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1.
Int J Infect Dis ; 118: 144-149, 2022 May.
Article in English | MEDLINE | ID: covidwho-1838857

ABSTRACT

BACKGROUND: Rhinoviruses are commonly considered simple "common cold" agents. The link between their molecular epidemiology and patient clinical presentation and outcomes remains unclear in adult populations. MATERIALS/METHODS: All nasopharyngeal or bronchoalveolar lavages were screened using multiplex PCR in 3 Parisian hospitals from January 2018 to September 2018. For all detected rhinoviruses, the VP2/VP4 region was subtyped by sequencing. RESULTS: The study included 178 unique patients who were positive for human rhinovirus (HRV). They were primarily men (56%), with a median age of 62.2 years (IQR: 46.8-71.4), frequently presenting chronic respiratory diseases (56%) and/or immunosuppression (46%). Of these, 63% were admitted for respiratory distress, including 25% for pneumonia; 95 (53%), 27 (15%), and 56 (32%) were positive for HRV-A, -B, and -C, respectively. HRV-B appeared to be more associated with immunosuppressive treatments (58% vs 30% and 36% of patients for HRV-A and -C, respectively, p = 0.038), higher coinfection rates (54% vs 34% and 23%, p = 0.03), and higher intensive care unit (ICU) admission rates (35% vs 17% and 13%, p = 0.048). Conversely, HRV-A was more frequently associated with pneumonia (54% vs 31% and 11% for HRV-B and -C, respectively, p = 0.01). CONCLUSIONS: This study highlights the high proportion of chronic respiratory diseases or immunosuppression among hospitalized patients infected with a rhinovirus. IMPORTANT: Human rhinoviruses (HRVs) are frequently detected in patients hospitalized for respiratory distress. Understanding their molecular differences is crucial to finding target treatments and improving patient outcomes.


Subject(s)
Picornaviridae Infections , Respiratory Distress Syndrome , Respiratory Tract Infections , Adult , Aged , Enterovirus , Humans , Male , Middle Aged , Phylogeny , Picornaviridae Infections/epidemiology , Respiratory Tract Infections/epidemiology , Rhinovirus/genetics
2.
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
3.
J Virol ; 96(2): e0106021, 2022 01 26.
Article in English | MEDLINE | ID: covidwho-1759286

ABSTRACT

Rhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways. IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.


Subject(s)
Capsid/chemistry , Mutation/drug effects , Rhinovirus/physiology , Virus Uncoating/physiology , Antiviral Agents/pharmacology , Capsid/drug effects , Capsid Proteins/genetics , Capsid Proteins/metabolism , Drug Resistance, Viral/drug effects , Drug Resistance, Viral/genetics , Endosomes/chemistry , Endosomes/drug effects , Endosomes/metabolism , HeLa Cells , Humans , Hydrogen-Ion Concentration , Intercellular Adhesion Molecule-1/metabolism , Protein Conformation , Rhinovirus/chemistry , Rhinovirus/drug effects , Rhinovirus/genetics , Virion/chemistry , Virion/genetics , Virion/metabolism , Virus Internalization/drug effects , Virus Uncoating/drug effects , Virus Uncoating/genetics
4.
BMC Infect Dis ; 22(1): 253, 2022 Mar 14.
Article in English | MEDLINE | ID: covidwho-1741929

