Microbiome and virome on indoor surfaces of an Antarctic research ship

BACKGROUND Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. FINDINGS Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. MAIN CONCLUSIONS This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.

Relevance of national, regional and global virome projects on pandemics prediction, prevention, and control: a social network analysis of GVP-citing articles

BACKGROUND The Global Virome Project (GVP) was proposed in 2018 as an evolution of the USAID PREDICT project and was presented as a "collaborative scientific initiative to discover zoonotic viral threats and stop future pandemics". The immediate response was mixed, with public health and scientific communities representatives showing skepticism, if not direct opposition. OBJECTIVES The economic, social, and health consequences of the coronavirus disease 2019 (COVID-19) pandemic demonstrated how unprepared the world was in the face of new pandemics. This paper analyses the impact of the GVP on the scientific and public health communities. METHODS Published scientific articles that cited the two 2018 seminal publications proposing the project were analysed using social network analysis methods. FINDINGS Encompassing the periods before and after the onset of the Covid-19 pandemic, the results indicate that (i) the concepts of the GVP have received more support than opposition in the scientific literature; (ii) its foundations should be updated to address the specific criticisms. MAIN CONCLUSIONS Shifting focus to national virome projects can provide tangible, regional benefits that can positively contribute towards a consensus on achieving a high level of preparedness for the ever-present possibility of the following global viral pandemic.

Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China / 生物医学与环境科学（英文）

OBJECTIVE@#To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China.@*METHODS@#Ten smear samples were collected in March 2019. Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus.@*RESULTS@#We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01-S09 and S10. In S01-S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01-S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B.@*CONCLUSION@#This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds.

Urine virology and clinical characteristics of female patients with overactive bladder / 中华泌尿外科杂志

Objective:To investigate the urinary virology and clinical characteristics of female overactive bladder (OAB) patients.Methods:Catheterized urine samples were collected from 55 women with OAB and 18 control individuals between January 2021 and August 2021. Inclusion criteria were: female with age>18, diagnosed as OAB, OABSS total score≥3 and item Urgency score≥2, informed consent signed. Exclusion criteria were: Urine culture positive, urinary catheter indwelling status, antibiotic usage in recent 30 days, other disease leading to OAB-like symptoms, pelvic organ prolapse and current pregnancy, immunosuppressive therapy or status. Clinical characteristic and history were collected. OAB symptoms were assessed via both OABSS (overactive bladder symptom score) and OAB-V8 (8-item overactive bladder questionnaire). The urine specimens were analyzed using mNGS for identifying viral infections. The correlation between the disease and JC virus infection was analyzed by t test, chi-square test, binary logistic regression analysis and Spearman correlation matrix, and the Nomogram map for predicting the risk of viral infection was constructed. Results:In total, 55 women with OAB and 18 healthy controls were recruited in the study. There are significant difference in terms of UTI history, pelvic surgery history and the habit of holding urine [60.0%(n=33)to 16.7%(n=3), P=0.002; 43.6%(n=24)to 0.0%(n=0), P<0.01; 36.4%( n=20)to 5.6%( n=1), P=0.015]. Based on mNGS results, OAB patients were identified with more positive viral infection [47.3%(n=26)to 33.3%(n=6)] and more JC virus infection. In the OAB group, subtype 7B of JCV ( n=8) was identified, while in the control group, subtype 7A(n=2) was identified. Pairwise Spearman correlation analysis indicated high correlations between viral infection and OABSS ( r=0.58), age and pausimenia ( r=0.68), hypertension and age ( r=0.53), respectively. Estimates from binary logistic regression model indicated risk factors for virus infection in OAB patients including age ( OR=1.99, 95% CI 0.02-2.61), holding urine habit( OR=2.16, 95% CI 0.18-3.85) and pelvic surgery ( OR=2.53, 95% CI 0.54-4.27). Conclusions:Urinary viral infections appear to be associated with more severe OAB symptoms and JC virus may be a potential therapeutic target for OAB.

