Virucidal activity of chemical biocides against mimivirus, a putative pneumonia agent

A history of over 40 years of potentially pathogenic free-living amoeba studies in Brazil - a systematic review

Free-living amoeba (FLA) group includes the potentially pathogenic genera Acanthamoeba, Naegleria, Balamuthia, Sappinia, and Vermamoeba, causative agents of human infections (encephalitis, keratitis, and disseminated diseases). In Brazil, the first report on pathogenic FLA was published in the 70s and showed meningoencephalitis caused by Naegleria spp. FLA studies are emerging, but no literature review is available to investigate this trend in Brazil critically. Thus, the present work aims to integrate and discuss these data. Scopus, PubMed, and Web of Science were searched, retrieving studies from 1974 to 2020. The screening process resulted in 178 papers, which were clustered into core and auxiliary classes and sorted into five categories: wet-bench studies, dry-bench studies, clinical reports, environmental identifications, and literature reviews. The papers dating from the last ten years account for 75% (134/178) of the total publications, indicating the FLA topic has gained Brazilian interest. Moreover, 81% (144/178) address Acanthamoeba-related matter, revealing this genus as the most prevalent in all categories. Brazil’s Southeast, South, and Midwest geographic regions accounted for 96% (171/178) of the publications studied in the present work. To the best of our knowledge, this review is the pioneer in summarising the FLA research history in Brazil.

Outdoor disinfectant sprays for the prevention of COVID-19: Are they safe for the environment?

Due to the wide range of viability on inanimate surfaces and fomite transmission of SARS-CoV-2, hydrogen peroxide (0.5%, HP) and hypochlorite-based (0.1%, HC) disinfectants (common biocides) are proposed by World Health Organization to mitigate the spread of this virus in healthcare settings. They can be adopted and applied to outdoor environments. However, many studies have shown that these two disinfectants are toxic to fishes and aquatic non-target organisms (primary producers and macroinvertebrates). The global market of these disinfectants will increase in coming years due to COVID-19. Therefore, it is urgent to highlight the toxicities of these disinfectants. The main findings of this article allow the community to develop a new strategy to protect the environment against the hazardous effects of disinfectants. Therefore, we use the "toxicity calculated ratio (TC ratio)" that refers to the fold increase or decrease in the toxicities reported in the literature (NOEC, LOEC, LC50 and EC50) relative to the WHO-recommended dose of HP and HC. The calculated TC ratios are valuable for policy makers to formulate the regulations to prevent disinfectant exposure in the environment. Our results were collected via PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analysis) guidelines and showed that the TC ratios are from the single digits to several thousand-fold lower than the HP and HC recommended dose, which means these disinfectants are potentially dangerous to non-target organisms. The results also showed that HP and HC are toxic to the growth and reproduction of non-target organisms. Therefore, we recommend policymakers formulate protocols for critical assessment and monitoring of the environment-especially on non-target organisms in water bodies located in and around disinfectant-exposed areas to safeguard the environment in the future.

A critical evaluation of current protocols for self-sterilizing surfaces designed to reduce viral nosocomial infections

BACKGROUND

Biocidal high-touch surfaces contact surfaces can be used to help reduce healthcare-acquired infections (HAIs). While the bactericidal protocols are well developed, there remains high variability in the methods used to evaluate the virucidal properties of such surfaces. This paper seeks to identify the most commonly used methods and critically evaluate the strengths of each method by comparing tests from standard testing organisations and related bactericidal protocols.

METHODS

Three databases and grey literature were queried using a key-word search for relevant articles. Articles were selected if they met the criteria of virucidal properties of self-sterilizing surfaces designed to prevent HAIs. Of the resulting 177 articles, 38 met the inclusion criteria.

RESULTS

The resulting papers varied greatly in their testing methods and recommendations. Further, no standard test adequately meets the needs for specifically testing virucidal properties of self-sterilizing surfaces.

CONCLUSIONS

Studies have shown that temperature and humidity can affect the performance of virucidal touch-surfaces, but no standard protocols were found to test these factors.

Sanitizing agents for virus inactivation and disinfection

Viral epidemics develop from the emergence of new variants of infectious viruses. The lack of effective antiviral treatments for the new viral infections coupled with rapid community spread of the infection often result in major human and financial loss. Viral transmissions can occur via close human-to-human contact or via contacting a contaminated surface. Thus, careful disinfection or sanitization is essential to curtail viral spread. A myriad of disinfectants/sanitizing agents/biocidal agents are available that can inactivate viruses, but their effectiveness is dependent upon many factors such as concentration of agent, reaction time, temperature, and organic load. In this work, we review common commercially available disinfectants agents available on the market and evaluate their effectiveness under various application conditions. In addition, this work also seeks to debunk common myths about viral inactivation and highlight new exciting advances in the development of potential sanitizing agents.

Structural and Proteomic Characterization of the Initiation of Giant Virus Infection

Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.

