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1.
Viruses ; 14(1)2022 01 13.
Article in English | MEDLINE | ID: covidwho-1632083

ABSTRACT

Rhinoviruses (RVs) have been reported as one of the main viral causes for severe respiratory illnesses that may require hospitalization, competing with the burden of other respiratory viruses such as influenza and RSV in terms of severity, economic cost, and resource utilization. With three species and 169 subtypes, RV presents the greatest diversity within the Enterovirus genus, and despite the efforts of the research community to identify clinically relevant subtypes to target therapeutic strategies, the role of species and subtype in the clinical outcomes of RV infection remains unclear. This review aims to collect and organize data relevant to RV illness in order to find patterns and links with species and/or subtype, with a specific focus on species and subtype diversity in clinical studies typing of respiratory samples.


Subject(s)
Picornaviridae Infections/virology , Rhinovirus/classification , Rhinovirus/genetics , Asthma/etiology , Coinfection/virology , Enterovirus , Enterovirus Infections/virology , Genotyping Techniques , Hospitalization , Humans , Respiratory Tract Infections/virology , Serotyping
2.
MMWR Morb Mortal Wkly Rep ; 70(47): 1623-1628, 2021 Nov 26.
Article in English | MEDLINE | ID: covidwho-1534933

ABSTRACT

Enterovirus D68 (EV-D68) is associated with a broad spectrum of illnesses, including mild to severe acute respiratory illness (ARI) and acute flaccid myelitis (AFM). Enteroviruses, including EV-D68, are typically detected in the United States during late summer through fall, with year-to-year fluctuations. Before 2014, EV-D68 was infrequently reported to CDC (1). However, numbers of EV-D68 detection have increased in recent years, with a biennial pattern observed during 2014-2018 in the United States, after the expansion of surveillance and wider availability of molecular testing. In 2014, a national outbreak of EV-D68 was detected (2). EV-D68 was also reported in 2016 via local (3) and passive national (4) surveillance. EV-D68 detections were limited in 2017, but substantial circulation was observed in 2018 (5). To assess recent levels of circulation, EV-D68 detections in respiratory specimens collected from patients aged <18 years* with ARI evaluated in emergency departments (EDs) or admitted to one of seven U.S. medical centers† within the New Vaccine Surveillance Network (NVSN) were summarized. This report provides a provisional description of EV-D68 detections during July-November in 2018, 2019 and 2020, and describes the demographic and clinical characteristics of these patients. In 2018, a total of 382 EV-D68 detections in respiratory specimens obtained from patients aged <18 years with ARI were reported by NVSN; the number decreased to six detections in 2019 and 30 in 2020. Among patients aged <18 years with EV-D68 in 2020, 22 (73%) were non-Hispanic Black (Black) persons. EV-D68 detections in 2020 were lower than anticipated based on the biennial circulation pattern observed since 2014. The circulation of EV-D68 in 2020 might have been limited by widespread COVID-19 mitigation measures; how these changes in behavior might influence the timing and levels of circulation in future years is unknown. Ongoing monitoring of EV-D68 detections is warranted for preparedness for EV-D68-associated ARI and AFM.


Subject(s)
Disease Outbreaks , Enterovirus D, Human/isolation & purification , Enterovirus Infections/epidemiology , Population Surveillance/methods , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Adolescent , Child , Child, Preschool , Enterovirus D, Human/genetics , Enterovirus Infections/virology , Female , Humans , Infant , Male , United States/epidemiology
3.
Viruses ; 13(9)2021 09 10.
Article in English | MEDLINE | ID: covidwho-1411079

ABSTRACT

We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900-2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.


Subject(s)
Enterovirus Infections/epidemiology , Enterovirus Infections/virology , Enterovirus/genetics , Waste Water/microbiology , Water Microbiology , Arizona/epidemiology , Enterovirus/isolation & purification , Enterovirus Infections/history , High-Throughput Nucleotide Sequencing , History, 21st Century , Humans , Phylogeny , RNA, Viral , Seasons , Wastewater-Based Epidemiological Monitoring
4.
Viruses ; 13(1)2021 Jan 07.
Article in English | MEDLINE | ID: covidwho-1389524

ABSTRACT

We describe the complete capsid of a genotype C1-like Enterovirus A71 variant recovered from wastewater in a neighborhood in the greater Tempe, Arizona area (Southwest United States) in May 2020 using a pan-enterovirus amplicon-based high-throughput sequencing strategy. The variant seems to have been circulating for over two years, but its sequence has not been documented in that period. As the SARS-CoV-2 pandemic has resulted in changes in health-seeking behavior and overwhelmed pathogen diagnostics, our findings highlight the importance of wastewater-based epidemiology (WBE ) as an early warning system for virus surveillance.


