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1.
Virol J ; 18(1): 174, 2021 08 23.
Article in English | MEDLINE | ID: covidwho-1770553

ABSTRACT

BACKGROUND: Human rhinovirus (HRV) is one of the major viruses of acute respiratory tract disease among infants and young children. This work aimed to understand the epidemiological and phylogenetic features of HRV in Guangzhou, China. In addition, the clinical characteristics of hospitalized children infected with different subtype of HRV was investigated. METHODS: Hospitalized children aged < 14 years old with acute respiratory tract infections were enrolled from August 2018 to December 2019. HRV was screened for by a real-time reverse-transcription PCR targeting the viral 5'UTR. RESULTS: HRV was detected in 6.41% of the 655 specimens. HRV infection was frequently observed in children under 2 years old (57.13%). HRV-A and HRV-C were detected in 18 (45%) and 22 (55%) specimens. All 40 HRV strains detected were classified into 29 genotypes. The molecular evolutionary rate of HRV-C was estimated to be 3.34 × 10-3 substitutions/site/year and was faster than HRV-A (7.79 × 10-4 substitutions/site/year). Children who experienced rhinorrhoea were more common in the HRV-C infection patients than HRV-A. The viral load was higher in HRV-C detection group than HRV-A detection group (p = 0.0148). The median peak symptom score was higher in patients with HRV-C infection as compared to HRV-A (p = 0.0543), even though the difference did not significance. CONCLUSION: This study revealed the molecular epidemiological characteristics of HRV in patients with respiratory infections in southern China. Children infected with HRV-C caused more severe disease characteristics than HRV-A, which might be connected with higher viral load in patients infected with HRV-C. These findings will provide valuable information for the pathogenic mechanism and treatment of HRV infection.


Subject(s)
Picornaviridae Infections , Respiratory Tract Infections , Rhinovirus , Adolescent , Child , Child, Preschool , China/epidemiology , Enterovirus , Genetic Variation , Humans , Infant , Phylogeny , Picornaviridae Infections/epidemiology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Rhinovirus/genetics
2.
Nat Commun ; 13(1): 1406, 2022 03 17.
Article in English | MEDLINE | ID: covidwho-1750000

ABSTRACT

Human rhinovirus (HRV), like coronavirus (HCoV), are positive-strand RNA viruses that cause both upper and lower respiratory tract illness, with their replication facilitated by concentrating RNA-synthesizing machinery in intracellular compartments made of modified host membranes, referred to as replication organelles (ROs). Here we report a non-canonical, essential function for stimulator of interferon genes (STING) during HRV infections. While the canonical function of STING is to detect cytosolic DNA and activate inflammatory responses, HRV infection triggers the release of STIM1-bound STING in the ER by lowering Ca2+, thereby allowing STING to interact with phosphatidylinositol 4-phosphate (PI4P) and traffic to ROs to facilitates viral replication and transmission via autophagy. Our results thus hint a critical function of STING in HRV viral replication and transmission, with possible implications for other RO-mediated RNA viruses.


Subject(s)
Enterovirus , RNA Viruses , Humans , Organelles , Rhinovirus , Virus Replication/physiology
3.
Viruses ; 14(3)2022 02 27.
Article in English | MEDLINE | ID: covidwho-1744919

ABSTRACT

Respiratory viruses play an important role in asthma exacerbation, and early exposure can be involved in recurrent bronchitis and the development of asthma. The exact mechanism is not fully clarified, and pathogen-to-host interaction studies are warranted to identify biomarkers of exacerbation in the early phase. Only a limited number of international exacerbation cohorts were studied. Here, we have established a local pediatric exacerbation study in Germany consisting of children with asthma or chronic, recurrent bronchitis and analyzed the viriome within the nasopharyngeal swab specimens derived from the entire cohort (n = 141). Interestingly, 41% of exacerbated children had a positive test result for human rhinovirus (HRV)/human enterovirus (HEV), and 14% were positive for respiratory syncytial virus (RSV). HRV was particularly prevalent in asthmatics (56%), wheezers (50%), and atopic (66%) patients. Lymphocytes were decreased in asthmatics and in HRV-infected subjects, and patients allergic to house dust mites were more susceptible to HRV infection. Our study thus confirms HRV infection as a strong 'biomarker' of exacerbated asthma. Further longitudinal studies will show the clinical progress of those children with a history of an RSV or HRV infection. Vaccination strategies and novel treatment guidelines against HRV are urgently needed to protect those high-risk children from a serious course of disease.


