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Guo Q, Zhu S, Wang D, Li X, Zhu H, Song Y, Liu X, Xiao F, Zhao H, Lu H, Xiao J, Yu L, Wang W, He Y, Liu Y, Li J, Zhang Y, Xu W, Yan D. Genetic characterization and molecular evolution of type 3 vaccine-derived polioviruses from an immunodeficient patient in China. Virus Res 2023; 334:199177. [PMID: 37479187 PMCID: PMC10388201 DOI: 10.1016/j.virusres.2023.199177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/06/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
In 2013, a case of immunodeficiency vaccine-derived poliovirus (iVDPV) was identified in Jiangxi Province, China. In this study, we purified 14 type 3 original viral isolates from this case and characterized the molecular evolution of these iVDPVs for 298 days. Genetic variants were found in most of the original viral isolates, with complex genetic and evolutionary relationships among the variants. A phylogenetic tree constructed based on the P1 region showed that these iVDPVs were classified into lineage A and B. The dominant lineage B represents a major trend in virus evolution. The nucleotide substitution rate at the third codon position (3CP) estimated by the BEAST program was 1.76 × 10-2 substitutions/site/year (95% HPD: 1.23-2.39 × 10-2). The initial OPV dose was given dating back to March 2013, which was close to the time of the last OPV vaccination, suggesting that OPV infection may have originated with the last dose of vaccine. Recombinant analysis showed that these iVDPVs were inter-vaccine recombinants with two recombination patterns, S3/S2/S1 and S3/S2/S3/S2/S1. Whole genome sequence analysis revealed that key nucleotide sites (C472U, C2034U, U2493C) associated with the attenuated phenotype of Sabin 3 have been replaced. Temperature sensitivity test showed that all tested strains were temperature-sensitive, except for the variant Day11-5. Interestingly, we observed that the variant Day11-5 temperature resistance properties may be associated with the Lys to Met substitution at the VP2-162 site. Serological test and whole genome sequence analysis showed that the seropositivity rate remained high, and mutations in the antigenic sites did not significantly alter neutralization ability.
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Affiliation(s)
- Qin Guo
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China; Da Zhou Vocational College of Chinese Medicine, Dazhou, China
| | - Shuangli Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Dongyan Wang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Xiaolei Li
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Hui Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Yang Song
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Xiaoqing Liu
- Jiangxi Center for Disease Control and Prevention, Nanchang, China
| | - Fang Xiao
- Jiangxi Center for Disease Control and Prevention, Nanchang, China
| | - Hehe Zhao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Huanhuan Lu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Jinbo Xiao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Liheng Yu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Wenhui Wang
- School of Public Health and Management, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, China
| | - Yun He
- School of Public Health and Management, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, China
| | - Ying Liu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Jichen Li
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Yong Zhang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Wenbo Xu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Dongmei Yan
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China.
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Fall A, Forman M, Morris CP, Gniazdowski V, Luo CH, Hanlon A, Miller H, Bergman Y, Mostafa HH. Enterovirus characterized from cerebrospinal fluid in a cohort from the Eastern United States. J Clin Virol 2023; 161:105401. [PMID: 36805602 DOI: 10.1016/j.jcv.2023.105401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Enteroviruses (EVs) are predominant causes of a spectrum of neurological diseases. To better understand the origins of the outbreaks of disease associated with EV, it is essential to develop an efficient surveillance system that identifies the circulating EVs and correlate their genomic evolution with the disease presentations. METHODS The clinical presentations of patients with positive EV from cerebrospinal fluid (CSF) between 2014 and 2022, diagnosed at the Johns Hopkins Medical Microbiology Laboratory, were compared from year to year. EV typing and whole genome sequencing were performed and correlated to the spectrum of disease. RESULTS A total of 95 CSF specimens were positive for EV between 2014 and 2022. The percentage positivity ranged from the lowest of 1.1% in 2020 to the highest of 3.2% in 2015. The median ages declined from 22 years in 2014 to less than one year starting in 2016 to 34 in 2022. Typing using VP1 sequencing revealed that E30 and E6 were associated with meningitis in adults but coxsackieviruses (CVs-B3 and B5) were detected from pediatric patients with fever. Whole genome sequencing revealed multiple recombination events. In 2020, a recombinant CV-A9 was detected in a CSF sample associated with unusual presentation of sepsis, profound acute bilateral sensory neural hearing loss, and myofasciitis. CONCLUSIONS EV genomic surveillance is needed for a better understanding of the genetic determinants of neurovirulence. Whole genome sequencing can reveal recombination events missed by traditional molecular surveillance methods.