Mimiviruses and the Human Interferon System: Viral Evasion of Classical Antiviral Activities, But Inhibition By a Novel Interferon-β Regulated Immunomodulatory Pathway

In this review we discuss the role of mimiviruses as potential human pathogens focusing on clinical and evolutionary evidence. We also propose a novel antiviral immunomodulatory pathway controlled by interferon-β (IFN-β) and mediated by immune-responsive gene 1 (IRG1) and itaconic acid, its product. Acanthamoeba polyphaga Mimivirus (APMV) was isolated from amoebae in a hospital while investigating a pneumonia outbreak. Mimivirus ubiquity and role as protist pathogens are well understood, and its putative status as a human pathogen has been gaining strength as more evidence is being found. The study of APMV and human cells interaction revealed that the virus is able to evade the IFN system by inhibiting the regulation of interferon-stimulated genes, suggesting that the virus and humans have had host-pathogen interactions. It also has shown that the virus is capable of growing on IFN-α2, but not on IFN-β-treated cells, hinting at an exclusive IFN-β antiviral pathway. Our hypothesis based on preliminary data and published articles is that IFN-β preferentially upregulates IRG1 in human macrophagic cells, which in turn produces itaconic acid. This metabolite links metabolism to antiviral activity by inactivating the virus, in a novel immunomodulatory pathway relevant for APMV infections and probably to other infectious diseases as well.

Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes

Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.

Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa

The Megavirales are a newly described order capable of infecting different types of eukaryotic hosts. For the most part, the natural host is unknown. Several methods have been used to detect these viruses, with large discrepancies between molecular methods and co-cultures. To isolate giant viruses, we propose the use of different species of amoeba as a cellular support. The aim of this work was to isolate new Brazilian giant viruses by comparing the protozoa Acanthamoeba castellanii, A. polyphaga, A. griffini, and Vermamoeba vermiformis (VV) as a platform for cellular isolation using environmental samples. One hundred samples were collected from 3 different areas in September 2014 in the Pampulha lagoon of Belo Horizonte city, Minas Gerais, Brazil. PCR was used to identify the isolated viruses, along with hemacolor staining, labelling fluorescence and electron microscopy. A total of 69 viruses were isolated. The highest ratio of isolation was found in A. polyphaga (46.38%) and the lowest in VV (0%). Mimiviruses were the most frequently isolated. One Marseillevirus and one Pandoravirus were also isolated. With Brazilian environmental samples, we demonstrated the high rate of lineage A mimiviruses. This work demonstrates how these viruses survive and circulate in nature as well the differences between protozoa as a platform for cellular isolation.

Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries

In 2003, Acanthamoeba polyphaga mimivirus (APMV) was first described and began to impact researchers around the world, due to its structural and genetic complexity. This virus founded the family Mimiviridae. In recent years, several new giant viruses have been isolated from different environments and specimens. Giant virus research is in its initial phase and information that may arise in the coming years may change current conceptions of life, diversity and evolution. Thus, this review aims to condense the studies conducted so far about the features and peculiarities of APMV, from its discovery to its clinical relevance.

Growing a giant: evaluation of the virological parameters for mimivirus production

Acanthamoeba polyphaga mimivirus (APMV) was described in 2003, and due to its unique structural and genetic complexity, the viral family Mimiviridae was created. APMV prompted the creation of an open field of study on the function of hundreds of never-before-seen open reading frames (ORFs) and their roles in virus-host interactions. In recent years, several giant viruses have been isolated from different environments and specimens. Although the scientific community has experienced a remarkable advancement in the comprehension of the mimivirus replication cycle in the last years, few studies have been devoted to the investigation of the methodological features and conditions for mimivirus cultivation. In this work, conditions for the cultivation of mimivirus isolates were investigated to obtain relevant information about the production of infectious particles, total viral particles and viral DNA. The results suggest that low viral doses are more efficient for the production of infectious particles, yielding up to 5000 TCID50 for each inoculated TCID50. Besides methodological information, these data also reveal, for the first time, the ratio between total and infectious particles (in TCID50) that are produced during mimivirus cultivation in laboratory conditions. All of this information can be used as a worldwide guide for the production of mimiviruses and can help prompt mimivirological studies in different fields.

The virus of my virus is my friend: ecological effects of virophage with alternative modes of coinfection

Virophages are viruses that rely on the replication machinery of other viruses to reproduce within eukaryotic hosts. Two different modes of coinfection have been posited based on experimental observation. In one mode, the virophage and the virus enter the host independently. In the other mode, the virophage adheres to the virus so both virophage and virus enter the host together. Here we ask: what are the ecological effects of these different modes of coinfection? In particular, what ecological effects are common to both infection modes, and what are the differences particular to each mode? We develop a pair of biophysically motivated ODE models of viral-host population dynamics, corresponding to dynamics arising from each mode of infection. We find that both modes of coinfection allow for the coexistence of the virophage, virus, and host either at a stable fixed point or through cyclical dynamics. In both models, virophage tends to be the most abundant population and their presence always reduces the viral abundance and increases the host abundance. However, we do find qualitative differences between models. For example, via extensive sampling of biologically relevant parameter space, we only observe bistability when the virophage and the virus enter the host together. We discuss how such differences may be leveraged to help identify modes of infection in natural environments from population level data.