ABSTRACT

BACKGROUND: Human rhinovirus (HRV) is the predominant etiological agent of the common cold in children and adults. A recent study showed that the inhibitory effect of face masks on viral shedding of HRV was less prominent than that on other respiratory viruses. Considering that most Chinese people have worn face masks in public area since the outbreak of coronavirus disease 2019, we aimed to find out whether HRV prevailed among children in 2020 and demonstrate the details of the epidemiological features of HRV under such a special circumstance. METHODS: We summarized the incidences of various respiratory virus infections in patients who visited the Children's Hospital of Fudan University during 2018-2020, and genotyped HRV positive nasopharyngeal specimens collected from 316 inpatients and 72 outpatients that visited the hospital in 2020. RESULTS: There was a major prevalence of HRV among children in the latter half of 2020, with a clear seasonality that HRV-As prevailed in summer while HRV-Cs in autumn. HRV-As were more prone to cause severe lower respiratory tract infections (LRTI), while HRV-Cs were closely associated with childhood wheezing. The predominant genotypes were A11, A28, A47, A82, A101, C40 and C43. Notably, A21, A82 and A101 took up larger proportions in severe cases than in non-severe cases. CONCLUSIONS: Our findings described a major prevalence of HRVs among children in 2020, which highlight the unique transmitting pattern of HRV and help to narrow the targets for antiviral strategies.


Subject(s)
COVID-19 , Picornaviridae Infections , Adult , Child , China/epidemiology , Humans , Masks , Picornaviridae Infections/epidemiology , Picornaviridae Infections/prevention & control , Rhinovirus/genetics
5.
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
6.
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
7.
Infect Genet Evol ; 96: 105106, 2021 12.
Article in English | MEDLINE | ID: covidwho-1506080

ABSTRACT

Coronaviruses (especially SARS-CoV-2) are characterized by rapid mutation and wide spread. As these characteristics easily lead to global pandemics, studying the evolutionary relationship between viruses is essential for clinical diagnosis. DNA sequencing has played an important role in evolutionary analysis. Recent alignment-free methods can overcome the problems of traditional alignment-based methods, which consume both time and space. This paper proposes a novel alignment-free method called the correlation coefficient feature vector (CCFV), which defines a correlation measure of the L-step delay of a nucleotide location from its location in the original DNA sequence. The numerical feature is a 16×L-dimensional numerical vector describing the distribution characteristics of the nucleotide positions in a DNA sequence. The proposed L-step delay correlation measure is interestingly related to some types of L+1 spaced mers. Unlike traditional gene comparison, our method avoids the computational complexity of multiple sequence alignment, and hence improves the speed of sequence comparison. Our method is applied to evolutionary analysis of the common human viruses including SARS-CoV-2, Dengue virus, Hepatitis B virus, and human rhinovirus and achieves the same or even better results than alignment-based methods. Especially for SARS-CoV-2, our method also confirms that bats are potential intermediate hosts of SARS-CoV-2.


Subject(s)
Genome, Viral/genetics , Phylogeny , Sequence Analysis, DNA/methods , Coronavirus/genetics , Dengue Virus/genetics , Hepatitis B/genetics , Humans , Models, Genetic , Rhinovirus/genetics , SARS-CoV-2/genetics , Sequence Alignment
8.
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
9.
Influenza Other Respir Viruses ; 15(6): 721-731, 2021 11.
Article in English | MEDLINE | ID: covidwho-1360496

ABSTRACT

BACKGROUND: After the detection of the first case of coronavirus disease 2019 (COVID-19) in South Korea on January 20, 2019, it has triggered three major outbreaks. To decrease the disease burden of COVID-19, social distancing and active mask wearing were encouraged, reducing the number of patients with influenza-like illness and altering the detection rate of influenza and respiratory viruses in the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS). We examined the changes in respiratory viruses due to COVID-19 in South Korea and virological causes of the high detection rate of human rhinovirus (hRV) in 2020. METHODS: We collected 52 684 oropharyngeal or nasopharyngeal swab samples from patients with influenza-like illness in cooperation with KINRESS from 2016 to 2020. Influenza virus and other respiratory viruses were confirmed using real-time RT-PCR. The weekly detection rate was used to compare virus detection patterns. RESULTS: Non-enveloped virus (hRV, human bocavirus, and human adenovirus) detection rates during the COVID-19 pandemic were maintained. The detection rate of hRV significantly increased in 2020 compared with that in 2019 and was negatively correlated with number of COVID-19-confirmed cases in 2020. The distribution of strains and genetic characteristics in hRV did not differ between 2019 and 2020. CONCLUSIONS: The COVID-19 pandemic impacted the respiratory virus detection rate. The extremely low detection rate of enveloped viruses resulted from efforts to prevent the spread of COVID-19 in South Korea. The high detection rate of hRV may be related to resistance against environmental conditions as a non-enveloped virus and the long period of viral shedding from patients.


