Figure 3 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
Classical and novel human astrovirus viral load in stool samples. The horizontal lines denote median log values. ***Po0.001. human astrovirus, HAstV.
Source publication
Classical human astroviruses (HAstV) are the third most common cause of non-bacterial acute gastroenteritis. Due to the lack of routine molecular assays, novel HAstV are underdiagnosed and the magnitude of their contribution to clinical disease remains unknown. To better understand their prevalence and the susceptible patient profile, we conducted...
Context in source publication
Context 1
... viral load was estimated for each positive case (Table 1 and Figure 3) and ranged from 7.1 × E2 to 3.3 × E9 for MLB2, 3.3 × E2 to 5.5 × E4 for MLB1, 3.4 × E2 to 8.4 × E2 for VA2 and 2.1 × E5 to 6.0 × E11 for classical HAstV. Overall, the viral load was significantly lower (P = 0.0007) in novel HAstV-positive (MLB1, MLB2 and VA2) than in classical HAstV-positive samples (Table 2). This latter observation did not result from different time intervals between the symptom onsets and the collection of samples (P = 0.95). Due to the small number of positive samples, a statistical analysis could not be performed to compare viral loads between the different groups of novel HAstV. The mean viral load of all HAstV-positive samples was similar between adults and children (P = 0.137) and when novel and classical HAstV were considered separately (P = 0.433 and P = 0.253, respectively). The distribution of novel and classical HAstV-positive cases was uniform throughout the year, irrespective of the studied population ( Figure ...
Similar publications
Background:
Until today, classic human astroviruses have not been associated with central nervous system infections in immunocompetent patients.
Case presentation:
A 16-month-old Caucasian girl presented with repetitive generalized seizures with a 4-day history of watery diarrhea, which had already gradually improved. Initially, the prolonged se...
Citations
... Hence, as in the case of CMV, the prevalence of viral infections with transient and/or rare viremia may have been underestimated. Furthermore, due to the limited volume of each sample, we were unable to screen for astroviruses, which are associated with disseminated infections among immunocompromised patients [4,5,[56][57][58]. Corticosteroid treatments as well as antiviral prophylaxis/treatments were not systematically recorded, although institutional strategies were unchanged. ...
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients’ plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26–36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
... According to the phylogenetic tree analysis of classic HAstV, only two genotypes, including HAstV-1 and HAstV-5, were identified in Shanghai from 2017 to 2018. HAstV-1 (95.24%) was the predominant genotype detected in children with diarrhea, which is consistent with the findings of our previous study from 2008 to 2011 as well as with other reports conducted in Japan, Switzerland, Asian Russia, Korea, Germany, and Brazil [36,37,39,[48][49][50][51]. Moreover, HAstV-5 was only detected in two samples in early 2018; to the best of our knowledge, this study is the first to report the appearance of HAstV-5 in Shanghai. ...
Background
In addition to rotavirus and norovirus, human adenovirus (HAdV) and classic human astrovirus (classic HAstV) are important pathogens of acute diarrhea in infants and young children. Here, we present the molecular epidemiology of HAdV and classic HAstV in children with acute diarrhea in Shanghai.
Methods
Fecal specimens were collected from 804 outpatient infants and young children diagnosed with acute diarrhea in Shanghai from January 2017 to December 2018. All of the samples were screened for the presence of HAdV and classic HAstV. HAdV and classic HAstV were detected using traditional PCR and reverse-transcription PCR, respectively. All of the HAdV and classic HAstV positive samples were genotyped by phylogenetic analysis.