Subject(s)
Capsid Proteins/genetics , Enterovirus A, Human/genetics , Enterovirus A, Human/isolation & purification , High-Throughput Nucleotide Sequencing/methods , Waste Water/virology , Wastewater-Based Epidemiological Monitoring , Arizona/epidemiology , Capsid/chemistry , Enterovirus Infections/epidemiology , Enterovirus Infections/virology , Humans , Molecular Epidemiology , Pandemics , Phylogeny
5.
Viruses ; 13(5)2021 05 06.
Article in English | MEDLINE | ID: covidwho-1224252

ABSTRACT

Due to the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), combined with the risk of polio importation from Ukraine, we evaluated the presence of SARS-CoV-2 and enteroviruses in 25 sewage water samples from Romania, concentrated using the WHO method between January 2020 and January 2021. Surveillance for enteroviruses and SARS-CoV-2 are relevant in the calculation of prevalence estimates as well as early detection of the introduction or disappearance of these viruses. For SARS-CoV-2 detection, we used two immunochromatographic nucleocapsid antigenic tests as well as real-time PCR assays, produced for respiratory samples. The isolation of cell culture lines, in accordance with the WHO recommendations, was carried out for enterovirus detection. Twenty-three of the samples investigated were positive in rapid tests for SARS-CoV-2, while the RNA of SARS-CoV-2, detected with Respiratory 2.1 plus a panel Biofire Film array, was present in eight samples. The Allplex 2019-nCoV assay was used for the validation of the tests. There were three genes detected in one sample, E, RdPR, and N, two genes, E and RdPR, in one sample, two genes, RdPR and N, in four samples, one gene, RdPR, in five samples and one gene, N, in one sample. Eight samples were positive for non-polio enteroviruses, and no poliovirus strains were isolated. This study suggests the presence of SARS-CoV-2 and enteroviruses in Romanian sewage water in 2020. As such, our results indicate that a rapid, more specific test should be developed especially for the detection of SARS-CoV-2 in sewage water.


Subject(s)
Environmental Monitoring/methods , SARS-CoV-2/isolation & purification , Sewage/virology , COVID-19/genetics , COVID-19/metabolism , Disease Outbreaks , Enterovirus/genetics , Enterovirus Infections/virology , Humans , Pilot Projects , Real-Time Polymerase Chain Reaction , Romania/epidemiology , SARS-CoV-2/pathogenicity , Water
6.
Stem Cell Reports ; 16(3): 493-504, 2021 03 09.
Article in English | MEDLINE | ID: covidwho-1099264

ABSTRACT

Enteroviruses, such as EV-A71 and CVA16, mainly infect the human gastrointestinal tract. Human coronaviruses, including SARS-CoV and SARS-CoV-2, have been variably associated with gastrointestinal symptoms. We aimed to optimize the human intestinal organoids and hypothesize that these optimized intestinal organoids can recapitulate enteric infections of enterovirus and coronavirus. We demonstrate that the optimized human intestinal organoids enable better simulation of the native human intestinal epithelium, and that they are significantly more susceptible to EV-A71 than CVA16. Higher replication of EV-A71 than CVA16 in the intestinal organoids triggers a more vigorous cellular response. However, SARS-CoV and SARS-CoV-2 exhibit distinct dynamics of virus-host interaction; more robust propagation of SARS-CoV triggers minimal cellular response, whereas, SARS-CoV-2 exhibits lower replication capacity but elicits a moderate cellular response. Taken together, the disparate profile of the virus-host interaction of enteroviruses and coronaviruses in human intestinal organoids may unravel the cellular basis of the distinct pathogenicity of these viral pathogens.


Subject(s)
COVID-19/virology , Enterovirus A, Human/pathogenicity , Enterovirus Infections/virology , Intestines/virology , Organoids/virology , SARS-CoV-2/pathogenicity , Animals , Cell Line , Chlorocebus aethiops , Host Microbial Interactions/physiology , Humans , Intestinal Mucosa/virology , Vero Cells , Virus Replication/physiology
7.
Diagn Microbiol Infect Dis ; 100(2): 115352, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1086876

ABSTRACT

The emergence of SARS-CoV-2 and subsequent COVID-19 pandemic highlights the morbidity and potential disease severity caused by respiratory viruses. To elucidate pathogen prevalence, etiology of coinfections and URIs from symptomatic adult Emergency department patients in a pre-SARS-CoV-2 environment, we evaluated specimens from four geographically diverse Emergency departments in the United States from 2013-2014 utilizing ePlex RP RUO cartridges (Genmark Diagnostics). The overall positivity was 30.1% (241/799), with 6.6% (16/241) coinfections. Noninfluenza pathogens from most to least common were rhinovirus/enterovirus, coronavirus, human metapneumovirus and RSV, respectively. Broad differences in disease prevalence and pathogen distributions were observed across geographic regions; the site with the highest detection rate (for both mono and coinfections) demonstrated the greatest pathogen diversity. A variety of respiratory pathogens and geographic variations in disease prevalence and copathogen type were observed. Further research is required to evaluate the clinical relevance of these findings, especially considering the SARS-CoV-2 pandemic and related questions regarding SARS-CoV-2 disease severity and the presence of co-infections.