Subject(s)
COVID-19 , Influenza, Human , Respiratory Tract Infections , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Pandemics , Republic of Korea/epidemiology , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/epidemiology , Rhinovirus/genetics , SARS-CoV-2
10.
Viruses ; 13(8)2021 08 12.
Article in English | MEDLINE | ID: covidwho-1355050

ABSTRACT

We aimed to assess the duration of nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA persistence in adults self-confined at home after acute infection; and to identify the associations of SARS-CoV-2 persistence with respiratory virus co-detection and infection transmission. A cross-sectional intra-household study was conducted in metropolitan Barcelona (Spain) during the time period of April to June 2020. Every adult who was the first family member reported as SARS-CoV-2-positive by reverse transcription polymerase chain reaction (RT-PCR) as well as their household child contacts had nasopharyngeal swabs tested by a targeted SARS-CoV-2 RT-PCR and a multiplex viral respiratory panel after a 15 day minimum time lag. Four-hundred and four households (404 adults and 708 children) were enrolled. SARS-CoV-2 RNA was detected in 137 (33.9%) adults and 84 (11.9%) children. Rhinovirus/Enterovirus (RV/EV) was commonly found (83.3%) in co-infection with SARS-CoV-2 in adults. The mean duration of SARS-CoV-2 RNA presence in adults' nasopharynx was 52 days (range 26-83 days). The persistence of SARS-CoV-2 was significantly associated with RV/EV co-infection (adjusted odds ratio (aOR) 9.31; 95% CI 2.57-33.80) and SARS-CoV-2 detection in child contacts (aOR 2.08; 95% CI 1.24-3.51). Prolonged nasopharyngeal SARS-CoV-2 RNA persistence beyond the acute infection phase was frequent in adults quarantined at home during the first epidemic wave; which was associated with RV/EV co-infection and could enhance intra-household infection transmission.


Subject(s)
COVID-19/complications , COVID-19/virology , Coinfection , Enterovirus Infections/complications , Picornaviridae Infections/complications , SARS-CoV-2/isolation & purification , Adolescent , Adult , Antibodies, Viral/blood , COVID-19/epidemiology , COVID-19/transmission , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Cross-Sectional Studies , Enterovirus/genetics , Enterovirus/isolation & purification , Family Health , Female , Humans , Infant , Male , Middle Aged , Nasopharynx/virology , Quarantine , RNA, Viral/analysis , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Time Factors , Young Adult
11.
Influenza Other Respir Viruses ; 15(6): 711-720, 2021 11.
Article in English | MEDLINE | ID: covidwho-1340182

ABSTRACT

BACKGROUND: Respiratory syncytial virus (RSV) and human rhinovirus (HRV) commonly cause influenza-like illness in young children. The global coronavirus pandemic beginning in 2020 altered the seasonality and prevalence of these respiratory infections in Thailand. We aimed to characterize the upsurge of HRV and the subsequent RSV infection observed among young children who sought medical care at a hospital in Bangkok. METHODS: From July to December 2020, nasopharyngeal swabs from children ≤5 years of age presented with influenza-like illness were tested for RSV and HRV using reverse-transcription polymerase chain reaction. Positive samples were Sanger sequenced. Genotyping was performed using sequence and phylogenetic analysis. RESULTS: Upsurge of HRV infection began in July and was subsequently replaced by a surge of RSV infection from September onward. In 6 months, HRV was detected in 27.5% (158/574) of the samples, of which 44% (69/158) were HRV-A, 7% (11/158) were HRV-B, and 36% (57/158) were HRV-C. Meanwhile, RSV was detected in 40.4% (232/574) of the samples, of which 78% (181/232) were RSV-A and 6% (14/232) were RSV-B. RSV peaked in October 2020, approximately 2 months later than typically seen in previous years. All RSV-A were of subgenotype ON1. Codetection of HRV and RSV was found in 5.1% (29/574). CONCLUSIONS: HRV and RSV infection among young children coincided with relaxed local coronavirus public health measures, including the return to in-class schooling. The delayed RSV season in 2020 was predominantly associated with RSV-A.