Subject(s)
Asthma , Bronchitis , Enterovirus Infections , Enterovirus , Picornaviridae Infections , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Viruses , Asthma/epidemiology , Biomarkers , Child , Humans , Infant , Respiratory Tract Infections/epidemiology , Rhinovirus
4.
Viruses ; 14(2)2022 02 10.
Article in English | MEDLINE | ID: covidwho-1715772

ABSTRACT

Enterovirus genus has over one hundred genotypes and could cause several kinds of severe animal and human diseases. Understanding the role of conserved residues in the VP1 capsid protein among the enterovirus genus may lead to anti-enteroviral drug development. The highly conserved residues were found to be located at the loop and ß-barrel intersections. To elucidate the role of these VP1 residues among the enterovirus genus, alanine substitution reverse genetics (rg) variants were generated, and virus properties were investigated for their impact. Six highly conserved residues were identified as located near the inside of the canyon, and four of them were close to the ß-barrel and loop intersection. The variants rgVP1-R86A, rgVP1-P193A, rgVP1-G231A, and rgVP1-K256A were unable to be obtained, which may be due to disruption in the virus replication process. In contrast, rgVP1-E134A and rgVP1-P157A replicated well and rgVP1-P157A showed smaller plaque size, lower viral growth kinetics, and thermal instability at 39.5°C when compared to the rg wild type virus. These findings showed that the conserved residues located at the ß-barrel and loop junction play roles in modulating viral replication, which may provide a pivotal role for pan-enteroviral inhibitor candidate.


Subject(s)
Capsid Proteins/chemistry , Enterovirus/physiology , Virus Replication , Amino Acid Sequence , Antiviral Agents/chemistry , Capsid Proteins/genetics , Cell Line, Tumor , Conserved Sequence , Humans , Mutation , Protein Conformation , Protein Stability , RNA, Viral/metabolism , Small Molecule Libraries/chemistry , Temperature , Viral Load
5.
Sci Total Environ ; 824: 153886, 2022 Jun 10.
Article in English | MEDLINE | ID: covidwho-1692894

ABSTRACT

Enteric viruses are of great importance in wastewater due to their high excretion from infected individuals, low removal in wastewater treatment processes, long-time survival in the environment, and low infectious dose. Among the other viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance in wastewater systems has received particular attention as a result of the current COVID-19 epidemic. Viruses adhering to solid particles in wastewater treatment processes will end up as sewage sludge, and therefore insufficient sludge treatment may result in viral particles dissemination into the environment. Here, we review data on viruses' presence in sewage sludge, their detection and concentration methods, and information on human health issues associated with sewage sludge land application. We used combinations of the following keywords in the Scopus, Web of Science (WOS), and PubMed databases, which were published between 2010 and January 21th, 2022: sludge (sewage sludge, biosolids, sewage solids, wastewater solids) and virus (enteric virus, viral particles, viral contamination, SARS-CoV-2, coronavirus). The sources were searched twice, once with and then without the common enteric virus names (adenovirus, rotavirus, norovirus, enterovirus, hepatitis A virus). Studies suggest adenovirus and norovirus as the most prevalent enteric viruses in sewage sludge. Indeed, other viruses include rotavirus, hepatitis A virus, and enterovirus were frequently found in sewage sludge samples. Untreated biological sludge and thickened sludge showed more viral contamination level than digested sludge and the lowest prevalence of viruses was reported in lime stabilized sludge. The review reveals that land application of sewage sludge may pose viral infection risks to people due to accidently ingestion of sludge or intake of crops grown in biosolids amended soil. Moreover, contamination of groundwater and/or surface water may occur due to land application of sewage sludge.


