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2.
Emerg Microbes Infect ; 11(1): 168-171, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1623181

ABSTRACT

HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.


Subject(s)
Common Cold/epidemiology , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/genetics , Genome, Viral , Genotype , Pneumonia, Viral/epidemiology , Base Sequence , Bayes Theorem , Child , Child, Hospitalized , Child, Preschool , China/epidemiology , Common Cold/pathology , Common Cold/transmission , Common Cold/virology , Coronavirus Infections/pathology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Coronavirus OC43, Human/classification , Coronavirus OC43, Human/pathogenicity , Epidemiological Monitoring , Female , Humans , Infant , Male , Monte Carlo Method , Mutation , Phylogeny , Pneumonia, Viral/pathology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Recombination, Genetic
4.
J Clin Virol ; 136: 104754, 2021 03.
Article in English | MEDLINE | ID: covidwho-1385860

ABSTRACT

OBJECTIVES: The four seasonal coronaviruses 229E, NL63, OC43, and HKU1 are frequent causes of respiratory infections and show annual and seasonal variation. Increased understanding about these patterns could be informative about the epidemiology of SARS-CoV-2. METHODS: Results from PCR diagnostics for the seasonal coronaviruses, and other respiratory viruses, were obtained for 55,190 clinical samples analyzed at the Karolinska University Hospital, Stockholm, Sweden, between 14 September 2009 and 2 April 2020. RESULTS: Seasonal coronaviruses were detected in 2130 samples (3.9 %) and constituted 8.1 % of all virus detections. OC43 was most commonly detected (28.4 % of detections), followed by NL63 (24.0 %), HKU1 (17.6 %), and 229E (15.3 %). The overall fraction of positive samples was similar between seasons, but at species level there were distinct biennial alternating peak seasons for the Alphacoronaviruses, 229E and NL63, and the Betacoronaviruses, OC43 and HKU1, respectively. The Betacoronaviruses peaked earlier in the winter season (Dec-Jan) than the Alphacoronaviruses (Feb-Mar). Coronaviruses were detected across all ages, but diagnostics were more frequently requested for paediatric patients than adults and the elderly. OC43 and 229E incidence was relatively constant across age strata, while that of NL63 and HKU1 decreased with age. CONCLUSIONS: Both the Alphacoronaviruses and Betacoronaviruses showed alternating biennial winter incidence peaks, which suggests some type of immune mediated interaction. Symptomatic reinfections in adults and the elderly appear relatively common. Both findings may be of relevance for the epidemiology of SARS-CoV-2.


Subject(s)
COVID-19/epidemiology , Common Cold/epidemiology , Coronavirus 229E, Human/isolation & purification , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/isolation & purification , Deltacoronavirus/isolation & purification , Female , Humans , Male , Retrospective Studies , SARS-CoV-2 , Seasons , Sweden
5.
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
6.
BMC Emerg Med ; 21(1): 64, 2021 05 29.
Article in English | MEDLINE | ID: covidwho-1247575

ABSTRACT

BACKGROUND: Trends in the characteristics and disease severity of patients using an after-hours house call (AHHC) medical service changed during the coronavirus disease (COVID-19) pandemic. However, there have been no reports on this issue since the start of the COVID-19 pandemic. This study aimed to investigate patients' tendencies to utilize an AHHC medical service for fever or common cold symptoms during the COVID-19 pandemic. METHODS: This retrospective cohort study compared the characteristics and disease severity of patients with fever or common cold symptoms utilizing an AHHC medical service offered by a single large company between the control period (December 1, 2018 to April 30, 2019) and the COVID-19 pandemic exposure period (December 1, 2019 to April 30, 2020). We also assessed the proportion of these patients in relation to all patients calling the service for any reason. RESULTS: During the control and COVID-19 pandemic exposure periods, a total of 6462 and 10,003 patients consulted the AHHC medical service, respectively. Of these, 5335 (82.6%) and 7423 (74.2%) patients had fever and common cold symptoms, respectively, during the control and COVID-19 pandemic exposure periods (P < 0.001). The corresponding median (interquartile range) ages were 8 (3-11) and 10 (4-33) years, respectively. The distribution of disease severity differed between the groups. The proportions of patients with mild, moderate, and severe illness were 71.1, 28.7, and 0.2% in the control period and 42.3, 56.7, and 0.9% in the COVID-19 pandemic exposure period, respectively (P < 0.001). CONCLUSIONS: During the COVID-19 pandemic, the proportion of patients with fever or common cold symptoms was lower than that in the control period, but disease severity was significantly higher.


