Genetic diversity and molecular evolution of human adenovirus serotype 41 strains circulating in Beijing, China, during 2010-2019

Molecular Epidemiology of Human Adenovirus from Acute Gastroenteritis Cases in Brazil After the COVID-19 Pandemic Period, 2021-2023

Human enteric adenoviruses (HAdV-F40/41) play a crucial role as causative agents of acute gastroenteritis (AGE), particularly affecting children in low-and middle-income countries. This study investigated the prevalence, genetic diversity, and molecular characteristics of HAdV-F40/41 in AGE cases reported in Brazil from 2021 to 2023, a period after the COVID-19 pandemic. A total of 1980 stool samples collected from medically attended AGE patients from nine states were analyzed by TaqMan-based qPCR. Overall, HAdV was detected in 16.6% (n = 328/1980) of cases, with the highest prevalence observed in children under five years of age. The positive HAdV samples were genotyped through partial sequencing of the hexon and/or fiber genes followed by phylogenetic analysis. Enteric HAdVs (HAdV-F40/41) were detected in 3.2% (n = 63/1980) of samples, with HAdV-F41 (44.1%) being the most common genotype. Among the non-enteric types, HAdV-C (29.4%) was the most prevalent, followed by HAdV-B (13.2%), HAdV-A (10.3%), and HAdV-D (2.9%). Phylogenetic analysis of the hexon (HVR1-HVR6) and fiber (Shaft) gene regions identified two major clusters, H-GTC1 and F-GTC2, showing close genetic relationships with global strains. HAdV-F40/41 demonstrated significantly higher viral loads compared to non-enteric HAdVs. These findings highlight the importance of continued surveillance of HAdV-F to better understand its role in AGE cases and support public health strategies, including potential vaccine development.

Immunological pathogenesis and treatment progress of adenovirus pneumonia in children

Human adenovirus is an infectious agent that causes respiratory infections in adults and children. It has been found that immunocompromised children are highly susceptible to this pathogen, as it can swiftly evolve into severe pneumonia with multiple sequelae. Due to the lack of immunity in children, the body's response mechanisms to innate and acquired immunity are specialized. We first examined the infection classification and clinical characteristics associated with adenovirus in children. Subsequently, we explored the in-depth understanding of the pathogenic mechanism of adenovirus pneumonia in children, focusing on immunological and cellular biological aspects. Adenovirus infection in children can disrupt the balance of the innate immune response, inducing immune cells to secrete an abundance of pro-inflammatory cytokines. This cascade results in a cytokine storm, which triggers an inflammatory response and causes lung tissue damage. As a result, the infection may progress to a severe state, potentially leading to multi-organ failure. Immunocompromised children exhibit impaired immune cell numbers and functions, which affects both the secretion of antibodies to humoral immunity and the immune response of cellular immunity to adenovirus. Lastly, we reviewed the progress in treating adenovirus pneumonia in children. There are many treatments for adenovirus pneumonia in children, which must be personalized based on a thorough assessment to optimize treatment outcomes. Recent advancements in pharmaceutical development have provided new treatment options for children. Immunomodulatory therapy can reduce inflammation in children, while adjuvant therapy can improve respiratory function; however, it can also lead to complications. Further, co-infections increased the complexity of diagnosis and treatment, necessitating dynamic adjustments to treatment regimens. This review could serve as the basis for identifying potential therapeutic approaches to alleviate the symptoms associated with adenovirus infections in children.

Hybrid sequencing for detailed genetic characterization of human adenoviruses

Human adenoviruses (HAdVs) are highly contagious and have significant clinical implications in the pediatric population. In the present study, we employed a combination of long-read sequencing and short-read sequencing to accurately reconstruct 32 genomes of HAdVs. The phylogenetic analyses based on the whole genome and genes revealed distinct sub-clusters within HAdV-B and -E. For HAdV-C, the phylogenetic trees constructed from hexon, fiber, and E3 gene sequences consistently matched the whole-genome phylogeny, reflecting the high sequence diversity in these regions. Notably, in regions with high sequence diversity, we observed a higher number of recombination breakpoints and lower GC content. Additionally, the E4 gene region of HAdV-C exhibited a Ka/Ks ratio > 1, indicating that positive selection may be driving the fixation of advantageous mutations. These genetic characterization analyses are crucial for enhancing future surveillance of HAdVs, facilitating a more strategic and proactive approach to monitoring their evolution, diversity, and epidemiological trends.

Adenovirus 41 diversity in Arizona (USA) using wastewater-based epidemiology, long-range PCR, and pathogen sequencing between October 2019 and March 2020

By coupling long-range polymerase chain reaction, wastewater-based epidemiology, and pathogen sequencing, we show that adenovirus type 41 hexon-sequence lineages, described in children with hepatitis of unknown origin in the United States in 2021, were already circulating within the country in 2019. We also observed other lineages in the wastewater, whose complete genomes have yet to be documented from clinical samples.