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Affiliation(s)
- Amary Fall
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Michael Forman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - C Paul Morris
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA; National Institute of Allergy and Infectious Disease, National Institutes of Health, Frederick, MD, USA
| | - Victoria Gniazdowski
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Ann Hanlon
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Heather Miller
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Yehudit Bergman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA.
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Wang X, Ren R, Ma B, Xie J, Ma Y, Luo H, Guo Y, Ding L, Zhang L, Zhang M, Wang T, Shuang Z, Zhu X. Comparative Study on MNVT of OPV Type I and III Reference Products in Different Periods. Diseases 2023; 11:diseases11010028. [PMID: 36810542 PMCID: PMC9944487 DOI: 10.3390/diseases11010028] [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] [Received: 12/27/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
Widespread vaccination using the oral live attenuated polio vaccine (OPV) and Sabin strain inactivated vaccine (sIPV) have greatly reduced the incidence of polio worldwide. In the period post-polio, the virulence of reversion of the Sabin strain makes the use of OPV gradually becoming one of the major safety hazards. The verification and release of OPV has become the top priority. The monkey neurovirulence test (MNVT) is the gold standard for detecting whether OPV meets the criteria, which are recommended by the WHO and Chinese Pharmacopoeia. Therefore, we statistically analyzed the MNVT results of type I and III OPV at different stages: 1996-2002 and 2016-2022. The results show that the upper and lower limits and C value of the qualification standard of type I reference products in 2016-2022 have decreased compared with the corresponding scores in the 1996-2002 period. The upper and lower limit and C value of the qualified standard of type III reference products were basically the same as the corresponding scores in the 1996-2002. We also found significant differences in the pathogenicity of the type I and III in the cervical spine and brain, with the decreasing trend in the diffusion index of the type I and type III in the cervical spine and brain. Finally, two evaluation criteria were used to judge the OPV test vaccines from 2016 to 2022. The vaccines all met the test requirements under the evaluation criteria of the above two stages. Based on the characteristics of OPV, data monitoring was one of the most intuitive methods to judge changes in virulence.
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Kitamura K, Shimizu H. Outbreaks of Circulating Vaccine-derived Poliovirus in the World Health Organization Western Pacific Region, 2000-2021. Jpn J Infect Dis 2022; 75:431-444. [PMID: 36047174 DOI: 10.7883/yoken.jjid.2022.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The World Health Organization Western Pacific Region (WPR) has maintained the polio-free status for more than two decades. At the global level, there were only 6 confirmed polio cases due to wild type 1 poliovirus in Pakistan, Afghanistan, and Malawi in 2021, therefore, the risk of the importation of wild poliovirus from the endemic countries to the WPR is considerably lower than ever before. On the other hand, the risk of polio outbreaks associated with circulating vaccine-derived polioviruses (cVDPVs) still cannot be ignored even in the WPR. Since late 2010s, cVDPV outbreaks in the WPR have appeared to be more extensive in frequency and magnitude. Moreover, the emergence of concomitant polio outbreaks of type 1 and type 2 cVDPVs in the Philippines and Malaysia during 2019-2020 has highlighted the remaining risk of cVDPV outbreaks in high-risk areas and/or communities in the WPR. The previous cVDPV outbreaks in the WPR have been rapidly and effectively controlled, however, the future risk of polio outbreaks associated with cVDPVs needs to be reconsidered and polio immunization and surveillance strategies should be updated accordingly.