Subject(s)
Coronavirus , Picornaviridae Infections , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Child , Child, Preschool , Humans , Infant , Pandemics , Phylogeny , Picornaviridae Infections/epidemiology , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Tract Infections/epidemiology , Rhinovirus/genetics , Seasons , Thailand/epidemiology
12.
J Med Virol ; 93(7): 4392-4398, 2021 07.
Article in English | MEDLINE | ID: covidwho-1263103

ABSTRACT

With the arrival of coronavirus disease 2019 (COVID-19) in Brazil in February 2020, several preventive measures were taken by the population aiming to avoid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection including the use of masks, social distancing, and frequent hand washing then, these measures may have contributed to preventing infection also by other respiratory viruses. Our goal was to determine the frequencies of Influenza A and B viruses (FLUAV/FLUBV), human mastadenovirus C (HAdV-C), Enterovirus 68 (EV-68), and rhinovirus (RV) besides SARS-CoV-2 among hospitalized patients suspect of COVID-19 with cases of acute respiratory disease syndrome (ARDS) in the period of March to December 2020 and to detect possible coinfections among them. Nucleic acid detection was performed using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) in respiratory samples using naso-oropharyngeal swabs and bronchoalveolar lavage. A total of 418 samples of the 987 analyzed (42.3%) were positive for SARS-CoV-2, 16 (1.62%) samples were positive for FLUAV, no sample was positive for FLUBV or EV-68, 67 (6.78%) samples were positive for HAdV-C, 55 samples were positive for RV 1/2 (26.3%) and 37 for RV 2/2 (13.6%). Coinfections were also detected, including a triple coinfection with SARS-CoV-2, FLUAV, and HAdV-C. In the present work, a very low frequency of FLUV was reported among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID-19 and the high influenza vaccination coverage in the region in which this study was performed.


Subject(s)
Adenoviridae Infections/epidemiology , COVID-19/epidemiology , Common Cold/epidemiology , Enterovirus Infections/epidemiology , Influenza, Human/epidemiology , Physical Distancing , Adenoviridae Infections/prevention & control , Adolescent , Adult , Aged , Aged, 80 and over , Brazil/epidemiology , COVID-19/prevention & control , Child , Child, Preschool , Coinfection/epidemiology , Coinfection/virology , Common Cold/prevention & control , Enterovirus D, Human/genetics , Enterovirus D, Human/isolation & purification , Enterovirus Infections/prevention & control , Female , Humans , Infant , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza B virus/genetics , Influenza B virus/isolation & purification , Influenza, Human/prevention & control , Male , Masks , Mastadenovirus/genetics , Mastadenovirus/isolation & purification , Middle Aged , Nucleic Acid Amplification Techniques/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Young Adult
13.
J Med Virol ; 93(2): 1002-1007, 2021 02.
Article in English | MEDLINE | ID: covidwho-1196430

