International Committee On Taxonomy Of Viruses Research Articles

A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses.

Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order Pimascovirales of the phylum Nucleocytoviricota. However, they were not classified previously by the International Committee on Taxonomy of Viruses (ICTV). Here, we present a comprehensive analysis of the gene content, morphology, and phylogenomics of these viruses, providing data that underpinned the recent proposal to establish new taxa for their initial classification. The new taxonomy, which has now been ratified by the ICTV, includes the family Orpheoviridae and genus Alphaorpheovirus, the family Pithoviridae and genus Alphapithovirus, and the family Cedratviridae and genus Alphacedratvirus, aiming to formally catalogue the isolates covered in this study. Additionally, as per the newly adopted rules, we applied standardized binomial names for the virus species created to classify isolates with complete genome sequences available in public databases at the time of the proposal. The specific epithet of each virus species was chosen as a reference to the location where the exemplar virus was isolated.

Epidemiological, clinical and biological profile of COVID-19 in patients hospitalized at the Avicenne Military Hospital in Marrakech

In late December 2019, a series of cases of viral pneumonia caused by a novel coronavirus emerged in Wuhan, China, and quickly spread to all continents. This coronavirus, identified in respiratory tract samples, was named SARS-CoV-2 for Severe Acute Respiratory Syndrome Coronavirus-2 by the ICTV (International Committee on Taxonomy of Viruses). The disease it causes was designated COVID-19 for Coronavirus Disease 2019 by the Word Health Organization. Most often, SARS-CoV-2 infection is responsible for a mild or moderate form, with the most typical clinical presentation being that of a febrile respiratory infection with dry cough, dyspnea, fatigue, and myalgia. Approximately 10-15% of cases are severe, and 5% are critical. Cases of reinfection have been described. Treatment for COVID-19 is currently symptomatic, relying on supportive care. The present study aims to investigate the demographic, clinical, and diagnostic aspects, as well as the study of risk factors associated with SARS-CoV-2 infection among 318 patients admitted to the Avicenne Military Hospital in Marrakech during the first wave of the pandemic. This is a retrospective descriptive and analytical study involving 318 cases of SARS-CoV-2 infection, diagnosed at the microbiology-virology department, and followed up in various non-intensive care units of the Avicenna Military Hospital in Marrakech, during the period of the first wave of the epidemic in Morocco, schematically between March 22, 2020, and July 19, 2020. For patients who developed pneumonia, 20% were diabetic and 13.3% were hypertensive. A quarter of patients with pneumonia experienced desaturation upon admission. In the multivariate logistic regression model, risk factors associated with the development of pneumonia and the various disease outcomes included advanced age and absence of a history of contact with a confirmed case. In the univariate analysis, hyperleukocytosis, neutrophilia, lymphopenia, eosinopenia, anaemia, hyperferritinaemia with elevated aspartate aminotransferase, hyponatraemia and fasting hyperglycaemia were significantly associated with a higher risk of an unfavourable outcome. Patients who presented with pneumonia on admission had an unfavourable outcome during their hospitalisation compared with patients who did not develop pneumonia. The statistically significant risk factors associated with an unfavourable outcome were advanced age (>60 years) with p <0. 001: OR=1.194; 95%IC= [1.114-1.278], absence of contact with a confirmed case (p <0.001 : OR= 43.138; 95%IC= [8.893-209.263]), presence of comorbidity (P<0.001 : OR=11. 503; 95%CI= [3,306-40,028]), mainly diabetes (P<0.001: OR=16,971; 95%CI= [4,267-67,504]) and arterial hypertension (P<0.001: OR=18,812; 95%CI= [3,977-88,954]). The study of the epidemiological, clinical and biological characteristics of COVID 19 at the Avicenne military hospital in Marrakech has enabled us to gain a better understanding of the profile of our patients with SARS-CoV-2 infection, and then to detect shortcomings in terms of prophylaxis, diagnosis and management, in order to be able to provide the necessary solutions aimed at further improving the quality of care for this population.