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Affiliation(s)
- Kouichi Kitamura
- Department of Virology II, National Institute of Infectious Diseases, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Japan
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Abstract
Echovirus 30 (E30), a member of species B enterovirus, is associated with outbreaks of aseptic meningitis and has become a global health emergency. However, the pathogenesis of E30 remains poorly understood due to the lack of appropriate animal models. In this study, we established a mouse infection model to explore the pathogenicity of E30. The 2-day-old IFNAR-/- mice infected with E30 strain WZ16 showed lethargy and paralysis, and some died. Obvious pathological changes were observed in the skeletal muscle, brain tissue, and other tissues, with the highest viral load in the skeletal muscles. Transcriptome analysis of brain and skeletal muscle tissues from infected mice showed that significant differentially expressed genes were enriched in complement response and neuropathy-related pathways. Using immunofluorescence assay, we found that the viral double-stranded RNA (dsRNA) was detected in the mouse brain region and could infect human glioma (U251) cells. These results indicated that E30 affects the nervous system, and they provide a theoretical basis for understanding its pathogenesis. IMPORTANCE Echovirus 30 (E30) infection causes a wide spectrum of diseases with mild symptoms, such as hand, foot, and mouth disease (HFMD), acute flaccid paralysis, and aseptic meningitis and other diseases, especially one of the most common pathogens causing aseptic meningitis outbreaks. We established a novel mouse model of E30 infection by inoculating neonatal mice with clinical isolates of E30 and observed the pathological changes induced by E30. Using the E30 infection model, we found complement responses and neuropathy-related genes in the mice tissues at the transcriptome level. Moreover, we found that the viral dsRNA localized in the mouse brain and could replicate in human glioma cell line U251 rather than in the neuroblastoma cell line, SK-N-SH.
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6
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Abstract
Foot-and-mouth disease (FMD) field studies have suggested the occurrence of simultaneous infection of individual hosts by multiple virus strains; however, the pathogenesis of foot-and-mouth disease virus (FMDV) coinfections is largely unknown. In the current study, cattle were experimentally exposed to two FMDV strains of different serotypes (O and A). One cohort was simultaneously infected with both viruses, while additional cohorts were initially infected with FMDV A and subsequently superinfected with FMDV O after 21 or 35 days. Coinfections were confirmed during acute infection, with both viruses concurrently detected in blood, lesions, and secretions. Staggered exposures resulted in overlapping infections as convalescent animals with persistent subclinical FMDV infection were superinfected with a heterologous virus. Staggering virus exposure by 21 days conferred clinical protection in six of eight cattle, which were subclinically infected following the heterologous virus exposure. This effect was transient, as all animals superinfected at 35 days post-initial infection developed fulminant FMD. The majority of cattle maintained persistent infection with one of the two viruses while clearing the other. Analysis of viral genomes confirmed interserotypic recombination events within 10 days in the upper respiratory tract of five superinfected animals from which the dominant genomes contained the capsid coding regions of the O virus and nonstructural coding regions of the A virus. In contrast, there were no dominant recombinant genomes detected in samples from simultaneously coinfected cattle. These findings inculpate persistently infected carriers as potential FMDV mixing vessels in which novel strains may rapidly emerge through superinfection and recombination. IMPORTANCE Foot-and-mouth disease (FMD) is a viral infection of livestock of critical socioeconomic importance. Field studies from areas of endemic FMD suggest that animals can be simultaneously infected by more than one distinct variant of FMD virus (FMDV), potentially resulting in emergence of novel viral strains through recombination. However, there has been limited investigation of the mechanisms of in vivo FMDV coinfections under controlled experimental conditions. Our findings confirmed that cattle could be simultaneously infected by two distinct serotypes of FMDV, with different outcomes associated with the timing of exposure to the two different viruses. Additionally, dominant interserotypic recombinant FMDVs were discovered in multiple samples from the upper respiratory tracts of five superinfected animals, emphasizing the potential importance of persistently infected FMDV carriers as sources of novel FMDV strains.
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Lednicky JA, Tagliamonte MS, White SK, Elbadry MA, Alam MM, Stephenson CJ, Bonny TS, Loeb JC, Telisma T, Chavannes S, Ostrov DA, Mavian C, De Rochars VMB, Salemi M, Morris JG. Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33791709 PMCID: PMC8010738 DOI: 10.1101/2021.03.19.21253391] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, coronavirus emergence in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae – Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus, – human infections reported to date have been limited to alpha- and betacoronaviruses3. We identify, for the first time, porcine deltacoronavirus (PDCoV) strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the nsp15 and the spike glycoprotein genes by convergent evolution. In particular, structural analysis predicts that one of the changes in the Spike S1 subunit, which contains the receptor-binding domain, may affect protein’s flexibility and binding to the host cell receptor. Our findings not only underscore the ability of deltacoronaviruses to adapt and potentially lead to human-to-human transmission, but also raise questions about the role of such transmissions in development of pre-existing immunity to other coronaviruses, such as SARS-CoV-2.