ABSTRACT

Respiratory viral infection can cause severe disease and hospitalization, especially among children, the elderly, and patients with comorbidities. In Brazil, the official surveillance system of severe acute respiratory infection (SARI) investigates influenza A (IAV) and B (IBV) viruses, respiratory syncytial virus (RSV), adenovirus (HAdV), and parainfluenza viruses (hPIV 1-3). In Rio Grande do Sul (RS), Brazil, many fatalities associated with SARI between 2013 and 2017 occurred among patients without underlying diseases and for whom the causative agent had not been identified using official protocols. This cross-sectional study analyzed the presence of coronaviruses (HCoV), bocavirus (HBoV), metapneumovirus (hMPV), and rhinovirus in patients who died of SARI despite not having comorbidities, and that were negative for IAV, IBV, RSV, HAdV, and hPIV. Nasopharyngeal aspirates/swabs from patients were used for nucleic acid extraction. The presence of HCoVs OC43, HKU1, NL63, and 229E; HBoV; hMPV; and rhinovirus was assessed by quantitative reverse transcription-polymerase chain reaction. Clinical data were also analyzed. Between 2013 and 2017, 16 225 cases of SARI were reported in RS; 9.8% of the patients died; 20% of all fatal cases were patients without comorbidities and for whom no pathogen was detected using standard protocols. Analysis of 271 of these cases identified HCoV in nine cases; HBoV, hMPV, and rhinovirus were detected in 3, 3, and 10 cases, respectively. Of note, patients infected with HCoV were adults. Results reinforce the importance of including coronaviruses in diagnostic panels used by official surveillance systems because besides their pandemic potential, endemic HCoVs are associated to severe disease in healthy adults.


Subject(s)
Coronavirus Infections/mortality , Coronavirus Infections/virology , Coronavirus NL63, Human/pathogenicity , Coronavirus OC43, Human/pathogenicity , Adolescent , Adult , Aged , Brazil/epidemiology , Child , Child, Preschool , Common Cold/epidemiology , Common Cold/virology , Coronavirus/classification , Coronavirus/pathogenicity , Cross-Sectional Studies , Female , Healthy Volunteers , Humans , Infant , Male , Middle Aged , Nasopharynx/virology , Respiratory Tract Infections/virology , Rhinovirus/genetics , Severity of Illness Index , Young Adult
14.
Med Sci Monit ; 26: e929789, 2020 Nov 26.
Article in English | MEDLINE | ID: covidwho-948228

ABSTRACT

Recent studies have shown a significant level of T cell immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in convalescent coronavirus disease 2019 (COVID-19) patients and unexposed healthy individuals. Also, SARS-CoV-2-reactive T memory cells occur in unexposed healthy individuals from endemic coronaviruses that cause the 'common cold.' The finding of the expression of adaptive SARS-CoV-2-reactive T memory cells in unexposed healthy individuals may be due to multiple cross-reactive viral protein targets following previous exposure to endemic human coronavirus infections. The opinion of the authors is that determination of protein sequence homologies across seemingly disparate viral protein libraries may provide epitope-matching data that link SARS-CoV-2-reactive T memory cell signatures to prior administration of cross-reacting vaccines to common viral pathogens. Exposure to SARS-CoV-2 initiates diverse cellular immune responses, including the associated 'cytokine storm'. Therefore, it is possible that the intact virus possesses a required degree of conformational matching, or stereoselectivity, to effectively target its receptor on multiple cell types. Therefore, conformational matching may be viewed as an evolving mechanism of viral infection and viral replication by an evolutionary modification of the angiotensin-converting enzyme 2 (ACE2) receptor required for SARS-CoV-2 binding and host cell entry. The authors propose that convalescent memory T cell immunity in individuals with mild or asymptomatic SARS-CoV-2 infection may result from an evolutionarily adapted immune response to coronavirus and the 'common cold'.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , Asymptomatic Infections , COVID-19/immunology , Common Cold/immunology , Immunologic Memory/genetics , Antibodies, Viral , COVID-19/blood , COVID-19/diagnosis , COVID-19/virology , Common Cold/prevention & control , Common Cold/virology , Cross Reactions/genetics , Epitopes, T-Lymphocyte/genetics , Epitopes, T-Lymphocyte/immunology , Evolution, Molecular , Humans , Immunity, Cellular/genetics , Immunogenicity, Vaccine , Rhinovirus/genetics , Rhinovirus/immunology , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Sequence Homology , Severity of Illness Index , T-Lymphocyte Subsets/immunology , T-Lymphocytes/immunology , Viral Proteins/genetics , Viral Proteins/immunology , Viral Vaccines/administration & dosage , Viral Vaccines/immunology , Virus Internalization , Virus Replication/genetics , Virus Replication/immunology
15.
Rev Med Virol ; 31(4): e2193, 2021 07.
Article in English | MEDLINE | ID: covidwho-938540

