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Liu S, Niu R, Wang X, Cui J, Cui M, Zhou H, Li J, Holmes EC, Shi W, Li C. Meta-transcriptomic sequencing reveals divergent RNA viruses in geckos. Virus Res 2025; 354:199551. [PMID: 39999926 PMCID: PMC11919394 DOI: 10.1016/j.virusres.2025.199551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 02/20/2025] [Accepted: 02/22/2025] [Indexed: 02/27/2025]
Abstract
Geckos are generally small, predominantly nocturnal reptiles, with several species commonly found close to human habitations. However, little is known about viral diversity in geckos. Using meta-transcriptomic sequencing we identified four novel RNA viruses - provisionally denoted Gecko astrovirus, Gecko parechovirus, Gecko reptillovirus, and Gecko hartmanivirus - in geckos sampled in October 2019 from Hainan Province, China. The presence of these viruses was confirmed by reverse transcription (RT)-PCR. Phylogenetic analyses revealed that these viruses were most closely related to those identified in various gecko species from China and Australia, such that they represent gecko-specific lineages, yet were also genetically distinct, with amino acid sequence identities to their closest relatives ranging from 38.6 % to 74.2 %. A co-phylogeny analysis revealed a complex interplay between long-term virus-host co-divergence and more recent host jumping, which differed in frequency among groups. In sum, we demonstrate the presence of four novel gecko-associated RNA viruses, expanding our understanding of viral diversity in these common animal species.
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Affiliation(s)
- Shuqi Liu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Ruiling Niu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Xinrui Wang
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Jingxuan Cui
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Mingxue Cui
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Hong Zhou
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Juan Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Weifeng Shi
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Cixiu Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China; School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China.
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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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Sasidharan A, Harrison CJ, Selvarangan R. Diagnosis, management, and outcomes of parechovirus infections in infants: an overview. J Clin Microbiol 2024; 62:e0113923. [PMID: 38647282 PMCID: PMC11237800 DOI: 10.1128/jcm.01139-23] [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] [Indexed: 04/25/2024] Open
Abstract
Parechovirus A (PeV-A) infections have been detected with increasing frequency in US infants under 6 months of age, leading to a Centers for Disease Control and Prevention (CDC) health advisory in July 2022. Clinicians are advised to consider PeV-A laboratory testing of blood and cerebrospinal fluid when infants present with unexplained fever, sepsis-like illness, or neurological issues. Clinical laboratories are encouraged to offer in-house molecular testing for PeV-A to avoid diagnostic delays, unnecessary use of antibiotics, and prolonged hospitalization of infants presenting with sepsis-like illness. While data are evolving on potential neurodevelopmental sequelae after PeV-A infant central nervous system infections, most infected infants return to baseline health for age. This review examines the PeV-A literature with a focus on PeV-A3, including aspects of epidemiology, clinical presentations/management, laboratory diagnostics, genotyping, and post-infectious sequelae related to PeV-A infections in infants.
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Affiliation(s)
- Anjana Sasidharan
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital and Clinics, Kansas City, Missouri, USA
| | | | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital and Clinics, Kansas City, Missouri, USA
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Coutinho CRM, Cardoso JF, Siqueira JAM, Machado RS, Chagas Júnior WDD, Tavares FN, Gabbay YB. Diversity of picornaviruses detected in diarrheal samples from children in Belém, Brazilian Amazon (1982-2019). J Med Virol 2023; 95:e28873. [PMID: 37349989 DOI: 10.1002/jmv.28873] [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: 01/10/2023] [Revised: 05/06/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
In this investigation, fecal specimens from children with diarrhea were collected from four community studies conducted between 1982 and 2019 in Belém, Brazilian Amazon. A total of 234 samples were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to detect infections by picornaviruses of the Enterovirus (EV), Parechovirus (HPeV), Cosavirus (HCoSV), Kobuvirus (Aichivirus - AiV) and Salivirus (SalV) genera. The positive samples were subjected to different amplification protocols of the VP1 region of the genome, such as nested PCR or snPCR, and were subsequently genotyped by sequencing VP1 and VP3 of the viral genome. Positivity was observed in 76.5% (179/234) of the samples tested using RT-qPCR for at least one virus, and co-infection was observed in 37.4% (67/179) of the cases. EV was detected in 50.8% (119/234), HPeV in 29.9% (70/234), HCoSV in 27.3% (64/234), and AiV/SalV in 2.1% (5/234) of the specimens tested by RT-qPCR. Using nested PCR and/or snPCR techniques, the positivity rates were 94.11% (112/119) for EV, 72.85% (51/70) for HPeV, and 20.31% (13/64) for HCoSV. It was not possible to amplify the samples that were positive for AiV/SalV. Sequencing revealed 67.2% (80/119) EV, 51.4% (36/70) HPeV, and 20.31% (13/64) HCoSV. Forty-five different types of EV were found among species A, B, and C; HCoSV identified five species, including a possible recombinant strain; all HPeV were identified as belonging to species A, in two samples a possible recombination involving three different strains was verified. This study demonstrated the high circulation and diversity of different types of picornaviruses in fecal samples, including those collected more than 30 years ago. This endorsed the evaluation of important points in the epidemiology of these viruses, such as the presence of co-infection and the possibility of knowing more about these agents, considering that some were recently described; therefore, their detection in older samples can provide more data about their ancestry.
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Affiliation(s)
| | - Jedson Ferreira Cardoso
- Laboratório de Bioinformática-BIOINFO, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Jones Anderson Monteiro Siqueira
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Raiana Scerni Machado
- Programa de Pós-graduação em Medicina Tropical, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - Wanderley Dias das Chagas Júnior
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Fernando Neto Tavares
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
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