Results
Among the 804 fecal samples, 8.58% (69/804) of samples were infected with either HAdV or classic HAstV, and five were co-infected with two diarrhea viruses. The overall detection rates of HAdV and classic HAstV were 3.47% (28/804) and 5.22% (42/804), respectively. Four subgroups (A, B, C, and F) and seven genotypes (HAdV-C1, −C2, −B3, −C5, −A31, −F40, and -F41) of HAdV were detected. Subgroup F had the highest constituent ratio at 64.29% (18/28), followed by non-enteric HAdV of subgroup C (21.43%, 6/28) and subgroup B 10.71% (3/28). HAdV-F41 (60.71%, 17/28) was the dominant genotype, followed by HAdV-C2 (14.29%, 4/28) and HAdV-B3 (10.71%, 3/28). Two genotypes of classic HAstV (HAstV-1 and HAstV-5) were identified in 42 samples during the study period; HAstV-1 (95.24%, 40/42) was the predominant genotype, and the other two strains were genotyped as HAstV-5. No significant differences were found between boys and girls in the detection rates of HAdV ( P = 0.604) and classic HAstV ( P = 0.275). Over half of the HAdV infections (82.14%, 23/28) and classic HAstV infections (66.67%, 28/42) occurred in children less than 36 months. Seasonal preferences of HAdV and classic HAstV infections were summer and winter, respectively. In this study, the common clinical symptoms of children with acute diarrhea were diarrhea, vomiting, fever and abdominal pain.
Conclusions
Our findings indicate that HAdV and classic HAstV play important roles in the pathogenesis of acute diarrhea in children in Shanghai. Systematic and long-term surveillance of HAdV and classic HAstV are needed to monitor their prevalence in children and prevent major outbreak.
... Our results further highlight that HAstV has a significant circulation in the global population, with a higher prevalence of novel HAstV (2.1%) than classical HAstV (0.9%). This observation is in agreement with previous reports and underscores the clinical pertinence of novel HAstV in the paediatric population [44][45][46]. ...
Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.
Trial registration: ClinicalTrials.gov identifier: NCT02225769.
... Clinically unrecognized mNGS findings were confirmed on unpooled plasma by specific semi-quantitative or quantitative r(RT-)PCR assays as previously published; additional specimens (including plasma, cerebrospinal fluid, bronchoalveolar lavage (BAL) fluids, nasopharyngeal swabs, native urines, stools suspension, tissue biopsies or bone marrow) were tested when available and pertinent. Quantitative r(RT-)PCR assays were done for Mamastrovirus 1 (classical) using the updated human astrovirus (HAstV) combination [21], Mamastrovirus 6 (MLB2) using the MLB2 assay [22], Usutu virus [23], and bufavirus using the BuV (NS1) assay [24]. Semiquantitative r(RT-)PCR assays were done for cutavirus using the CuV (VP2) assay [24], human polyomavirus (HPyV) 6 using the VP2 assay [25], HPyV-7 using the VP2 assay [25], and rubella virus [26]. ...
Background
Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated pipeline and de novo analysis on pooled routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal, and unexpected viruses.
Results
Median duration of intensive immunosuppression was 5.1 months (IQR 5.5). GvHD-related mortality rate was 36%. mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥ 3 distinct viruses were detected in 16/25 patients; Anelloviridae (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7 patients with fatal outcomes, viral sequences not assessed by routine investigations were identified with mNGS and confirmed by RT-PCR. These cases included Usutu virus (1), rubella virus (1 vaccine strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1).
Conclusions
Clinically unrecognized viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid-refractory/dependent GvHD in consecutive samples. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations, or re-infection.
... According to the phylogenetic tree analysis of classic HAstV, only two genotypes including HAstV-1 and HAstV-5 were identi ed in Shanghai from 2017 to 2018. HAstV-1 (95.24%) was the absolute predominant genotype detected in children with diarrhea which is consistent with our previous study from 2008 to 2011 as well as with other reports conducted in Japan, Switzerland, Asian Russia, Korea, German and Brazil [36,37,39,[48][49][50][51]. HAstV-5 was only detected in two samples in early 2018. ...
Background: In addition to rotavirus and norovirus, human adenovirus (HAdV) and classic human astrovirus (classic HAstV) have been identified as important pathogens of acute diarrhea in infants and young children. Here, we presented the molecular epidemiology of HAdV and classic HAstV in children with acute diarrhea in Shanghai.
Methods: Fecal specimens were collected from 804 outpatient infants and young children diagnosed as acute diarrhea in Shanghai from January 2017 to December 2018. All the samples were screened for the presence of HAdV and classic HAstV. HAdV and Classic HAstV were detected using traditional PCR and reverse-transcription PCR, respectively. All the HAdV and classic HAstV positive samples were genotyped by phylogenetic analysis.