Acanthamoeba polyphaga mimivirus stability in environmental and clinical substrates: implications for virus detection and isolation

Viruses are extremely diverse and abundant and are present in countless environments. Giant viruses of the Megavirales order have emerged as a fascinating research topic for virologists around the world. As evidence of their ubiquity and ecological impact, mimiviruses have been found in multiple environmental samples. However, isolation of these viruses from environmental samples is inefficient, mainly due to methodological limitations and lack of information regarding the interactions between viruses and substrates. In this work, we demonstrate the long-lasting stability of mimivirus in environmental (freshwater and saline water) and hospital (ventilator plastic device tube) substrates, showing the detection of infectious particles after more than 9 months. In addition, an enrichment protocol was implemented that remarkably increased mimivirus detection from all tested substrates, including field tests. Moreover, biological, morphological and genetic tests revealed that the enrichment protocol maintained mimivirus particle integrity. In conclusion, our work demonstrated the stability of APMV in samples of environmental and health interest and proposed a reliable and easy protocol to improve giant virus isolation. The data presented here can guide future giant virus detection and isolation studies.

Amoebas as mimivirus bunkers: increased resistance to UV light, heat and chemical biocides when viruses are carried by amoeba hosts

Amoebas of the genus Acanthamoeba are protists that are associated with human disease and represent a public health concern. They can harbor pathogenic microorganisms, acting as a platform for pathogen replication. Acanthamoeba polyphaga mimivirus (APMV), the type species of the genus Mimivirus, family Mimiviridae, represents the largest group of amoeba-associated viruses that has been described to date. Recent studies have demonstrated that APMV and other giant viruses may cause pneumonia. Amoebas can survive in most environments and tolerate various adverse conditions, including UV light irradiation, high concentrations of disinfectants, and a broad range of temperatures. However, it is unknown how the amoebal intracellular environment influences APMV stability and resistance to adverse conditions. Therefore, in this work, we evaluated the stability of APMV, either purified or carried by the amoeba host, under extreme conditions, including UV irradiation, heat and exposure to six different chemical biocides. After each treatment, the virus was titrated in amoebas using the TCID50 method. APMV was more stable in all resistance tests performed when located inside its host. Our results demonstrate that Acanthamoeba acts as a natural bunker for APMV, increasing viral resistance to extreme physical and chemical conditions. The data raise new questions regarding the survival of APMV in nature and in hospital environments.

Giant viruses of amoebae as potential human pathogens

Giant viruses infecting phagocytic protists are composed of mimiviruses, the record holders of particle and genome size amongst viruses, and marseilleviruses. Since the discovery in 2003 at our laboratory of the first of these giant viruses, the Mimivirus, a growing body of data has revealed that they are common inhabitants of our biosphere. Moreover, from the outset, the story of Mimivirus has been linked to that of patients exhibiting pneumonia and it was shown that patients developed antibodies to this amoebal pathogen. Since then, there have been several proven cases of human infection or colonization with giant viruses of amoebae, which are known to host several bacteria that are human pathogens. Mimiviruses and marseilleviruses represent a major challenge in human pathology, as virological procedures implemented to date have not used appropriate media to allow their culture, and molecular techniques have used filtration steps that likely prevented their detection. Nevertheless, there is an increasing body of evidence that mimiviruses might cause pneumonia and that humans carry marseilleviruses, and re-analyses of metagenomic databases have provided evidence that these giant viruses can be common in human samples. The proportion of human infections related to these giant mimiviruses and marseilleviruses and the precise short- and long-term consequences of these infections have been scarcely investigated so far and should be the subject of future works.

A decade of improvements in Mimiviridae and Marseilleviridae isolation from amoeba

Since the isolation of the first giant virus, the Mimivirus, by T.J. Rowbotham in a cooling tower in Bradford, UK, and after its characterisation by our group in 2003, we have continued to develop novel strategies to isolate additional strains. By first focusing on cooling towers using our original time-consuming procedure, we were able to isolate a new lineage of giant virus called Marseillevirus and a new Mimivirus strain called Mamavirus. In the following years, we have accumulated the world's largest unique collection of giant viruses by improving the use of antibiotic combinations to avoid bacterial contamination of amoeba, developing strategies of preliminary screening of samples by molecular methods, and using a high-throughput isolation method developed by our group. Based on the inoculation of nearly 7,000 samples, our collection currently contains 43 strains of Mimiviridae (14 in lineage A, 6 in lineage B, and 23 in lineage C) and 17 strains of Marseilleviridae isolated from various environments, including 3 of human origin. This study details the procedures used to build this collection and paves the way for the high-throughput isolation of new isolates to improve the record of giant virus distribution in the environment and the determination of their pangenome.