ABSTRACT

Human rhinoviruses (RVs) are the primary aetiological agent of the common cold. Generally, the associated infection is mild and self-limiting, but may also be associated with bronchiolitis in infants, pneumonia in the immunocompromised and exacerbation in patients with pulmonary conditions such as asthma or chronic obstructive pulmonary disease. Viral infection accounts for as many as two thirds of asthma exacerbations in children and more than half in adults. Allergy and asthma are major risk factors for more frequent and severe RV-related illnesses. The prevalence of RV-induced wheezing will likely continue to increase given that asthma affects a significant proportion of the population, with allergic asthma accounting for the majority. Several new respiratory viruses and their subgroups have been discovered, with various degrees of relevance. This review will focus on RV infection in the context of the epidemiologic evidence, genetic variability, pathobiology, clinical studies in the context of asthma, differences with other viruses including COVID-19 and current treatment interventions.


Subject(s)
Asthma/etiology , Picornaviridae Infections/complications , Rhinovirus , Asthma/virology , Common Cold/complications , Common Cold/virology , Genetic Variation , Humans , Picornaviridae Infections/virology , Rhinovirus/genetics
16.
Viruses ; 12(10)2020 10 09.
Article in English | MEDLINE | ID: covidwho-906169

ABSTRACT

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate "self". This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate "self") with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural "self" traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses.


Subject(s)
Adenoviridae/metabolism , Capsid Proteins/metabolism , Coronavirus/metabolism , Protein Structure, Tertiary/physiology , Rhinovirus/metabolism , Adenoviridae/genetics , Coronavirus/genetics , Crystallography, X-Ray , Genome, Viral/genetics , Rhinovirus/genetics , Viral Structures/metabolism
18.
Int J Pharm ; 589: 119826, 2020 Nov 15.
Article in English | MEDLINE | ID: covidwho-733806

ABSTRACT

Viral infections represent 44% of newly emerging infections, and as is shown by the COVID-19 outbreak constitute a major risk to human health and wellbeing. Although there are many efficient antiviral agents, they still have drawbacks such as development of virus resistance and accumulation within off-target organs. Encapsulation of antiviral agents into nanoparticles (NPs) has been shown to improve bioavailability, control release, and reduce side effects. However, there is little quantitative understanding of how the uptake of NPs into virally infected cells compares to uninfected cells. In this work, the uptake of fluorescently labeled polymer NPs was investigated in several models of rhinovirus (RV) infected cells. Different multiplicities of RV infections (MOI) and timings of NPs uptake were also investigated. In some cases, RV infection resulted in a significant increase of NPs uptake, but this was not universally noted. For HeLa cells, RV-A16 and RV-A01 infection elevated NPs uptake upon increasing the incubation time, whereas at later timepoints (6 h) a reduced uptake was noted with RV-A01 infection (owing to decreased cell viability). Beas-2B cells exhibited more complex trends: decreases in NPs uptake (cf. uninfected cells) were observed at short incubation times following RV-A01 and RV-A16 infection. At later incubation times (4 h), we found a marked decrease of NPs uptake for RV-A01 infected cells but an increase in uptake with RV-A16 infected cells. Where increases in NPs uptake were found, they were very modest compared to results previously reported for a hepatitis C/ Huh7.5 cell line model. An increase in RV dose (MOI) was not associated with any notable change of NPs uptake. We argue that the diverse endocytic pathways among the different cell lines, together with changes in virus nature, size, and entry mechanism are responsible for these differences. These findings suggest that NPs entry into virally infected cells is a complex process, and further work is required to unravel the different factors which govern this. Undertaking this additional research will be crucial to develop potent nanomedicines for the delivery of antiviral agents.