Results: Among these 804 fecal samples, 8.58% (69/804) samples were infected with at least one of HAdV or classic HAstV, and one of them was co-infected with these two viruses. The overall detection rates of HAdV and classic HAstV were 3.47% (28/804) and 5.22% (42/804), respectively. Four subgroups (A, B, C and F) of HAdV were detected and seven different genotypes (HAdV-C1, -C2, -B3, -C5, -A31, -F40 and -F41) were identified. Subgroup F had the highest constituent ratio at 64.29% (18/28) followed by non-enteric HAdV of subgroup C (21.43%, 6/28) and subgroup B 10.71% (3/28). HAdV-F41 (60.71%, 17/28) was the dominant genotype, followed by HAdV-C2 (14.29%, 4/28) and HAdV-B3 (10.71%, 3/28). Two different genotypes of classic HAstV (HAstV-1 and HAstV-5) were identified in 42 samples during the study period. HAstV-1 (95.24%, 40/42) was the predominant genotype and the other two strains were genotyped as HAstV-5.
Conclusions: Those findings indicate that HAdV and classic HAstV play an important role in the pathogenesis of acute diarrhea in children in Shanghai. Systematic and long-term surveillance of HAdV and classic HAstV are needed to monitor their prevalence in children and prevent major outbreak.
... Our results further highlight that HAstV has a signi cant circulation in the global population, with a higher prevalence of novel HAstV (2.1%) than classical HAstV (0.9%). This observation is in agreement with previous reports and underscores the clinical pertinence of novel HAstV in the paediatric population [40][41][42]. ...
Background: Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Untargeted metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes.
Results: Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half the population (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.
Conclusions: This study highlighted several DNA and RNA viral sequences on a population of young children with fever of unknown origin and/or severe outcomes living in Tanzania, and provides a large list of novel viruses that should be considered as a potential cause of human infections.
... The same group performed a retrospective screen for classic and novel HAstVs in stool and CSF samples from pediatric and adult patients at a tertiary hospital, with a specially designed real-time RT-PCR (rRT-PCR) panel for novel HAstV-MLB1 to -MLB3 and HAstV-VA1 to -VA4 detection. Results showed that 20/654 stool samples were positive for novel HAstV, of which 40% were from SOT and HSCT recipients, but none of the available serum or plasma samples of these patients were positive (409). Novel HAstV-VA1 RNA was detected by mNGS and real-time RT-PCR in CSF and serum samples of an 18-month-old HSCT recipient from the United Kingdom with encephalitis (410). ...
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae , Anelloviridae , Flaviviridae , and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians’ radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
... A human astrovirus belonging to genotype 8 (HAstV-8) detected in a recent study carried out in Geneva, Switzerland (44), was propagated in Caco-2 cells. For isolation of the virus, a stool sample was diluted 1:10 in PBS and filtered through a 0.45-m-pore-size membrane. ...
To ensure transmission, enteric viruses must maintain their infectivity during the various environmental challenges that they face in transit within and between hosts. Increased knowledge of the factors affecting enteric virus survival may help to control their transmission. This study reveals that specific fecal bacterial components preserve classic human astrovirus infectivity by stabilizing viral particles. However, the outcomes of stool-virus interactions are very variable, ranging from protection to a reduction of viral infectivity, depending on the viral genotype and the individual from whom the stool has been collected. We show that the transmissibility of enteric viruses is dependent on the intestinal contents of the infected individual and highlight the complex multiple interactions that could explain the stochastic nature of enteric virus transmission in humans.
... Both groups of novel HAstVs have been further divided into several genotypes: MLB1-3 for the MLB astroviruses and VA1-5 for the VA astroviruses [3,4]. To date, no definitive association between novel astroviruses and gastroenteritis has yet been established, but further epidemiologic studies have confirmed the presence of novel HAstVs worldwide [9,[11][12][13][14][15][16]. Interestingly, novel HAstVs have been associated with unexpected central nervous system infections in-mostly immunocompromised-humans [17][18][19][20][21][22][23]. ...