Subject(s)
After-Hours Care/statistics & numerical data , COVID-19/epidemiology , Common Cold/epidemiology , Fever/epidemiology , House Calls/statistics & numerical data , Severity of Illness Index , Adult , COVID-19/therapy , Continuity of Patient Care/statistics & numerical data , Humans , Japan , Male , Middle Aged , Retrospective Studies
7.
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
8.
Adv Clin Exp Med ; 30(1): 109-114, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1059687

ABSTRACT

BACKGROUND: This review focuses on the frequency of symptoms in COVID-19 in comparison to SARS, influenza and common cold. OBJECTIVES: To evaluate and compare the knowledge about the clinical features, symptoms and differences between patients with COVID-19, SARS, influenza, and common cold. The research can help ear, nose and throat specialists and other health practitioners manage patients during the COVID-19 pandemic. MATERIAL AND METHODS: The biomedical databases used in the study included PubMed and MEDLINE. Statistical analysis using the Z-score test assessed which symptoms were more characteristic of COVID-19 than other viral diseases. RESULTS: Among individuals with COVID-19, the most frequently reported symptoms were cough (70%), fever (45%), muscular pain (29%), and headache (21%), whereas sore throat (12%), and rhinorrhea (4%) were observed at lower rates. Fever was identified as most frequent in COVID-19 (74%), appearing at a higher rate in those cases than in influenza (68%) or the common cold (40%) (p < 0.05). In comparison to other viral diseases, sore throat was rarely reported in COVID-19 and SARS (12% and 18%, respectively) (p < 0.05). In influenza and common cold, a cough was identified in 93% and 80% of cases (p < 0.05). Headache, rhinorrhea, muscular pain, and sore throat were more common in influenza (91%, 91%, 94%, and 84%, respectively) and common cold (89%, 81%, 94%, and 84%, respectively) than in COVID-19 (21%, 4%, 29%, and 12%, respectively) and SARS (45%, 12%, 55%, and 18%, respectively) (p < 0.05). CONCLUSION: The results of the analysis show that a greater number of general symptoms should lead to a diagnosis of influenza or common cold rather than COVID-19.


Subject(s)
COVID-19 , Common Cold , Influenza, Human , Common Cold/diagnosis , Common Cold/epidemiology , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Pandemics , SARS-CoV-2
9.
JCI Insight ; 6(4)2021 02 22.
Article in English | MEDLINE | ID: covidwho-1047074

ABSTRACT

Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory infection in humans. B cell responses to these "common cold" viruses remain incompletely understood. Here we report a comprehensive analysis of CoV-specific antibody repertoires in 231 children and 1168 adults using phage immunoprecipitation sequencing. Seroprevalence of antibodies against endemic HCoVs ranged between approximately 4% and 27% depending on the species and cohort. We identified at least 136 novel linear B cell epitopes. Antibody repertoires against endemic HCoVs were qualitatively different between children and adults in that anti-HCoV IgG specificities more frequently found among children targeted functionally important and structurally conserved regions of the spike, nucleocapsid, and matrix proteins. Moreover, antibody specificities targeting the highly conserved fusion peptide region and S2' cleavage site of the spike protein were broadly cross-reactive with peptides of epidemic human and nonhuman coronaviruses. In contrast, an acidic tandem repeat in the N-terminal region of the Nsp3 subdomain of the HCoV-HKU1 polyprotein was the predominant target of antibody responses in adult donors. Our findings shed light on the dominant species-specific and pan-CoV target sites of human antibody responses to coronavirus infection, thereby providing important insights for the development of prophylactic or therapeutic monoclonal antibodies and vaccine design.