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Tagliamonte MS, Abid N, Borocci S, Sangiovanni E, Ostrov DA, Kosakovsky Pond SL, Salemi M, Chillemi G, Mavian C. Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements. Int J Mol Sci 2020; 22:E80. [PMID: 33374797 PMCID: PMC7794730 DOI: 10.3390/ijms22010080] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/12/2023] Open
Abstract
Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has mainly been driven by purifying selection, suggesting the presence of conserved structural features. Our dynamic simulations identified two main long-range covariant dynamic movements of the novel glycoprotein, and showed that, as a result of the evolutionary duality, they are preserved. The first movement involves the receptor binding domain with the N-terminal domain and the C-terminal domain 2 and is maintained across human, bat and pangolin coronaviruses. The second is a complex network of long-range dynamics specific to SARS-CoV-2 involving the novel PRRA and the conserved KR*SF cleavage sites, as well as conserved segments in C-terminal domain 3. These movements, essential for host cell binding, are maintained by hinges conserved across human, bat, and pangolin coronaviruses glycoproteins. The hinges, located around Threonine 333 and Proline 527 within the N-terminal domain and C-terminal domain 2, represent candidate targets for the future development of novel pan-coronavirus inhibitors. In summary, we show that while recombination created a new configuration that increased the covariant dynamic movements of the SARS-CoV-2 glycoprotein, negative selection preserved its inter-domain structure throughout evolution in different hosts and inter-species transmissions.
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Affiliation(s)
- Massimiliano S. Tagliamonte
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, 5000 Monastir, Tunisia;
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute for Biological Systems, National Research Council, Via Salaria, Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Elisa Sangiovanni
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | | | - Marco Salemi
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Carla Mavian
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
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Zhang G, Hu B, Huo Y, Lu J, Guo J, Deng M, Li P, Wang W, Li L, Meng S, Wang Z, Shen S. Amino acid substitutions in VP2, VP1, and 2C attenuate a Coxsackievirus A16 in mice. Microb Pathog 2020; 150:104603. [PMID: 33271234 DOI: 10.1016/j.micpath.2020.104603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 09/21/2020] [Accepted: 10/30/2020] [Indexed: 11/29/2022]
Abstract
Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD), a common acute infectious disease affecting infants and young children. Severe symptoms of the central nervous system may develop and even lead to death. Here, a plaque-purified CVA16 strain, L731-P1 (P1), was serially passaged in Vero cells for six times and passage 6 (P6) stock became highly attenuated in newborn mice. Genomic sequencing of the P1 and P6 revealed seven nucleotide substitutions at positions 1434 (C to U), 2744 (A to G), 2747 (A to G), 3161 (G to A), 3182 (A to G), 4968 (C to U), and 6064 (C to U). Six of these substitutions resulted in amino acid changes at VP2-T161 M, VP1-N102D, VP1-T103A, VP1-E241K, VP1-T248A, and 2C-S297F, respectively. P1-based infectious cDNA was generated to further investigate these virulent determinants. Independent reverse transcription-polymerase chain reaction (RT-PCR) amplifications for mutant constructions and plaque-purification of the P6 for isolation of variants were performed to determine dominant mutations and strains more related to attenuation. The virulent P1, attenuated P6, as well as a plaque purified strain (PP) and other four recombinant mutants, were inoculated into one-day-old BALB/c mice and the 50% lethal dose of each strain was determined. Comparison of virulence among these strains indicated that amino acid changes of VP1-N102D, VP1-E241K and 2C-S297F might be associated more closely with a high level attenuation of CVA16-L731-P6 than other mutations. Identification of novel residues associated with virulence may contribute to understanding of molecular basis of virulence of CVA16 and other enteroviruses.
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Affiliation(s)
- Gaobo Zhang
- Wuhan Huaxia University of Technology, Wuhan, 430223, China.
| | - Bing Hu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430000, China
| | - Yuqi Huo
- The Sixth People' s Hospital of Zhengzhou, Zhengzhou, 450000, China
| | - Jia Lu
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Jing Guo
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Mi Deng
- Worldwide Safety and Regulatory Pfizer, Inc., Wuhan, 430000, China
| | - Pengfei Li
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Weishan Wang
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Li Li
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Shengli Meng
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China
| | - Zejun Wang
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China.
| | - Shuo Shen
- Laboratory of Viral Vaccine Research, Wuhan Institute of Biological Products (WIBP) Co. Ltd., Wuhan, 430207, China.