... Interestingly, novel HAstVs have been associated with unexpected central nervous system infections in-mostly immunocompromised-humans [17][18][19][20][21][22][23]. While novel astroviruses have been identified in every continent, data in Europe are scarce, and so far only three countries have reported a systematic screening [12,14,18]. ...
... RNA was extracted from 200 µL of a 30% stool suspension using the Viasure RNA-DNA Extraction Kit (Certest Biotec, Zaragoza, Spain) following the manufacturer's instruction. Real-time RT-PCR specific assays for HAstV-MLB and HAstV-VA were performed using primers and probes previously published [14]. The standard curves and positive controls for MLB1, MLB2, MLB2-3, VA1, VA2, VA3, VA4 real-time RT-PCR assays were obtained using plasmid constructs kindly provided by Dr. S. Cordey from the Geneva University Hospitals. ...
A remarkable percentage of acute gastroenteritis cases remain etiologically undiagnosed. The aim of the study was to determine the prevalence of common and emerging enteric viruses, such as novel human astroviruses, among undiagnosed samples from children with acute gastroenteritis. Epidemiological studies for novel human astroviruses are still scarce. Stool samples collected over two consecutive winter seasons (2016–2017) from children with gastroenteritis in Spain, which were negative for bacteria, rotavirus, and adenovirus by routine diagnostics were screened by real-time RT-PCR assays for the presence of classical and novel astrovirus, rotavirus, norovirus GI and GII, sapovirus, and adenovirus. Overall, 220/384 stool samples (57.3%) were positive for at least one virus. Co-infections were identified in 21% of cases. Among a total of 315 viruses identified, adenovirus was the most prevalent (n = 103), followed by rotavirus (n = 51), sapovirus (n = 50), classical astrovirus (n = 43), novel astroviruses (n = 42), and norovirus (n = 26). Novel astroviruses were present in 13.3% of virus-positive cases. Most novel astroviruses were found in children <2-year-old (30/39 children, 77%, p = 0.01) and were found in co-infection (66%). Only classical astroviruses demonstrated significant differences in the Cq values during mono-infections compared to co-infections. In conclusion, common enteric viruses may be frequently found in children with undiagnosed gastroenteritis, indicating the need to implement more sensitive diagnostic methods. Novel astroviruses circulate in the community and could be the cause of gastroenteritis among young children.
... With the advent of next-generation sequencing technologies, two novel groups of highly divergent HAstVs (named MLB and VA/HMO) which are more closely related to certain animal astroviruses than to the classic HAstVs, have been identified in human stools of individuals with diarrhea (7)(8)(9)(10)(11)(12)(13) but also in asymptomatic healthy controls (14,15). To date, no definitive association between novel astroviruses and gastroenteritis has yet been established, but further epidemiologic studies have confirmed the presence of novel HAstVs worldwide (14,(16)(17)(18)(19)(20)(21). In addition, novel HAstVs have been recently identified as the cause of unexpected central nervous system infections in (mostly immunocompromised) humans (22)(23)(24)(25)(26)(27)(28). ...
... Viral RNA extraction and quantitative reverse transcription-PCR assay. RNA was extracted from the cell culture supernatants using the NucleoSpin RNA virus kit (Macherey-Nagel), following the manufacturer's instructions, and RT-qPCR-specific assays for MLB astroviruses were performed as previously published (19). Briefly, the following primers and probe for MLB1 were used: forward primer 4320, to 3848 from the virus with GenBank accession no. ...
MLB astroviruses are emerging viruses infecting humans. More studies are required to determine their exact epidemiology, but several reports have already identified them as the cause of unexpected clinical diseases, including severe neurologic diseases. Our study provides the first description of a cell culture system for the propagation of MLB astroviruses, enabling the study of their replicative cycle. Moreover, we demonstrated the unknown capacity of MLB astrovirus to establish persistent infections in cell culture. Whether these persistent infections are also established in vivo remains unknown, but the clinical consequences would be of high interest if persistence was confirmed in vivo . Finally, our analysis of IFN expression provides some trails to understand the mechanism by which MLB astroviruses can cause persistent infections in the assayed cultures.