Different strategies of reducing non-viral nucleic acid of meta-virome in plasma: a comparative study / 中国输血杂志

【Objective】 To explore the influence of common methods of reducing non-viral nucleic acid on the abundance of plasma virus group. 【Methods】 Three kinds of library construction, five kinds of centrifugation conditions, two kinds of filters, four kinds of enzymes and four concentrations of chloroform were used to treat plasma samples added quantitatively 2.16 mL of pseudorabies virus(PRV) and 2.16 mL of porcine parvovirus(PPV). A total of 21.6 mL of plasma samples were processed, including 54 samples. Subsequently, nucleic acid was extracted, mitochondrial DNA(mtDNA) and two viruses were quantitated, the library of the next generation sequencing was constructed, Illumina NovaSeq 6000 was used for the next generation sequencing. The sequencing data were compared with Kraken Py 2.0 software, and the species annotation analysis was conducted. The corresponding species classification information of each segment was obtained to analyze the impact of different reducing non-viral nucleic acid methods on the relative abundance of microorganisms and two indicator viruses. 【Results】 After sequencing by Illumina NovaSeq 6000, 306.27 GB raw data and 193.17 GB clean data were obtained, with Q20>90%, Q30>85%, Error Rate of 0.03%, and average GC Content of 45.02%. The DNA library construction process significantly increased the proportion of microbial sequences and the PRV abundance [(91.8±0.5)%](P<0.05); RNA library construction and combined library construction can increase the abundance of Pestivirus, an RNA virus, and the PRV abundance was(17.7±3.3)% and(8.1±1.5)% respectively. The Ct value of mtDNA was increased and the proportion of human sequence decreased to less than(89.5±1)%, while the proportion of microbial sequence increased to (2.4±0.03)% after treatment of five centrifugation conditions(P<0.05); After centrifugation at 4℃, 100 g, 30 min, the PRV abundance was increased to (40.6±6)%, and centrifugation at 4℃, 4 000 g, 45 min reduced the PRV abundance to (4.1±0.01)%(P<0.05). Both of 0.22-μm filter and 0.45-μm filter increased the Ct value of mtDNA to above 25.56±0.13, decreased the proportion of human sequence to less than (86.1±0.6)%, increased the proportion of microbial sequence to (3.1±0.1)% and (3.4±0.2)%, and decreased the PRV abundance to (1.6±0.3)% and (4.1±0.7)%(P<0.05), while there was no statistical difference in the effect on PPV concentration and abundance. DNase Ⅰ and Benzonase increased the Ct value of PPV to 25.65±0.06 and 25.36±0.45, decreased the proportion of human sequence to (81.7±5.6)% and (72.8±6.7)%, and increased the proportion of microbial sequence and PRV abundance to (11.0±4.1)% and (16.1±4.7)%, (55.8±2.3)% and (39.0±8.9)%, respectively(P<0 05); After treatment with RNase A, the Ct value of PRV increased to 25.20±0.11, and the human sequence proportion decreased to (85.4±5.6)%(P<0 05); Lysozyme had no effect on removing non-viral nucleic acid. The chloroform of 1%, 5%, 10% and 20% increased Ct value of PRV and mtDNA to no less than 27.17±0.21 and 25.68±0.04; Only 10% chloroform increased the proportion of microbial sequences to (3.1±1.2)%(P<0.05); The abundance of PRV with 1% and 5% chloroform treatment was increased to (48.7±13.3)% and (42.1±5.5)%(P<0.05), while 10% and 20% chloroform reduced PRV abundance to (1.0±0.5)% and (3.4±2.8)%(P<0.05). There was no statistical difference in the effect of chloroform with four contents on PPV abundance. 【Conclusion】 Centrifugation at 4℃, 5 000 g, 10 min is suitable for increasing the overall abundance of virus, and centrifugation at 4℃, 100 g, 30 min is suitable for increasing the content of virus similar to PRV. 0.45-μm filter, DNase Ⅰ, Benzonase and low concentration chloroform can effectively reduce the proportion of non-viral nucleic acid sequence in plasma to increase the abundance of the indicated virus group. Thus, the enrichment effect of plasma meta-virome is closely related to the nature of the virus, and the appropriate virus enrichment method should be selected according to the research purpose to establish the corresponding enrichment strategy.

Comparative metavirome analysis in polytransfused patients

Due to the high transfusion volume, polytransfused patients with sickle cell disease (SCD) and beta-thalassemia are constantly exposed to parenterally transmitted infections. Currently, we have little information about the virome of such patients and how the virological composition might be influenced by the hemotherapy procedures that these patients receive. The objective of this study was to compare the viral diversity between these two groups with respect to the viral abundance and how it might be affected by the specific conditions of these groups. We sequenced by next-generation sequencing (NGS) and compared the virome of 30 patients with beta-thalassemia major, 45 with SCD, and 16 blood donors from the Blood Center of Ribeirão Preto, Brazil. Predominantly, commensal viruses including Torque teno virus (TTV) genotypes and human pegiviris-1 (HPgV-1) were identified in each group. Strikingly, while HPgV-1 reads were dominant in the SCD group, thalassemic patients showed high TTV abundance, expressed both in viral reads and genotypes. We speculated that the commensal virome of polytransfused patients might be influenced by the transfusion frequency and disease characteristics and that commensal viruses might be used as important genetic biomarkers for these hematological disturbances. Nevertheless, more specific studies are necessary to confirm a relationship between blood virome and transfusion treatment.