Subject(s)
Antibodies, Viral/isolation & purification , Common Cold/virology , Coronavirus Infections/immunology , Coronavirus/immunology , Endemic Diseases , Adult , Antibodies, Viral/blood , Antibodies, Viral/immunology , Antibody Specificity , Antigens, Viral/blood , Antigens, Viral/immunology , Child , Child, Preschool , Common Cold/blood , Common Cold/epidemiology , Common Cold/immunology , Coronavirus/isolation & purification , Coronavirus Infections/blood , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Cross Reactions , Epitopes, B-Lymphocyte/blood , Epitopes, B-Lymphocyte/immunology , Female , Humans , Male , Middle Aged , Protein Domains/immunology , Retrospective Studies , Seroepidemiologic Studies , Viral Proteins/immunology
10.
Arch Virol ; 166(3): 929-933, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1046769

ABSTRACT

This is the first study of respiratory infections in Córdoba, Argentina, caused by endemic human coronavirus (HCoV)-OC43 and HCOV-229E, which circulated during 2011-2012 at a 3% rate, either as single or multiple infections. They were detected mainly in children, but HCoV-229E was also found in adults. HCoV-229E was detected in five out of 631 samples (0.8%), and HCoV-OC43 was found in 14 out of 631 (2.2%) samples. Clinical manifestations ranged from fever to respiratory distress, and a significant association of HCoV-229E with asthma was observed. Further studies and surveillance are needed to provide better clinical insights, early diagnosis, and medical care of patients, as well as to contribute to epidemiology modeling and prevention.


Subject(s)
Common Cold/epidemiology , Coronavirus 229E, Human/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/isolation & purification , Adolescent , Adult , Aged , Argentina , Child , Child, Preschool , Common Cold/virology , Coronavirus 229E, Human/genetics , Coronavirus Infections/virology , Coronavirus OC43, Human/genetics , Cross-Sectional Studies , Humans , Infant , Middle Aged , Retrospective Studies , Seasons , Young Adult
11.
J Clin Invest ; 131(1)2021 01 04.
Article in English | MEDLINE | ID: covidwho-1011061

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic continues to cause morbidity and mortality. Since SARS coronavirus 2 (SARS-CoV-2) was identified as the cause for COVID-19, some have questioned whether exposure to seasonal common cold coronaviruses (CCCs) could provide tangible protection against SARS-CoV-2 infection or disease. In this issue of the JCI, Sagar et al. examined SARS-CoV-2 infections and outcomes of patients who had previously tested positive or negative for CCC infection (CCC+ or CCC-) by a comprehensive respiratory panel using PCR. No differences were seen between groups in terms of susceptibility to SARS-CoV-2 infection. However, hospitalized patients with a documented history of CCC infection had lower rates of intensive care unit (ICU) admissions and higher rates of survival than hospitalized CCC- patients. While these findings are associative and not causative, they highlight evidence suggesting that previous CCC infection may influence the disease course of SARS-CoV-2 infection.


Subject(s)
COVID-19 , Common Cold/immunology , Pandemics , SARS-CoV-2/immunology , COVID-19/epidemiology , COVID-19/immunology , COVID-19/prevention & control , Common Cold/epidemiology , Humans , Male , Middle Aged
14.
J Med Virol ; 92(11): 2623-2630, 2020 11.
Article in English | MEDLINE | ID: covidwho-935126

ABSTRACT

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread around the world, causing serious illness and death and creating a heavy burden on the healthcare systems of many countries. Since the virus first emerged in late November 2019, its spread has coincided with peak circulation of several seasonal respiratory viruses, yet some studies have noted limited coinfections between SARS-CoV-2 and other viruses. We use a mathematical model of viral coinfection to study SARS-CoV-2 coinfections, finding that SARS-CoV-2 replication is easily suppressed by many common respiratory viruses. According to our model, this suppression is because SARS-CoV-2 has a lower growth rate (1.8/d) than the other viruses examined in this study. The suppression of SARS-CoV-2 by other pathogens could have implications for the timing and severity of a second wave.