Complete genome sequence of a novel totivirus isolated from the leaves of Myrica rubra.

Chinese bayberry is a fruit that is appreciated for its taste. A novel totivirus associated with rolling, disfiguring, chlorotic and vein-clearing symptoms on the leaf apices of Chinese bayberry was identified by transcriptome sequencing and reverse transcription PCR (RT-PCR). The complete genome of the virus was determined to be 4959 nucleotides long, and it contains two open reading frames (ORFs). Its genomic organization is similar to that of previously reported totiviruses. ORF1 encodes a putative coat protein (CP) of 765 aa, and ORF2 encodes an RNA-dependent RNA polymerase (RdRp) of 815 aa. These two putative proteins share 55.1% and 62.6%, amino acid sequence identity, respectively, with the corresponding proteins of Panax notoginseng virus A, respectively. According to the demarcation criteria for totivirus species established by the International Committee on Taxonomy of Viruses (ICTV), the new virus should be considered a member of a new species in the genus totivirus, family Orthototiviridae, which we have tentatively named ''Myrica rubra-associated totivirus'' (MRaTV).

ICTV Virus Taxonomy Profile: Nairoviridae 2024.

Nairoviridae is a family for negative-sense RNA viruses with genomes of about 17.2-21.1 kb. These viruses are maintained in and/or transmitted by arthropods among birds, reptiles and mammals. Norwaviruses and orthonairoviruses can cause febrile illness in humans. Several orthonairoviruses can infect mammals, causing mild, severe and sometimes, fatal diseases. Nairovirids produce enveloped virions containing two or three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), sometimes a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Nairoviridae, which is available at www.ictv.global/report/nairoviridae.

ICTV Virus Taxonomy Profile: Fusariviridae 2024.

Fusariviridae is a family of mono-segmented, positive-sense RNA viruses with genome sizes of 5.9-10.7 kb. Most genomic RNAs are bicistronic, but exceptions have up to four predicted ORFs. In bicistronic genomes, the 5'-proximal ORF codes for a single protein with both RNA-directed RNA polymerase (RdRP) and RNA helicase (Hel) domains; little is known about the protein encoded by the second ORF. Fusarivirids do not appear to form virions. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Fusariviridae, which is available at ictv.global/report/fusariviridae.

ICTV Virus Taxonomy Profile: Hantaviridae 2024.

Hantaviridae is a family for negative-sense RNA viruses with genomes of about 10.5-14.6 kb. These viruses are maintained in and/or transmitted by fish, reptiles, and mammals. Several orthohantaviruses can infect humans, causing mild, severe, and sometimes-fatal diseases. Hantavirids produce enveloped virions containing three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Hantaviridae, which is available at ictv.global/report/hantaviridae.

Covid-19’s rampage in the human body

The Covid-19 (or Coronavirus Disease-19) was first detected in Wuhan, in the Hubei Province of China. Its causative agent got named as SARS-CoV-2 (or Severe Acute Respiratory Syndrome Coronavirus- 2) in 11 February, 2020 by the International Committee on Taxonomy of Viruses (ICTV). This virus is observed to infect the respiratory system in most patients. In this review, the aim was to discuss the potential of SARS-CoV-2 of affecting almost all the major organ systems of the body and to highlight the importance of interaction between spike glycoprotein of the virus and ACE2 receptor on a host cell. An analysis was made on the gfindings of the different kinds of manifestations of Covid-19 and 42 resources, including: scientific articles and websites, were used for writing this review. The resources were searched on the internet based on a set of keywords. In this review, first the pathophysiology and manifestations of the virus, based on target organ, are discussed. Later, the underlying mechanisms of infection for these organs are compared and a conclusion is drawn. Finally, few of the research works in progress were listed, which help highlight the importance of spike-ACE2 interactions. The result found was that: SARS-CoV-2 is capable of severely affecting: Central nervous system, Respiratory System, Skin, Eyes, Excretory system, Gastrointestinal system, Liver, Circulatory system and Reproductive system. The common mechanism of cellular entry of the virus has been observed to be: Interaction between spike glycoprotein with the ACE-2 receptor. While, many groups are currently conducting research based on this topic, hardly a hand few drugs have been approved for use. Thus, the conclusion is that: research should be focused on developing an approved, potent drug or therapy to inhibit the spike glycoprotein-ACE2 receptor interaction in order to tackle the raging pandemic.