Coinfection of human adenovirus and recombinant human astrovirus in a case of acute gastroenteritis: A report from China

Diarrhea is one of the major public health issues worldwide. Although the infections of individual enteric virus have been extensively studied, elucidation of the coinfection involving multiple viruses is still limited. In this study, we identified the coinfection of human adenovirus (HAdV) and human astrovirus (HAstV) in a child with acute gastroenteritis, analyzed their genotypes and molecular evolution characteristics. The sample was collected and identified using RT-PCR and subjected to whole-genome sequencing on the NovaSeq (Illumina) platform. Obtained sequences were assembled into the complete genome of HAdV and the ORF1 of HAstV. We conducted phylogenetic analysis using IQ-TREE software and conducted recombination analysis with the Recombination Detection Program. The sequenced HAdV was confirmed to be genotype 41, and was genetically close to some European strains. Phylogenetic analysis revealed that the HAstV was genetically close to both HAstV-2 and HAstV-4 and was different from the genotype prevalent in Shenzhen before. The recombination analysis confirmed that the sequenced HAstV strain is a recombinant of HAstV-2 and HAstV-4. Our analysis has shown that the strains in this coinfection are both uncommon variants in this geographical region, instead of dominant subtypes that have prevailed for years. This study presents a coinfection of HAdV and HAstV and conducts an evolutionary analysis on involved viruses, which reveals the genetic diversity of epidemic strains in Southern China and offers valuable insights into vaccine and medical research.

Clinical characteristics and phylogenetic analysis of human enteric adenovirus type 41 (HAdV-F41) from children with gastroenteritis during SARS-CoV-2 pandemic

Human adenovirus type 41 (HAdV-F41) usually causes pediatrics gastroenteritis. However, it was reported to be associated with the outbreaks of severe acute hepatitis of unknown aetiology (SAHUA) in pediatrics during COVID-19 pandemic. In this study, we investigated the prevalence of enteric HAdV-F41 in 37,920 paediatric gastroenteritis cases from 2017 to 2022 in Guangzhou, China. All children presented were tested negative for SARS-CoV-2 during the "zero-COVID" period. The main clinical symptom of the children was diarrhea (96.5%). No fatalities nor liver abnormal symptoms was found. In 2021, one year since the pandemic of COVID-19, the prevalence of HAdV-F41 abruptly increased from 3.71% to 8.64% (P < 0.001). All of HAdV-F41 circulating worldwide were classified into eight different subtypes (G1-G8) based on the phylogenetic clustering permutation of the four capsid genes of HAdV-F41. G3 was the predominant subtype (56.2%; 77/137). CRV5 isolates from SAHUA cases belong to this subtype, in which N312D and H335D mutations in the short fiber knob were identified in both Guangzhou and CRV5 isolates, presumably changing the virus tropism by directly interacting with the heparin sulfate (HS) receptor. Additionally, a novel recombinant G6 subtype, which is unique and only circulating in China was first identified in this study. This is the first study highlighting the prevalence of HAdV-F41 in paediatric cases of gastroenteritis during COVID-19 pandemic in China. The clinical and viral evolution finding of HAdV-F41 provide insight into the clinical characteristics of children with HAdV-F41 infections as well as the uncertain role of HAdV-F41 in the cause of SAHUA.

Molecular epidemiology of circulating human adenoviruses among acute respiratory infection patients seeking healthcare facilities in West Bengal, India

Human adenovirus (HAdV) causes acute respiratory infections leading to mortality in children. This study analyzes the circulating respiratory HAdV genotypes in West Bengal, India during 2018-2022 among symptomatic patients. The overall positivity rate was 6.8%, out of which 26.4% were co-infected with other respiratory viruses. Children aged 2 to 5 years were mostly infected. Phylogenetic analysis revealed that the recombinant HAdV-B type 7/3, which has remarkable outbreak potential, predominantly circulated in this region followed by the non-recombinant HAdV-B type 3/3. Moreover, the amino acid sequences encoded by both the hexon and fiber genes of these two circulating strains possessed a few mutations that mostly diverged from the prototype strain, although the divergence was less pronounced in case of the amino acids encoded by the fiber gene of HAdV-B type 3/3. Overall, the results underscore the need for continuous surveillance of respiratory HAdV types to combat future possible epidemics.

Molecular characterization of human adenovirus causing infantile acute gastroenteritis in Venezuela before and after rotavirus vaccine implementation

Human adenoviruses (HAdV) of species F are commonly involved in pediatric acute gastroenteritis (AGE). The real impact on Venezuelan health is unknown. To investigate the prevalence and molecular diversity of HAdV in Venezuela, 630 fecal samples collected from children with AGE in 3 cities, from 2001 to 2013, were tested by PCR. Species F and types F40/41 were identified by REA. HAdV was detected in 123 cases (19.5%), most from outpatient females under 24 months old. A progressive and substantial increase in the detection rate was observed over time, significantly higher in rotavirus vaccinated than unvaccinated children (28.4% vs. 9.5%, P = 0.00019). Phylogenetic analysis of 28 randomly selected genomes showed high similarity among HAdV-F40/41 and those worldwide. HAdV-F of type 41 prevailed (79.8%) and clustered into 2 intratypic major clades. The significant involvement of HAdV-F41 in AGE suggests the importance of actively monitoring viral agents other than rotavirus, especially after vaccine introduction.

Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance

Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.

Dissemination and genome characterization of a human adenovirus F41 in a patient with B-Cell lymphoma

Adenovirus (HAdV) F41 is a common cause of gastroenteritis and has rarely been reported associated with disseminated disease. In this report, an adult patient with a history of ulcerative colitis, cryptogenic cirrhosis, stage III adenocarcinoma, high-grade diffuse large B-cell lymphoma on chemotherapy was diagnosed with disseminated adenovirus infection. HAdV DNA was quantified in stool, plasma, and urine with viral loads of 7, 4, and 3 log10 copies/mL, respectively. The patient's course was rapidly progressive and he passed away 2 days after initiation of antiviral therapy. The patient's infecting virus was characterized as HAdV-F41 by whole genome sequencing.

Genetic Evolution and Variation of Human Adenovirus Serotype 31 Epidemic Strains in Beijing, China, during 2010-2022

Human adenovirus serotype 31 (HAdV-31) is closely associated with gastroenteritis in children and can cause fatal systemic disseminated diseases in immunocompromised patients. The lack of genomic data for HAdV-31, especially in China, will greatly limit research on its prevention and control. Sequencing and bioinformatics analyses were performed for HAdV-31 strains from diarrheal children in Beijing, China, during 2010-2022. Three capsid protein genes (hexon, penton, and fiber) were obtained in 37 cases, including one in which the whole genome was sequenced. HAdV-31 strains clustered into three distinct clades (I-III) in a phylogenetic tree constructed based on concatenated genes and the whole genome; the endemic strains only gathered into clade II, and most of the reference strains clustered into clade I. Compared with penton and hexon, fiber had a faster evolutionary rate (1.32 × 10^-4 substitutions/site/year), an earlier divergence time (1697), lower homology (98.32-100% at the amino acid level), and greater genetic variation (0.0032). Four out of the six predicted positive selection pressure codons were also in the knob of fiber. These results reveal the molecular evolution characteristics and variations of HAdV-31 in Beijing, and fiber may be one of the main evolution driving forces.

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children.

May 2022 acute hepatitis outbreak, is there a role for COVID-19 and other viruses?

There has been an increasing number of reported cases of acute hepatitis of unknown origin in previously healthy children since first reported on March 31, 2022. This clinical syndrome is identified by jaundice and markedly elevated liver enzymes with increased aspartate transaminase and/or alanine aminotransaminase (greater than 500 IU/L). We conducted an inclusive literature review with respect to acute hepatitis outbreaks in children using the search terms acute hepatitis, outbreak, children, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coronavirus disease 2019 (COVID-19), and adenovirus. According to the cumulative data presented in four main studies, the median age is 4 years, with a male predominance (1.3:1). Jaundice was the most common clinical manifestation (69%), followed by vomiting (63%), anorexia (52.9%), diarrhea (47.2%), abdominal pain (39%), pyrexia (33.3%), pale stool (30%), and dark urine (30%). Coryza and lethargy were reported in 16.6%, while pruritus was reported in 2% of cases. Acute liver failure was observed in 25% of cases. The exact mechanism of this acute hepatitis outbreak is still not entirely clear. Adenoviruses and SARS-CoV-2 were detected in a significant number of patients. Coinfection with adenovirus and SARS-CoV-2 could be a possible underlying mechanism. However, other possible infections and mechanisms must be considered in the pathogenesis of this condition. Acute hepatitis of unknown origin in children has been a serious problem since the start of the COVID-19 pandemic but has not yet been sufficiently addressed. Many questions remain regarding the underlying mechanisms leading to acute liver failure in children, and it is likely that extensive future research is needed.

First Isolation and Identification of Homologous Recombination Events of Porcine Adenovirus from Wild Boar

Porcine adenoviruses (PAdVs) are distributed in pig populations and classified into five immunologically distinct serotypes (PAdV-1 to 5). In this study, a PAdV was isolated from a fecal sample of wild boar for the first time. Whole-genome analysis revealed that this strain (Ino5) has sequence homology (approximately > 93%) throughout the genome with the PAdV-5 strain HNF-70 that was isolated from a pig in Japan in 1987, except for the hexon, E3 612R, and fiber coding regions. Two possible recombination breakpoints were detected in the hexon and E3 612R regions, which were found to have reduced GC content. Structural prediction analysis showed that a part of the hexon protein corresponding to the tower region of Ino5 had structural differences when compared with HNF-70, suggesting antigenic heterogeneity between these strains. PAdVs were detected in 1.77% (2/113) and 12% (12/100) of the fecal samples from wild boars and pigs collected in Japan by PCR, respectively. Phylogenetic analyses of the hexon and fiber genes revealed that some samples showed different grouping in the hexon and fiber genes, suggesting that these viruses have recombination events. These findings suggest that the PAdV-5 has evolved with homologous recombination events in the same manner as human adenoviruses among not only pig populations, but also wild boars in Japan.

Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology

The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.