Subject(s)
COVID-19/virology , Coinfection/virology , Common Cold/epidemiology , Influenza, Human/epidemiology , Models, Theoretical , COVID-19/epidemiology , Coinfection/epidemiology , Common Cold/virology , Humans , Influenza, Human/virology , Respiratory Syncytial Viruses/pathogenicity , Rhinovirus/pathogenicity , SARS-CoV-2/pathogenicity
15.
J Infect ; 81(6): 923-930, 2020 12.
Article in English | MEDLINE | ID: covidwho-894041

ABSTRACT

BACKGROUND: Immunological cross-reactivity between common cold coronaviruses (CCC) and SARS-CoV-2 might account for the reduced incidence of COVID-19 in children. Evidence to support speculation includes in vitro evidence for humoral and cellular cross-reactivity with SARS-CoV-2 in specimens obtained before the pandemic started. METHOD: We used retrospective health insurance enrollment records, claims, and laboratory results to assemble a cohort of 869,236 insured individuals who had a PCR test for SARS-CoV-2. We estimated the effects of having clinical encounters for various diagnostic categories in the year preceding the study period on the risk of a positive test result. FINDINGS: After adjusting for age, gender and care seeking behavior, we identified that individuals with diagnoses for common cold symptoms, including acute sinusitis, bronchitis, or pharyngitis in the preceding year had a lower risk of testing positive for SARS-CoV-2 (OR=0.76, 95%CI=0.75, 0.77). No reduction in the odds of a positive test for SARS-CoV-2 was seen in individuals under 18 years. The reduction in odds in adults remained stable for four years but was strongest in those with recent common cold symptoms. INTERPRETATION: While this study cannot attribute this association to cross-immunity resulting from a prior CCC infection, it is one potential explanation. Regardless of the cause, the reduction in the odds of being infected by SARS-CoV-2 among those with a recent diagnosis of common cold symptoms may have a role in shifting future COVD-19 infection patterns from endemic to episodic.


Subject(s)
COVID-19/epidemiology , Common Cold/epidemiology , Coronavirus Infections/epidemiology , SARS-CoV-2/immunology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/immunology , Child , Child, Preschool , Cohort Studies , Common Cold/immunology , Coronavirus/immunology , Coronavirus Infections/immunology , Cross Reactions , Female , Humans , Immunity , Incidence , Infant , Male , Middle Aged , Retrospective Studies , Risk Factors , Young Adult
16.
J Formos Med Assoc ; 120(1 Pt 3): 679-687, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-716804

ABSTRACT

BACKGROUND: The purpose of the work is to analyze population adaptation to SARS-CoV-2 in Europe in March-May 2020, predict herd immunity formation in the nearest several months on the basis of our SIR modified epidemiological model of the virus spread and elaborate recommendations to governments regarding a second wave of COVID-19 pandemic. METHODS: Outer (1,006,512 RT-PCR tests results for SARS-CoV-2) and proprietary (34,660 respiratory samples) epidemiological data was used. Fifteen European countries were studied. Dates of research: March 2 - May 22, 2020. RESULTS: As of April 21, 2020, the mean population infection rate (PIR) for the European countries considered, was 9.66%. It decreased to 6.85% by May 22, 2020. The model predicted 5.68% PIR, giving accuracy of 79.40%. SARS-CoV-2 basic reproduction number is limited by an extremum that may be observed for closed communities. A concept of effective reproduction number is introduced as a function of r0 with maximum at r0 = 4.671 and value reff. = 0.315 for the full-lockdown mode and r0 = 5.539 and reff. = 0.552 for the no-lockdown mode of SARS-CoV-2 containment. Full-lockdown and no-lockdown modes resulted in the outcomes not strikingly different from each other in terms of herd immunity values. CONCLUSION: In case of a second wave of COVID-19 disease in Europe, it will coincide with seasonal common cold surge, spanning from mid-September 2020 to mid-February 2021, with a median in November-December 2020. Strict epidemiological surveillance must be observed in Europe at that time.


Subject(s)
Basic Reproduction Number/statistics & numerical data , COVID-19 , Common Cold , Communicable Disease Control , Disease Transmission, Infectious , Immunity, Herd , Adaptation, Physiological/immunology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/immunology , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing/methods , Coinfection/epidemiology , Coinfection/prevention & control , Common Cold/epidemiology , Common Cold/prevention & control , Communicable Disease Control/organization & administration , Communicable Disease Control/statistics & numerical data , Disease Transmission, Infectious/prevention & control , Disease Transmission, Infectious/statistics & numerical data , Epidemiological Monitoring , Europe/epidemiology , Humans , Models, Statistical , SARS-CoV-2/isolation & purification , Seasons
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