISG in humans with antiviral activities against negative-sense RNA viruses via inhibiting viral transcription. Here, we aim to investigate if
MeSH term(s)	Animals ; Humans ; Interferons/genetics ; Chiroptera/genetics ; Tetratricopeptide Repeat ; RNA Viruses ; Antiviral Agents
Chemical Substances	Interferons (9008-11-1) ; Antiviral Agents
Language	English
Publishing date	2024-02-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1284056
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Article: Deep Structural Analysis of Myriads of Omicron Sub-Variants Revealed Hotspot for Vaccine Escape Immunity.

Gerardi, Valeria / Rohaim, Mohammed A / Naggar, Rania F El / Atasoy, Mustafa O / Munir, Muhammad

Vaccines

2023 Volume 11, Issue 3

Abstract: The emergence of the Omicron variant has reinforced the importance of continued SARS-CoV-2 evolution and its possible impact on vaccine effectiveness. Specifically, mutations in the receptor-binding domain (RBD) are critical to comprehend the flexibility ...

Abstract	The emergence of the Omicron variant has reinforced the importance of continued SARS-CoV-2 evolution and its possible impact on vaccine effectiveness. Specifically, mutations in the receptor-binding domain (RBD) are critical to comprehend the flexibility and dynamicity of the viral interaction with the human agniotensin-converting enzyme 2 (hACE2) receptor. To this end, we have applied a string of deep structural and genetic analysis tools to map the substitution patterns in the S protein of major Omicron sub-variants (n = 51) with a primary focus on the RBD mutations. This head-to-head comparison of Omicron sub-variants revealed multiple simultaneous mutations that are attributed to antibody escape, and increased affinity and binding to hACE2. Our deep mapping of the substitution matrix indicated a high level of diversity at the N-terminal and RBD domains compared with other regions of the S protein, highlighting the importance of these two domains in a matched vaccination approach. Structural mapping identified highly variable mutations in the up confirmation of the S protein and at sites that critically define the function of the S protein in the virus pathobiology. These substitutional trends offer support in tracking mutations along the evolutionary trajectories of SAR-CoV-2. Collectively, the findings highlight critical areas of mutations across the major Omicron sub-variants and propose several hotspots in the S proteins of SARS-CoV-2 sub-variants to train the future design and development of COVID-19 vaccines.
Language	English
Publishing date	2023-03-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines11030668
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Article: The Molecular Virology of Coronaviruses with Special Reference to SARS-CoV-2.

Clayton, Emily / Rohaim, Mohammed A / Bayoumi, Mahmoud / Munir, Muhammad

Advances in experimental medicine and biology

2022 Volume 1352, Page(s) 15–31

Abstract: Introduction: Coronaviruses (CoVs) are large, enveloped and positive-sense RNA viruses which are responsible for a range of upper respiratory and digestive tract infections. Interest in coronaviruses has recently escalated due to the identification of a ...

Abstract	Introduction: Coronaviruses (CoVs) are large, enveloped and positive-sense RNA viruses which are responsible for a range of upper respiratory and digestive tract infections. Interest in coronaviruses has recently escalated due to the identification of a newly emerged coronavirus named severe acute respiratory syndrome 2 (SARS-CoV-2), which is the causative agent of the COVID-19 pandemic. In this chapter, we summarise molecular virological features of coronaviruses and understand their molecular mechanisms of replication in guiding the control of the global COVID-19 pandemic. Methods: We applied a holistic and comparative approach to assess the current understanding of coronavirus molecular virology and identify research gaps among different human coronaviruses. Results: Coronaviruses can utilise unique strategies that aid in their pathogenicity, replication and survival in multiple hosts. Replication of coronaviruses involves novel mechanisms such as ribosomal frameshifting and the synthesis of both genomic and sub-genomic RNAs. We summarised the key components in coronavirus molecular biology and molecular determinants of pathogenesis. Focusing largely on SARS-CoV-2 due to its current importance, this review explores the virology of recently emerged coronaviruses to gain an in-depth understanding of these infectious diseases. Conclusions: The presented information provides fundamental bottlenecks to devise future disease control and management strategies to curtail the impact of coronaviruses in human populations.
MeSH term(s)	COVID-19 ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2022-02-07
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-030-85109-5_2
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Article ; Online: Structural topological analysis of spike proteins of SARS-CoV-2 variants of concern highlight distinctive amino acid substitution patterns

Filips Peisahovics / Mohammed A. Rohaim / Muhammad Munir

European Journal of Cell Biology, Vol 101, Iss 4, Pp 151275- (2022)

2022

Abstract	Since the onset of pandemic in 2019, SARS-CoV-2 has diverged into numerous variants driven by antigenic and infectivity-oriented selection. Some variants have accumulated fitness-enhancing mutations, evaded immunity and spread despite global vaccination campaigns. The spike (S) glycoprotein of SARS-CoV-2 demonstrated the greatest immunogenicity and amino acid substitution diversity owing to its importance in the interaction with human angiotensin receptor 2 (hACE2). The S protein consistently emerges as an amino acid substitution (AAS) hotspot in all six lineages, however, in Omicron this enrichment is significantly higher. This study attempts to design and validate a method of mapping S-protein substitution profile across variants to identify the conserved and AAS regions. A substitution matrix was created based on publicly available databases, and the substitution localization was illustrated on a cryo-electron microscopy generated S-protein model. Our analyses indicated that the diversity of N-terminal (NTD) and receptor-binding (RBD) domains exceeded that of any other regions but still contained extended low substitution density regions particularly considering significantly broader substitution profiles of Omicron BA.2 and BA.4/5. Finally, the substitution matrix was compared to a random sample alignment of variant sequences, revealing discrepancies. Therefore, it was suggested to improve matrix accuracy by processing a large number of S-protein sequences using an automated algorithm. Several critical immunogenic and receptor-interacting residues were identified in the conserved regions within NTD and RBD. In conclusion, the structural and topological analysis of S proteins of SARS-CoV-2 variants highlight distinctive amino acid substitution patterns which may be foundational in predicting future variants.
Keywords	Viruses ; Cell biology ; Variants ; Structural biology ; Evolution ; Cytology ; QH573-671
Subject code	570
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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