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Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2. Sci Rep 2020; 10:14502. [PMID: 32879332 PMCID: PMC7468141 DOI: 10.1038/s41598-020-71303-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution.
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Korotkova EA, Prostova MA, Gmyl AP, Kozlovskaya LI, Eremeeva TP, Baikova OY, Krasota AY, Morozova NS, Ivanova OE. Case of Poliomyelitis Caused by Significantly Diverged Derivative of the Poliovirus Type 3 Vaccine Sabin Strain Circulating in the Orphanage. Viruses 2020; 12:v12090970. [PMID: 32883046 PMCID: PMC7552002 DOI: 10.3390/v12090970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/26/2022] Open
Abstract
Significantly divergent polioviruses (VDPV) derived from the oral poliovirus vaccine (OPV) from Sabin strains, like wild polioviruses, are capable of prolonged transmission and neuropathology. This is mainly shown for VDPV type 2. Here we describe a molecular-epidemiological investigation of a case of VDPV type 3 circulation leading to paralytic poliomyelitis in a child in an orphanage, where OPV has not been used. Samples of feces and blood serum from the patient and 52 contacts from the same orphanage were collected twice and investigated. The complete genome sequencing was performed for five polioviruses isolated from the patient and three contact children. The level of divergence of the genomes of the isolates corresponded to approximately 9–10 months of evolution. The presence of 61 common substitutions in all isolates indicated a common intermediate progenitor. The possibility of VDPV3 transmission from the excretor to susceptible recipients (unvaccinated against polio or vaccinated with inactivated poliovirus vaccine, IPV) with subsequent circulation in a closed children’s group was demonstrated. The study of the blood sera of orphanage residents at least twice vaccinated with IPV revealed the absence of neutralizing antibodies against at least two poliovirus serotypes in almost 20% of children. Therefore, a complete rejection of OPV vaccination can lead to a critical decrease in collective immunity level. The development of new poliovirus vaccines that create mucosal immunity for the adequate replacement of OPV from Sabin strains is necessary.
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Affiliation(s)
- Ekaterina A. Korotkova
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia;
- Correspondence: (E.A.K.); (O.E.I.); Tel.: +7-916-169-86-12 (E.A.K.); +7-916-677-24-03 (O.E.I.)
| | - Maria A. Prostova
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Anatoly P. Gmyl
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
- Institute for Bionic Technologies and Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Liubov I. Kozlovskaya
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
- Institute for Bionic Technologies and Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Tatiana P. Eremeeva
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Olga Y. Baikova
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Alexandr Y. Krasota
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia;
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Nadezhda S. Morozova
- Federal Centre of Hygiene and Epidemiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 117105 Moscow, Russia;
| | - Olga E. Ivanova
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
- Institute for Bionic Technologies and Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (E.A.K.); (O.E.I.); Tel.: +7-916-169-86-12 (E.A.K.); +7-916-677-24-03 (O.E.I.)