A novel Betacoronavirus characterised in collared peccaries from the Rio de Janeiro Zoo (Brazil) killed by unknown disease

In an enclosure with nine collared peccaries (Pecari tajacu) from the Rio de Janeiro city Zoo, Brazil, one specimen was found dead and two others developed prostration, apathy and dehydration, resulting on its death. Necropsy of two animals pointed to pulmonary and renal damage. Histological examination revealed vasculitis in spleen from both P. tajacu, suggesting a systemic viral infection. Lungs from one specimen showed fibrinoid vasculitis, alveolar damage with hyaline membrane, and interstitial lymphocytes infiltration. Virome analysis in anal wash samples from the latter two animals revealed a new type of Betacoronavirus, lineage A, provisionally named Ptajacu-CoV.

El viroma humano. Implicaciones en la salud y enfermedad / The human virome. Its implications in health and disease

Introducción: El viroma humano se refiere al conjunto de todos los virus encontrados en el organismo humano. La diversidad viral del organismo humano bajo condiciones no patológicas ha sido subestimada. Se estima que hay 100 veces más virus en el cuerpo humano que células eucariotas. Objetivo: Realizar una revisión sistemática sobre las implicaciones del viroma humano para la salud y la enfermedad. Material y Métodos: Se realizó una revisión de artículos científicos publicados entre 2012 y 2017 en diversas bases de datos en línea. Se utilizaron en total 26 fuentes bibliográficas, incluidos artículos originales y revisiones. Desarrollo: Se presenta el conocimiento existente hasta el momento sobre las comunidades virales encontradas en diferentes sitios anatómicos como el sistema digestivo, respiratorio, genitourinario y sangre, los bacteriófagos y los Anellovirus son los virus más frecuentemente detectados. Si bien se hace evidente que el viroma tiene un papel tanto en el mantenimiento de la salud como en la enfermedad, estos mecanismos aún no se han esclarecido. Conclusiones: El organismo humano tiene una alta diversidad viral incluso bajo condiciones no patológicas. Aunque mucho se desconoce aún sobre las implicaciones del viroma, los avances en este campo abren nuevas perspectivas en la biomedicina(AU)

Introduction: The human virome refers to the collection of all viruses found in the human body. The viral diversity of the human body under non-pathological conditions has been underestimated. It is estimated that there are 100 times more viruses in the human body than eukaryotic cells. Objective: To carry out a systematic review of the human virome and its implications in health and disease. Materials and Methods: A review of scientific papers published between 2012 and 2017 in different online databases was made. A total of 26 bibliographic sources were used, including both original articles and reviews. Development: We present the existing knowledge to date about the viral communities found in different anatomical sites such as the digestive, respiratory, and genitourinary systems and the bloodstream; being the bacteriophages and Anellovirus the most frequently detected viruses. Although it is clear that the human virome plays a role both in maintaining health and in disease, these mechanisms have not yet been clarified. Conclusions: The human body has a high viral diversity even under non-pathological conditions. Although much is still unknown about the implications of these viruses on health and disease, advances in this field open new perspectives in the world of biomedicine(AU)

Microbiome: Paediatricians’ perspective.

Millions of microorganisms inhabit the human body and affect its homeostasis in multiple ways. Alterations in this microbial community have implications for the health and survival of the human hosts. It is believed that these microorganisms should be included as part of the human genome because of their influence on human physiology hence the term “microbiome” is commonly used to refer to these microbes along with their genetic make-up and their environmental interactions. In this article we attempt to provide an insight into this recently discovered vital organ of the human body which is yet to be fully explored. We herein discuss the composition and role of microbiome in human health and disease with a special emphasis in children and culture-independent techniques employed in mapping of the microbiome. Alteration in the gut microbiome has been associated with causation of several paediatric diseases like infantile colic, necrotizing enterocolitis, asthma, atopy, obesity, type -1 diabetes, and autism. Atopic dermatitis and psoriasis have also been associated with changes in the cutaneous microbiome. Respiratory microbial imbalances during infancy have been linked with wheezing and bronchial asthma. Dysbiosis in the regional microbiome has been linked with caries, periodontitis, and chronic rhinosinusitis. The future therapeutic implications of this rapidly evolving area of research are also highlighted.