Subject(s)
Nanoparticles/administration & dosage , Picornaviridae Infections/metabolism , Polyesters/administration & dosage , Rhinovirus , Cell Line , Cell Survival/drug effects , DNA, Viral , Endocytosis , Genome, Viral , Humans , Rhinovirus/genetics
19.
Int J Legal Med ; 134(4): 1271-1274, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-378237

ABSTRACT

In the setting of the coronavirus disease 2019 (COVID-19) pandemic, only few data regarding lung pathology induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is available, especially without medical intervention interfering with the natural evolution of the disease. We present here the first case of forensic autopsy of a COVID-19 fatality occurring in a young woman, in the community. Diagnosis was made at necropsy and lung histology showed diffuse alveolar damage, edema, and interstitial pneumonia with a geographically heterogeneous pattern, mostly affecting the central part of the lungs. This death related to COVID-19 pathology highlights the heterogeneity and severity of central lung lesions after natural evolution of the disease.


Subject(s)
Betacoronavirus , Coronavirus Infections/pathology , Lung/pathology , Pneumonia, Viral/pathology , Adenoviridae/genetics , Adenoviridae/isolation & purification , Adult , Autopsy , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Bocavirus/genetics , Bocavirus/isolation & purification , C-Reactive Protein/analysis , COVID-19 , Coronavirus/genetics , Coronavirus/isolation & purification , Female , Humans , Influenzavirus A/genetics , Influenzavirus A/isolation & purification , Influenzavirus B/genetics , Influenzavirus B/isolation & purification , Macrophages/pathology , Megakaryocytes/pathology , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Neutrophils/pathology , Obesity, Morbid , Pandemics , Procalcitonin/blood , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2 , Switzerland , T-Lymphocytes/pathology
20.
J Clin Lab Anal ; 34(1): e23032, 2020 Jan.
Article in English | MEDLINE | ID: covidwho-326814

ABSTRACT

BACKGROUND: Respiratory viruses, such as influenza viruses, initially infect the upper airways but can manifest as severe lower respiratory tract infections in high-risk patients with significant morbidity and mortality. For syndromic diagnosis, several multiplex nucleic acid amplification tests have been developed for clinics, of which SureX 13 Respiratory Pathogen Multiplex Kit (ResP) can simultaneously detect 13 pathogens directly from airway secretion specimens. The organisms identified are influenza virus A, influenza virus A pdmH1N1 (2009), influenza virus A H3N2, influenza virus B, adenovirus, boca virus, rhinovirus, parainfluenza virus, coronavirus, respiratory syncytial virus, human metapneumovirus, Mycoplasma pneumoniae, and Chlamydia. METHODS: This study provides performance evaluation data of this assay by comparing with pathogen-specific PCRs from oropharyngeal swab samples. RESULTS: Ten pathogens were detected in this assay, of which rhinovirus, adenovirus, and influenza virus A pdmH1N1 (2009) were the most common. The overall agreement between the ResP and the comparator tests was 93.8%. The ResP demonstrated 86.5% agreement for positive results and 97.8% agreement for negative results. CONCLUSION: The ResP assay demonstrated a highly concordant performance comparing with pathogen-specific PCRs for detection of respiratory pathogens in oropharyngeal swabs from outpatients and could aid in the diagnosis of respiratory infections in a variety of clinical scenarios.


Subject(s)
Ambulatory Care/methods , Multiplex Polymerase Chain Reaction/methods , Oropharynx/virology , Pneumonia, Mycoplasma , Pneumonia, Viral , Adenoviridae/genetics , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Influenza A virus/genetics , Male , Middle Aged , Mycoplasma pneumoniae/genetics , Pneumonia, Mycoplasma/diagnosis , Pneumonia, Mycoplasma/microbiology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , RNA, Viral/analysis , RNA, Viral/genetics , Rhinovirus/genetics , Young Adult
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