ICTV Virus Taxonomy Profile: Kolmioviridae 2024.

Kolmioviridae is a family for negative-sense RNA viruses with circular, viroid-like genomes of about 1.5-1.7 kb that are maintained in mammals, amphibians, birds, fish, insects and reptiles. Deltaviruses, for instance, can cause severe hepatitis in humans. Kolmiovirids encode delta antigen (DAg) and replicate using host-cell DNA-directed RNA polymerase II and ribozymes encoded in their genome and antigenome. They require evolutionary unrelated helper viruses to provide envelopes and incorporate helper virus proteins for infectious particle formation. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Kolmioviridae, which is available at ictv.global/report/kolmioviridae.

The Lithbea Domain.

The tree of life is the evolutionary metaphor for the past and present connections of all cellular organisms. Today, to speak of biodiversity is not only to speak of archaea, bacteria, and eukaryotes, but they should also consider the "new biodiversity" that includes viruses and synthetic organisms, which represent the new forms of life created in laboratories. There is even a third group of artificial entities that, although not living systems, pretend to imitate the living. To embrace and organize all this new biodiversity, I propose the creation of a new domain, with the name Lithbea (from life-on-the-border entites) The criteria for inclusion as members of Lithbea are: i) the acellular nature of the living system, ii) its origin in laboratory manipulation, iii) showing new biological traits, iv) the presence of exogenous genetic elements, v) artificial or inorganic nature. Within Lithbea there are two subdomains: Virworld (from virus world) which includes all viruses, regarded as lifeless living systems, and classified according to the International Committee on Taxonomy of Viruses (ICTV), and ii) Humade (from human-made) which includes all synthetic organisms and artificial entities. The relationships of Lithbea members to the three classical woesian domains and their implications are briefly discussed.

Identification and Genome Characterization of a Novel Virus within the Genus Totivirus from Chinese Bayberry (Myrica rubra).

Chinese bayberry (Myrica rubra) is an economically significant fruit tree native to eastern Asia and widely planted in south-central China. However, studies about the viruses infecting M. rubra remain largely lacking. In the present study, we employed the metatranscriptomic method to identify viruses in M. rubra leaves exhibiting yellowing and irregular margin symptoms collected in Fuzhou, a city located in China's Fujian province in the year 2022. As a consequence, a novel member of the genus Totivirus was identified and tentatively named "Myrica rubra associated totivirus 1" (MRaTV1). The genome sequencing of MRaTV1 was determined by overlapping reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The two deduced proteins encoded by MRaTV1 have the highest amino acid (aa) sequence identity to the coat protein (CP) and RNA-dependent RNA polymerase (RdRP) of Panax notoginseng virus A (PNVA), a member of the genus Totivirus within the family Totiviridae, at 49.7% and 61.7%, respectively. According to the results of the phylogenetic tree and the species demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV) for the genus Totivirus, MRaTV1 is considered a new member of the genus Totivirus.