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12
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Kempf BJ, Watkins CL, Peersen OB, Barton DJ. An Extended Primer Grip of Picornavirus Polymerase Facilitates Sexual RNA Replication Mechanisms. J Virol 2020; 94:e00835-20. [PMID: 32522851 PMCID: PMC7394906 DOI: 10.1128/jvi.00835-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/02/2020] [Indexed: 11/20/2022] Open
Abstract
Picornaviruses have both asexual and sexual RNA replication mechanisms. Asexual RNA replication mechanisms involve one parental template, whereas sexual RNA replication mechanisms involve two or more parental templates. Because sexual RNA replication mechanisms counteract ribavirin-induced error catastrophe, we selected for ribavirin-resistant poliovirus to identify polymerase residues that facilitate sexual RNA replication mechanisms. We used serial passage in ribavirin, beginning with a variety of ribavirin-sensitive and ribavirin-resistant parental viruses. Ribavirin-sensitive virus contained an L420A polymerase mutation, while ribavirin-resistant virus contained a G64S polymerase mutation. A G64 codon mutation (G64Fix) was used to inhibit emergence of G64S-mediated ribavirin resistance. Revertants (L420) or pseudorevertants (L420V and L420I) were selected from all independent lineages of L420A, G64Fix L420A, and G64S L420A parental viruses. Ribavirin resistance G64S mutations were selected in two independent lineages, and novel ribavirin resistance mutations were selected in the polymerase in other lineages (M299I, M323I, M392V, and T353I). The structural orientation of M392, immediately adjacent to L420 and the polymerase primer grip region, led us to engineer additional polymerase mutations into poliovirus (M392A, M392L, M392V, K375R, and R376K). L420A revertants and pseudorevertants (L420V and L420I) restored efficient viral RNA recombination, confirming that ribavirin-induced error catastrophe coincides with defects in sexual RNA replication mechanisms. Viruses containing M392 mutations (M392A, M392L, and M392V) and primer grip mutations (K375R and R376K) exhibited divergent RNA recombination, ribavirin sensitivity, and biochemical phenotypes, consistent with changes in the fidelity of RNA synthesis. We conclude that an extended primer grip of the polymerase, including L420, M392, K375, and R376, contributes to the fidelity of RNA synthesis and to efficient sexual RNA replication mechanisms.IMPORTANCE Picornaviruses have both asexual and sexual RNA replication mechanisms. Sexual RNA replication shapes picornavirus species groups, contributes to the emergence of vaccine-derived polioviruses, and counteracts error catastrophe. Can viruses distinguish between homologous and nonhomologous partners during sexual RNA replication? We implicate an extended primer grip of the viral polymerase in sexual RNA replication mechanisms. By sensing RNA sequence complementarity near the active site, the extended primer grip of the polymerase has the potential to distinguish between homologous and nonhomologous RNA templates during sexual RNA replication.
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Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Colorado, USA
| | - Colleen L Watkins
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Colorado, USA
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13
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Yeh MT, Bujaki E, Dolan PT, Smith M, Wahid R, Konz J, Weiner AJ, Bandyopadhyay AS, Van Damme P, De Coster I, Revets H, Macadam A, Andino R. Engineering the Live-Attenuated Polio Vaccine to Prevent Reversion to Virulence. Cell Host Microbe 2020; 27:736-751.e8. [PMID: 32330425 PMCID: PMC7566161 DOI: 10.1016/j.chom.2020.04.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 12/03/2019] [Accepted: 04/02/2020] [Indexed: 12/11/2022]
Abstract
The live-attenuated oral poliovirus vaccine (OPV or Sabin vaccine) replicates in gut-associated tissues, eliciting mucosa and systemic immunity. OPV protects from disease and limits poliovirus spread. Accordingly, vaccination with OPV is the primary strategy used to end the circulation of all polioviruses. However, the ability of OPV to regain replication fitness and establish new epidemics represents a significant risk of polio re-emergence should immunization cease. Here, we report the development of a poliovirus type 2 vaccine strain (nOPV2) that is genetically more stable and less likely to regain virulence than the original Sabin2 strain. We introduced modifications within at the 5' untranslated region of the Sabin2 genome to stabilize attenuation determinants, 2C coding region to prevent recombination, and 3D polymerase to limit viral adaptability. Prior work established that nOPV2 is immunogenic in preclinical and clinical studies, and thus may enable complete poliovirus eradication.
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Affiliation(s)
- Ming Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erika Bujaki
- National Institute for Biological Standards and Control (NIBSC), South Mimms, Herts EN6 3QG, UK
| | - Patrick T Dolan
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew Smith
- National Institute for Biological Standards and Control (NIBSC), South Mimms, Herts EN6 3QG, UK
| | - Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - John Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Amy J Weiner
- Bill and Melinda Gates Foundation, Seattle, WA 98109, USA
| | | | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium
| | - Ilse De Coster
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium
| | - Hilde Revets
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium
| | - Andrew Macadam
- National Institute for Biological Standards and Control (NIBSC), South Mimms, Herts EN6 3QG, UK.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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14
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Agol VI. In pursuit of intriguing puzzles. Virology 2020; 539:49-60. [PMID: 31670219 DOI: 10.1016/j.virol.2019.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 10/25/2022]
Abstract
This Invited Review is a kind of scientific autobiography based on the presentation at the Symposium "Viruses: Discovering Big in Small" held in honor of the author's 90th birthday (Moscow, March 2019).
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Affiliation(s)
- Vadim I Agol
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia; A. N. Belozersky Institute of Physical-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119899, Russia.