Subject(s)
COVID-19 , Enterovirus , Norovirus , Rotavirus , Viruses , Adenoviridae , Biosolids , Humans , SARS-CoV-2 , Sewage , Waste Water
9.
PLoS One ; 17(1): e0262874, 2022.
Article in English | MEDLINE | ID: covidwho-1643288

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated worldwide and causes coronavirus disease 2019 (COVID-19). At the onset of the COVID-19 pandemic, infection control measures were taken, such as hand washing, mask wearing, and behavioral restrictions. However, it is not fully clear how the effects of these non-pharmaceutical interventions changed the prevalence of other pathogens associated with respiratory infections. In this study, we collected 3,508 nasopharyngeal swab samples from 3,249 patients who visited the Yamanashi Central Hospital in Japan from March 1, 2020 to February 28, 2021. We performed multiplex polymerase chain reaction (PCR) using the FilmArray Respiratory Panel and singleplex quantitative reverse transcription PCR targeting SARS-CoV-2 to detect respiratory disease-associated pathogens. At least one pathogen was detected in 246 (7.0%) of the 3,508 samples. Eleven types of pathogens were detected in the samples collected from March-May 2020, during which non-pharmaceutical interventions were not well implemented. In contrast, after non-pharmaceutical interventions were thoroughly implemented, only five types of pathogens were detected, and the majority were SARS-CoV-2, adenoviruses, or human rhinoviruses / enteroviruses. The 0-9 year age group had a higher prevalence of infection with adenoviruses and human rhinoviruses / enteroviruses compared with those 10 years and older, while those 10 years and older had a higher prevalence of infection with SARS-CoV-2 and other pathogens. These results indicated that non-pharmaceutical interventions likely reduced the diversity of circulating pathogens. Moreover, differences in the prevalence of pathogens were observed among the different age groups.


Subject(s)
Adenoviruses, Human/genetics , COVID-19/epidemiology , Enterovirus/genetics , Respiratory Tract Infections/epidemiology , Rhinovirus/genetics , SARS-CoV-2/genetics , Adenoviruses, Human/classification , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19/virology , Child , Child, Preschool , Enterovirus/classification , Female , Hand Disinfection/methods , Humans , Infant , Infant, Newborn , Japan/epidemiology , Male , Masks/supply & distribution , Middle Aged , Multiplex Polymerase Chain Reaction , Nasopharynx/virology , Prevalence , Quarantine/organization & administration , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/prevention & control , Respiratory Tract Infections/virology , Rhinovirus/classification , SARS-CoV-2/pathogenicity
10.
Euro Surveill ; 26(45)2021 Nov.
Article in English | MEDLINE | ID: covidwho-1630353

ABSTRACT

We report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe.


Subject(s)
COVID-19 , Enterovirus D, Human , Enterovirus Infections , Enterovirus , Myelitis , Respiratory Tract Infections , Communicable Disease Control , Disease Outbreaks , Enterovirus D, Human/genetics , Enterovirus Infections/diagnosis , Enterovirus Infections/epidemiology , Europe/epidemiology , Humans , Myelitis/epidemiology , SARS-CoV-2
11.
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
12.
Sci Total Environ ; 799: 149386, 2021 Dec 10.
Article in English | MEDLINE | ID: covidwho-1545398

ABSTRACT

To support public-health-related disease surveillance and monitoring, it is crucial to concentrate both enveloped and non-enveloped viruses from domestic wastewater. To date, most concentration methods were developed for non-enveloped viruses, and limited studies have directly compared the recovery efficiency of both types of viruses. In this study, the effectiveness of two different concentration methods (Concentrating pipette (CP) method and an adsorption-extraction (AE) method amended with MgCl2) were evaluated for untreated wastewater matrices using three different viruses (SARS-CoV-2 (seeded), human adenovirus 40/41 (HAdV 40/41), and enterovirus (EV)) and a wastewater-associated bacterial marker gene targeting Lachnospiraceae (Lachno3). For SARS-CoV-2, the estimated mean recovery efficiencies were significantly greater by as much as 5.46 times, using the CP method than the AE method amended with MgCl2. SARS-CoV-2 RNA recovery was greater for samples with higher titer seeds regardless of the method, and the estimated mean recovery efficiencies using the CP method were 25.1 ± 11% across ten WWTPs when wastewater samples were seeded with 5 × 104 gene copies (GC) of SARS-CoV-2. Meanwhile, the AE method yielded significantly greater concentrations of indigenous HAdV 40/41 and Lachno3 from wastewater compared to the CP method. Finally, no significant differences in indigenous EV concentrations were identified in comparing the AE and CP methods. These data indicate that the most effective concentration method varies by microbial analyte and that the priorities of the surveillance or monitoring program should be considered when choosing the concentration method.