Characterization of a novel high-efficiency cracking Burkholderia gladiolus phage vB_BglM_WTB and its application in black fungus

Burkholderia gladiolus (B. gladiolus) is foodborne pathogenic bacteria producing bongkrekic acid (BA), which causes food poisoning and has a mortality rate of up to 40 % or more. However, no drugs have been reported in the literature for the prevention and treatment of this infection. In this study, a phage was identified to control B. gladiolus. The novel phage vB_BglM_WTB (WTB), which lyse B. gladiolus with high efficiency, was isolated from sewage of Huaihe Road Throttle Well Sewage Treatment Plant in Hefei. Transmission electron microscopy showed that WTB had an icosahedral head (69 ± 2 nm) and a long retractable tail (108 ± 2 nm). Its optimal temperature and pH ranges to control B. gladiolus were 25 °C -65 °C and 3–11 respectively. The phage WTB was identified as a linear double-stranded DNA phage of 68, 541 bp with 60.04 % G + C content, with a long latent period of 60 min. Phylogenetic analysis and comparative genetic analysis indicated that phage WTB has low identity (<50 %) with other phages, with the highest similarity to Burkholderia phage Maja (25.7 %), which showed that it does not belong to any previous genera recognized by the International Committee on Taxonomy of Viruses (ICTV) and was a candidate for a new genus within the Caudoviricetes. We have submitted a new proposal to ICTV to create a new genus, Bglawtbvirus. No transfer RNA (tRNA), virulence associated and antibiotic resistance genes were detected in phage WTB. Experimental results indicated that WTB at 4 °C and 25 °C had excellent inhibition activity against B. gladiolus in the black fungus, with an inhibition efficiency of over 99 %. The amount of B. gladiolus in the black fungus was reduced to a minimum of 89 CFU/mL when treated by WTB at 25 °C for 2 h. The inhibition rate remained at 99.97 % even after 12 h. The findings showed that the phage WTB could be applied as a food-cleaning agent for enhancing food safety and contributed to our understanding of phage biology and diversity.

ICTV Virus Taxonomy Profile: Filoviridae 2024.

Filoviridae is a family of negative-sense RNA viruses with genomes of about 13.1-20.9 kb that infect fish, mammals and reptiles. The filovirid genome is a linear, non-segmented RNA with five canonical open reading frames (ORFs) that encode a nucleoprotein (NP), a polymerase cofactor (VP35), a glycoprotein (GP1,2), a transcriptional activator (VP30) and a large protein (L) containing an RNA-directed RNA polymerase (RdRP) domain. All filovirid genomes encode additional proteins that vary among genera. Several filovirids (e.g., Ebola virus, Marburg virus) are pathogenic for humans and highly virulent. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Filoviridae, which is available at www.ictv.global/report/filoviridae.

Identification and Speciation of Various Fungal Co-infections in COVID-19 Patients by Different Laboratory Diagnostic Methods: A Retrospective Observational Study

Introduction: Respiratory illness caused by a novel coronavirus was first noted in December 2019 in Wuhan, Hubei Province, China. Later, the novel coronavirus was referred to as Severe and critical Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) by the International Committee on Taxonomy of Viruses (ICTV). However, the types of co-infected pathogens and the proportion of co-infection in SARS-CoV-2-positive patients were unclear. Co-infection with certain pathogens may also hinder accurate disease diagnosis. Aim: To determine the most suitable sample type for a better culture outcome and to identify the various opportunistic fungal infections related to Coronavirus Disease 2019 (COVID-19) patients. Materials and Methods: This retrospective observational study was conducted between November 2021 to January 2022 at Department of Microbiology, Government Medical College, Surat, Gujarat, India. The data collection was done in the month of November 2021 followed by data analysis in December 2021 to January 2022. A total of 252 suspected cases of fungal co-infection were sampled (including swabs, tissues, skin scrapings, Cerebrospinal fluid (CSF), sputum, pus, and drain) from different wards for fungal wet mount Potassium Hydroxide (KOH) and culture. The data was entered into Microsoft Excel (Windows 10), and analysis was performed using Microsoft Excel, including frequency distribution and percentage. Results: A total of 252 samples were received. Demographic details showed that individuals aged 41-50 years were more commonly affected, and males were affected more than females. Among the sample types, tissue samples showed the highest positivity 43 (17%), followed by scraping materials 14 (6%). Out of the total 252 cultures performed, 70 were positive. In terms of fungal speciation, Mucor species accounted for 24 (34.28%) isolates, while Aspergillus flavus accounted for 26 (37.14%), followed by other isolated fungal species. Conclusion: Fungal co-infection is observed in COVID-19 positive patients, which not only contributes to morbidity but also increases mortality. Tissue samples demonstrated the highest culture positivity. The culture results showed a higher frequency of Mucor species isolates and Aspergillus flavus compared to other isolates.