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15
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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16
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Kempf BJ, Watkins CL, Peersen OB, Barton DJ. Picornavirus RNA Recombination Counteracts Error Catastrophe. J Virol 2019; 93:e00652-19. [PMID: 31068422 PMCID: PMC6600191 DOI: 10.1128/jvi.00652-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/24/2023] Open
Abstract
Template-dependent RNA replication mechanisms render picornaviruses susceptible to error catastrophe, an overwhelming accumulation of mutations incompatible with viability. Viral RNA recombination, in theory, provides a mechanism for viruses to counteract error catastrophe. We tested this theory by exploiting well-defined mutations in the poliovirus RNA-dependent RNA polymerase (RDRP), namely, a G64S mutation and an L420A mutation. Our data reveal two distinct mechanisms by which picornaviral RDRPs influence error catastrophe: fidelity of RNA synthesis and RNA recombination. A G64S mutation increased the fidelity of the viral polymerase and rendered the virus resistant to ribavirin-induced error catastrophe, but only when RNA recombination was at wild-type levels. An L420A mutation in the viral polymerase inhibited RNA recombination and exacerbated ribavirin-induced error catastrophe. Furthermore, when RNA recombination was substantially reduced by an L420A mutation, a high-fidelity G64S polymerase failed to make the virus resistant to ribavirin. These data indicate that viral RNA recombination is required for poliovirus to evade ribavirin-induced error catastrophe. The conserved nature of L420 within RDRPs suggests that RNA recombination is a common mechanism for picornaviruses to counteract and avoid error catastrophe.IMPORTANCE Positive-strand RNA viruses produce vast amounts of progeny in very short periods of time via template-dependent RNA replication mechanisms. Template-dependent RNA replication, while efficient, can be disadvantageous due to error-prone viral polymerases. The accumulation of mutations in viral RNA genomes leads to error catastrophe. In this study, we substantiate long-held theories regarding the advantages and disadvantages of asexual and sexual replication strategies among RNA viruses. In particular, we show that picornavirus RNA recombination counteracts the negative consequences of asexual template-dependent RNA replication mechanisms, namely, error catastrophe.
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Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Colleen L Watkins
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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Lema C, Torres C, Van der Sanden S, Cisterna D, Freire MC, Gómez RM. Global phylodynamics of Echovirus 30 revealed differential behavior among viral lineages. Virology 2019; 531:79-92. [PMID: 30856485 DOI: 10.1016/j.virol.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/16/2019] [Accepted: 02/16/2019] [Indexed: 01/03/2023]
Abstract
Echovirus 30 (E30) is an important causative agent of aseptic meningitis worldwide. Despite this, the global and regional dispersion patterns, especially in South America, are still largely unknown. We performed an in-depth analysis of global E30 population dynamics, by using the VP1 sequences of 79 strains isolated in Argentina, between 1998 and 2012, and 856 sequences from GenBank. Furthermore, the 3Dpol regions of 329 sequences were analyzed to study potential recombination events. E30 evolution was characterized by co-circulation and continuous replacement of lineages over time, where four lineages appear to circulate at present and another four lineages appear to have stopped circulating. Five lineages showed a global distribution, whereas three other lineages had a more restricted circulation pattern. Strains isolated in South America belong to lineages E and F. Analysis of the 3Dpol region of Argentinean strains indicated that recombination events occurred in both lineages.
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Affiliation(s)
- Cristina Lema
- Neurovirosis Service at Virology Department, INEI-ANLIS, Dr. Carlos G. Malbran Institute, Argentina.
| | - Carolina Torres
- Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Argentina
| | | | - Daniel Cisterna
- Neurovirosis Service at Virology Department, INEI-ANLIS, Dr. Carlos G. Malbran Institute, Argentina
| | - María Cecilia Freire
- Neurovirosis Service at Virology Department, INEI-ANLIS, Dr. Carlos G. Malbran Institute, Argentina
| | - Ricardo M Gómez
- Institute of Biotechnology and Molecular Biology, CONICET-UNLP, 1900 La Plata, Argentina.
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Viral Recombination: Ecology, Evolution, and Pathogenesis. Viruses 2018; 10:v10070358. [PMID: 29986376 PMCID: PMC6070879 DOI: 10.3390/v10070358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 12/12/2022] Open
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Abstract
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.
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