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Afroz S, Saul S, Dai J, Surman S, Liu X, Park HS, Le Nouën C, Lingemann M, Dahal B, Coleman JR, Mueller S, Collins PL, Buchholz UJ, Munir S. Human parainfluenza virus 3 vaccine candidates attenuated by codon-pair deoptimization are immunogenic and protective in hamsters. Proc Natl Acad Sci U S A 2024; 121:e2316376121. [PMID: 38861603 PMCID: PMC11194498 DOI: 10.1073/pnas.2316376121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Human parainfluenza virus type 3 (HPIV3) is a major pediatric respiratory pathogen lacking available vaccines or antiviral drugs. We generated live-attenuated HPIV3 vaccine candidates by codon-pair deoptimization (CPD). HPIV3 open reading frames (ORFs) encoding the nucleoprotein (N), phosphoprotein (P), matrix (M), fusion (F), hemagglutinin-neuraminidase (HN), and polymerase (L) were modified singly or in combination to generate 12 viruses designated Min-N, Min-P, Min-M, Min-FHN, Min-L, Min-NP, Min-NPM, Min-NPL, Min-PM, Min-PFHN, Min-MFHN, and Min-PMFHN. CPD of N or L severely reduced growth in vitro and was not further evaluated. CPD of P or M was associated with increased and decreased interferon (IFN) response in vitro, respectively, but had little effect on virus replication. In Vero cells, CPD of F and HN delayed virus replication, but final titers were comparable to wild-type (wt) HPIV3. In human lung epithelial A549 cells, CPD F and HN induced a stronger IFN response, viral titers were reduced 100-fold, and the expression of F and HN proteins was significantly reduced without affecting N or P or the relative packaging of proteins into virions. Following intranasal infection in hamsters, replication in the nasal turbinates and lungs tended to be the most reduced for viruses bearing CPD F and HN, with maximum reductions of approximately 10-fold. Despite decreased in vivo replication (and lower expression of CPD F and HN in vitro), all viruses induced titers of serum HPIV3-neutralizing antibodies similar to wt and provided complete protection against HPIV3 challenge. In summary, CPD of HPIV3 yielded promising vaccine candidates suitable for further development.
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Affiliation(s)
- Sharmin Afroz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Sirle Saul
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Jin Dai
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Sonja Surman
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Xueqiao Liu
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Hong-Su Park
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Cyril Le Nouën
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Matthias Lingemann
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Bibha Dahal
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | | | | | - Peter Leon Collins
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ursula Johanna Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Shirin Munir
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
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Smielewska A, Emmott E, Ranellou K, Popay A, Goodfellow I, Jalal H. UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis. Wellcome Open Res 2018; 3:118. [PMID: 30569021 PMCID: PMC6281019 DOI: 10.12688/wellcomeopenres.14730.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3. Results: In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical. Conclusions: The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.
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Affiliation(s)
- Anna Smielewska
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Edward Emmott
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Department of Bioengineering, Northeastern University, Boston, MA, 02115-5000, USA
| | - Kyriaki Ranellou
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Ashley Popay
- Eastern Field Epidemiology Unit, Institute of Public Health, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Hamid Jalal
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
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Smielewska A, Emmott E, Ranellou K, Popay A, Goodfellow I, Jalal H. UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis. Wellcome Open Res 2018; 3:118. [PMID: 30569021 PMCID: PMC6281019 DOI: 10.12688/wellcomeopenres.14730.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 10/05/2023] Open
Abstract
Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3. Results: In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical. Conclusions: The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.
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Affiliation(s)
- Anna Smielewska
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Edward Emmott
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Department of Bioengineering, Northeastern University, Boston, MA, 02115-5000, USA
| | - Kyriaki Ranellou
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Ashley Popay
- Eastern Field Epidemiology Unit, Institute of Public Health, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB20QQ, UK
| | - Hamid Jalal
- Cambridge University Hospitals NHS Foundation Trust Laboratory, Public Health England, Cambridge, Cambridgeshire, CB20QQ, UK
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Slovic A, Kosutic-Gulija T, Santak M, Ivancic-Jelecki J, Jagusic M, Ljubin-Sternak S, Mlinarić-Galinović G, Vilibić-Čavlek T, Tabain I, Forcic D. Genetic Variability and Sequence Relatedness of Matrix Protein in Viruses of the Families Paramyxoviridae and Pneumoviridae. Intervirology 2018; 60:181-189. [PMID: 29510403 DOI: 10.1159/000487049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/22/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The families Paramyxoviridae and Pneumoviridae comprise a broad spectrum of viral pathogens that affect human health. The matrix (M) protein of these viruses has a central role in their life cycle. In line with this, molecular characteristics of the M proteins from variable viruses that circulated in Croatia were investigated. METHODS Sequences of the M proteins of human parainfluenza virus (HPIV) 1-3 within the family Paramyxoviridae, human metapneumovirus (HMPV), and human respiratory syncytial virus from the family Pneumoviridae were obtained and analyzed. RESULTS M proteins were very diverse among HPIVs, but highly conserved within each virus. More variability was seen in nucleotide sequences of M proteins from the Pneumoviridae family. An insertion of 8 nucleotides in the 3' untranslated region in 1 HMPV M gene sequence was discovered (HR347-12). As there are no samples with such an insertion in the database, this insertion is of interest and requires further research. CONCLUSION While we have confirmed that M proteins were conserved among individual viruses, any changes that are observed should be given attention and further researched. Of special interest is inclusion of HPIV2 M proteins in this analysis, as these proteins have not been studied to the same extent as other paramyxoviruses.
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Affiliation(s)
- Anamarija Slovic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Tanja Kosutic-Gulija
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Maja Santak
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Jelena Ivancic-Jelecki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Maja Jagusic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Sunčanica Ljubin-Sternak
- Teaching Institute of Public Health "Dr. Andrija Štampar", Zagreb, Croatia.,School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Tatjana Vilibić-Čavlek
- School of Medicine, University of Zagreb, Zagreb, Croatia.,Croatian National Institute of Public Health, Zagreb, Croatia
| | - Irena Tabain
- Croatian National Institute of Public Health, Zagreb, Croatia
| | - Dubravko Forcic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
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