Subject(s)
COVID-19 , Enterovirus , Viruses , Enterovirus/genetics , Humans , RNA, Viral , SARS-CoV-2 , Sewage , Waste Water
13.
Euro Surveill ; 26(43)2021 10.
Article in English | MEDLINE | ID: covidwho-1533602

ABSTRACT

We report a large-scale outbreak of hand, foot and mouth disease (HFMD) in France. As at 28 September 2021, 3,403 cases have been reported (47% higher than in 2018-19). We prospectively analysed 210 clinical samples; 190 (90.5%) were enterovirus-positive. Most children presented with atypical HFMD. Coxsackievirus (CV)A6 (49.5%; 94/190) was predominant; no enterovirus A71 was detected. Dermatological and neurological complications of HFMD justify prospective syndromic and virological surveillance for early detection of HFMD outbreaks and identification of associated types.


Subject(s)
Enterovirus Infections , Enterovirus , Hand, Foot and Mouth Disease , Child , Disease Outbreaks , Enterovirus Infections/epidemiology , Hand, Foot and Mouth Disease/diagnosis , Hand, Foot and Mouth Disease/epidemiology , Humans , Infant , Prospective Studies
14.
Influenza Other Respir Viruses ; 16(2): 190-192, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1505752

ABSTRACT

Stringent public health measures imposed across Canada to control the COVID-19 pandemic have nearly suppressed most seasonal respiratory viruses, with the notable exception of human rhinovirus/enterovirus (hRV/EV). Thanks to this unexpected persistence, we highlight that hRV/EV could serve as a sentinel for levels of contact rate in populations to inform on the efficiency, or the need of, public health measures to control the subsequent COVID-19 epidemic, but also for future epidemics from other seasonal or emerging respiratory pathogens.


Subject(s)
COVID-19 , Enterovirus , Respiratory Tract Infections , Viruses , Humans , Pandemics , Respiratory Tract Infections/epidemiology , Rhinovirus , SARS-CoV-2
15.
Clin Infect Dis ; 73(9): e2807-e2809, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1501044

ABSTRACT

Enteroviral meningitis is seasonal, typically exhibiting a rise in prevalence in late summer/early fall. Based on clinical microbiology laboratory testing data of cerebrospinal fluid, the expected August/September/October peak in enteroviral meningitis did not occur in 2020, possibly related to coronavirus disease 2019 (COVID-19) mitigation strategies.


Subject(s)
COVID-19 , Enterovirus Infections , Enterovirus , Meningitis, Viral , Enterovirus Infections/epidemiology , Enterovirus Infections/prevention & control , Humans , Infant , Meningitis, Viral/diagnosis , Meningitis, Viral/epidemiology , Meningitis, Viral/prevention & control , SARS-CoV-2
16.
Microbiol Spectr ; 9(2): e0083121, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1476399

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.


Subject(s)
COVID-19/complications , Coinfection/virology , Respiratory Tract Infections/complications , Respiratory Tract Infections/virology , Adenoviridae/genetics , Adenoviridae/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Child , Enterovirus/genetics , Enterovirus/isolation & purification , Female , Humans , Male , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Middle Aged , Retrospective Studies , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , Wisconsin , Young Adult
17.
Virol J ; 18(1): 202, 2021 10 09.
Article in English | MEDLINE | ID: covidwho-1463255

ABSTRACT

BACKGROUND: The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children. METHODS: This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children's Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed. RESULTS: A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p < 0.0001). CONCLUSIONS: Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.


Subject(s)
Antibiosis , COVID-19/epidemiology , Respiratory Tract Diseases/epidemiology , SARS-CoV-2/isolation & purification , Adenoviruses, Human/genetics , Adenoviruses, Human/isolation & purification , Adolescent , COVID-19/virology , Child , Child, Hospitalized , Child, Preschool , China , Enterovirus/genetics , Enterovirus/isolation & purification , Female , Humans , Infant , Influenza A virus/genetics , Influenza A virus/isolation & purification , Male , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Mycoplasma pneumoniae/genetics , Mycoplasma pneumoniae/isolation & purification , Nasopharynx/microbiology , Nasopharynx/virology , Prevalence , Respiratory Syncytial Viruses/genetics , Respiratory Syncytial Viruses/isolation & purification , Respiratory Tract Diseases/microbiology , Respiratory Tract Diseases/virology , Respirovirus/genetics , Respirovirus/isolation & purification , SARS-CoV-2/genetics
18.
Viruses ; 13(7)2021 07 15.
Article in English | MEDLINE | ID: covidwho-1448933