Subject(s)
Coinfection/virology , Emergency Service, Hospital , Influenza, Human/complications , Respiratory Tract Infections/virology , Adolescent , Adult , Aged , Aged, 80 and over , Coronavirus Infections/complications , Coronavirus Infections/virology , Emergency Service, Hospital/statistics & numerical data , Enterovirus Infections/complications , Enterovirus Infections/virology , Female , Humans , Influenza, Human/virology , Male , Metapneumovirus , Middle Aged , Paramyxoviridae Infections/complications , Paramyxoviridae Infections/virology , Picornaviridae Infections/complications , Picornaviridae Infections/virology , Prevalence , Respiratory Tract Infections/complications , Rhinovirus , Risk Factors , United States/epidemiology , Young Adult
8.
Commun Dis Intell (2018) ; 452021 Jan 29.
Article in English | MEDLINE | ID: covidwho-1080878

ABSTRACT

ABSTRACT: Significant reductions in the incidence of enteroviruses and noroviruses, both transmitted primarily by the faecal-oral route, were noted in 2020 compared to the previous decade, in Victoria, Australia. The enterovirus specimen positivity rate was reduced by 84.2% in 2020, while the norovirus outbreak positivity rate declined by 49.0%. The most likely explanation for these reductions is the concurrence of social restrictions, physical distancing, personal hygiene awareness and international and domestic border closures in response to the COVID-19 pandemic.


Subject(s)
COVID-19/epidemiology , Caliciviridae Infections/virology , Enterovirus , Gastroenteritis/epidemiology , Gastroenteritis/virology , Norovirus , Caliciviridae Infections/epidemiology , Enterovirus Infections/epidemiology , Enterovirus Infections/virology , Humans , Incidence , SARS-CoV-2 , Victoria/epidemiology
9.
Seizure ; 84: 69-77, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1065589

ABSTRACT

OBJECTIVE: There are limited data on the pathogen-related and host-related factors in the pathogenesis of febrile seizures (FS). We designed a controlled study to compare the role of different respiratory viruses and febrile response in FS. METHODS: In a prospective cohort study of 1899 pediatric emergency room patients aged 6 months-6 years with a positive respiratory virus multiplex PCR, we identified 225 patients with FSs. We first compared the distribution of respiratory viruses in age-stratified patients with FSs with that in other patients. In an embedded case-control study, we compared the febrile response in patients with FSs with that in the controls matched for age, season and the same respiratory virus. RESULTS: The relative risk for FS was the highest for coronavirus OC43, 229E, and NL63 infections [RR: 3.2, 95 % confidence interval (CI): 1.4-7.2) and influenza A and B [RR: 2.5, 95 % CI: 1.4-4.7] as compared to those with other respiratory viral infections. The patients with FSs had a stronger febrile response of 39.2 °C (difference: 0.8 °C, 95 % CI: 0.5-1.2) later during hospitalization after acute care than the controls matched for the same respiratory virus. CONCLUSIONS: Influenza and coronaviruses caused relatively more FS-related emergency room visits than other respiratory viruses. Furthermore, the febrile response was stronger in the patients with FSs than in the controls matched for the same respiratory virus. The results suggest that the pathomechanism of FSs includes modifiable pathogen-related and host-related factors with possible potential in the prevention of FSs.


Subject(s)
Coronavirus Infections/epidemiology , Enterovirus Infections/epidemiology , Influenza, Human/epidemiology , Paramyxoviridae Infections/epidemiology , Respiratory Tract Infections/epidemiology , Seizures, Febrile/epidemiology , Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/virology , Case-Control Studies , Child , Child, Preschool , Cohort Studies , Coronavirus 229E, Human , Coronavirus Infections/virology , Coronavirus NL63, Human , Coronavirus OC43, Human , Emergency Service, Hospital , Enterovirus Infections/virology , Female , Fever/physiopathology , Finland/epidemiology , Humans , Infant , Inflammation , Influenza A virus , Influenza B virus , Influenza, Human/virology , Male , Multiplex Polymerase Chain Reaction , Paramyxoviridae Infections/virology , Picornaviridae Infections/epidemiology , Picornaviridae Infections/virology , Prospective Studies , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/physiopathology , Respiratory Tract Infections/virology , Rhinovirus , Risk , Seizures, Febrile/virology
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