ICTV Virus Taxonomy Profile: Tulasviridae 2023.

Tulasviridae is a family of ambisense RNA viruses with genomes of about 12.2 kb that have been found in fungi. The tulasvirid genome is nonsegmented and contains three open reading frames (ORFs) that encode a nucleoprotein (NP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and a protein of unknown function (X). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Tulasviridae, which is available at ictv.global/report/tulasviridae.

ICTV Virus Taxonomy Profile: Cruliviridae 2023.

Cruliviridae is a family of negative-sense RNA viruses with genomes of 10.8-11.5 kb that have been found in crustaceans. The crulivirid genome consists of three RNA segments with ORFs that encode a nucleoprotein (NP), a glycoprotein (GP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and in some family members, a zinc-finger (Z) protein of unknown function. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Cruliviridae, which is available at ictv.global/report/cruliviridae.

ICTV Virus Taxonomy Profile: Wupedeviridae 2023.

Wupedeviridae is a family of negative-sense RNA viruses with genomes of about 20.5 kb that have been found in myriapods. The wupedevirid genome consists of three monocistronic RNA segments with open reading frames (ORFs) that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Wupedeviridae, which is available at ictv.global/report/wupedeviridae.

ICTV Virus Taxonomy Profile: Mypoviridae 2023.

Mypoviridae is a family of negative-sense RNA viruses with genomes of about 16.0 kb that have been found in myriapods. The mypovirid genome consists of three monocistronic RNA segments that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Mypoviridae, which is available at: ictv.global/report/mypoviridae.

ICTV Virus Taxonomy Profile: Jingchuvirales 2023.

Jingchuvirales is an order of negative-sense RNA viruses with genomes of 9.1-15.3 kb that have been associated with arachnids, barnacles, crustaceans, insects, fish and reptiles in Africa, Asia, Australia, Europe, North America and South America. The jingchuviral genome has two to four open reading frames (ORFs) that encode a glycoprotein (GP), a nucleoprotein (NP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and/or proteins of unknown function. Viruses in the order are only known from their genome sequences. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the order Jingchuvirales and on the families Aliusviridae, Chuviridae, Crepuscuviridae, Myriaviridae and Natareviridae, which are available at ictv.global/report/jingchuvirales, ictv.global/report/aliusviridae, ictv.global/report/chuviridae, ictv.global/report/crepuscuviridae, ictv.global/report/myriaviridae and ictv.global/report/natareviridae, respectively.

Diversity of Salmonella enterica phages isolated from chicken farms in Kenya.

Non-typhoidal Salmonella enterica infections are one of the leading causes of diarrhoeal diseases that spread to humans from animal sources such as poultry. Hence, keeping poultry farms free of Salmonella is essential for consumer safety and for a better yield of animal products. However, the emergence of antibiotic resistance due to over usage has sped up the search for alternative biocontrol methods such as the use of bacteriophages. Isolation and characterization of novel bacteriophages are key to adapt phage-based biocontrol applications. Here, we isolated and characterized Salmonella phages from samples collected at chicken farms and slaughterhouses in Kenya. The genomic characterization of these phage isolates revealed that they belong to four ICTV (International Committee on Taxonomy of Viruses) phage genera. All these phages are lytic and possibly suitable for biocontrol applications because no lysogenic genes or virulence factors were found in their genomes. Hence, we recommend further studies on these phages for their applications in Salmonella biocontrol.

Bacteriophage Taxonomy: A Continually Evolving Discipline.

While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.