ABSTRACT

Virus-induced infections of the central nervous system (CNS) are among the most serious problems in public health and can be associated with high rates of morbidity and mortality, mainly in low- and middle-income countries, where these manifestations have been neglected. Typically, herpes simplex virus 1 and 2, varicella-zoster, and enterovirus are responsible for a high number of cases in immunocompetent hosts, whereas other herpesviruses (for example, cytomegalovirus) are the most common in immunocompromised individuals. Arboviruses have also been associated with outbreaks with a high burden of neurological disorders, such as the Zika virus epidemic in Brazil. There is a current lack of understanding in Brazil about the most common viruses involved in CNS infections. In this review, we briefly summarize the most recent studies and findings associated with the CNS, in addition to epidemiological data that provide extensive information on the circulation and diversity of the most common neuro-invasive viruses in Brazil. We also highlight important aspects of the prion-associated diseases. This review provides readers with better knowledge of virus-associated CNS infections. A deeper understanding of these infections will support the improvement of the current surveillance strategies to allow the timely monitoring of the emergence/re-emergence of neurotropic viruses.


Subject(s)
Central Nervous System Diseases/virology , Central Nervous System Infections/epidemiology , Prion Diseases/epidemiology , Alphavirus/pathogenicity , Brazil/epidemiology , Central Nervous System/virology , Central Nervous System Diseases/metabolism , Central Nervous System Diseases/physiopathology , Central Nervous System Infections/virology , Central Nervous System Viral Diseases/physiopathology , Central Nervous System Viral Diseases/virology , Enterovirus/pathogenicity , Flavivirus/pathogenicity , Herpesviridae/pathogenicity , Humans , Nervous System Diseases/epidemiology , Nervous System Diseases/virology , Prion Diseases/physiopathology , Prions/metabolism , Prions/pathogenicity , Simplexvirus/pathogenicity , Virus Diseases/virology , Viruses/pathogenicity , Zika Virus/pathogenicity
19.
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
20.
Microbiol Spectr ; 9(2): e0043021, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1398597

ABSTRACT

Measures intended to limit the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus at the start of the coronavirus disease 2019 (COVID-19) pandemic resulted in a rapid decrease in other respiratory pathogens. Herein, we describe the trends of respiratory pathogens in a major metropolitan health care system central microbiology reference laboratory before and during the COVID-19 pandemic, with attention to when COVID-19 mitigation measures were implemented and relaxed. During the initial lockdown period, COVID-19 was the primary respiratory pathogen detected by multiplex respiratory panels. As COVID-19 containment measures were relaxed, the first non-COVID respiratory viruses to return to prepandemic levels were members of the rhinovirus/enterovirus family. After the complete removal of COVID-19 precautions at the state level, including an end to mask mandates, we observed the robust return of seasonal coronaviruses, parainfluenza virus, and respiratory syncytial virus. Inasmuch as COVID-19 has dominated the landscape of respiratory infections since early 2020, it is important for clinicians to recognize that the return of non-COVID respiratory pathogens may be rapid and significant when COVID-19 containment measures are removed. IMPORTANCE We describe the return of non-COVID respiratory viruses after the removal of COVID-19 mitigation measures. It is important for the public and physicians to recognize that, after months of COVID-19 being the primary driver of respiratory infection, more typical seasonal respiratory illnesses have returned, and this return is out of the normal season for some of these pathogens. Thus, clinicians and the public must now consider both COVID-19 and other respiratory illnesses when a patient presents with symptomatic respiratory illness.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Communicable Disease Control , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , Coxsackievirus Infections/epidemiology , Coxsackievirus Infections/prevention & control , Enterovirus/isolation & purification , Humans , Mandatory Programs/statistics & numerical data , Orthomyxoviridae/isolation & purification , Orthomyxoviridae Infections/epidemiology , Orthomyxoviridae Infections/prevention & control , Picornaviridae Infections/epidemiology , Picornaviridae Infections/prevention & control , Rhinovirus/isolation & purification , SARS-CoV-2/growth & development , Texas/epidemiology
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