Infections with human coronaviruses NL63 and OC43 among hospitalised and outpatient individuals in São Paulo, Brazil

HCoV-NL63 and HCoV-HKU1 seroprevalence and its relationship with the clinical features of COVID-19 patients from Villavicencio, Colombia

INTRODUCTION

Due to the cross-reactivity between SARS-CoV-2 and common human coronaviruses, previous infections with these viruses could contribute to serological or cellular cross-protection against severe COVID-19. However, protective immunity may not develop, or pre-existing immunity could increase COVID-19 severity.

OBJECTIVE

To determine the seroprevalence of IgG antibodies against HCoV-NL63 and HCoV-HKU1 and correlate previous exposure with COVID-19 signs in patients from Villavicencio.

MATERIALS AND METHODS

A cross-sectional retrospective study was conducted. ELISA technique was used to search for IgG antibodies against HCoV-NL3 and HCoV-HKU1 in patients with positive RT-qPCR results for SARS-CoV-2. Patients were grouped according to COVID-19 clinical characteristics in four groups: group 1: asymptomatic (n = 23); group 2: hospitalized (n = 24); group 3: intensive care units (n = 24), and group 4: dead (n = 22).

RESULTS

The overall seroprevalence of IgG antibodies against HCoV was 74.2% (n = 69; 95% CI: 65.3-83.1), with 66.7% of HCoV-NL63 (n = 62; 95% CI: 57,1-76,2), and 25.8% of HCoV-HKU1 (n = 24; 95% CI: 16,9-34,7). Based on crosstab analysis, prior exposure to HCoV-NL63 was associated with protection against severe COVID-19 (p = 0.042; adjusted OR = 0.159; 95% CI: 0.027-0.938), and previous coinfection of HCoV-NL63 and HCoVHKU1 was considered a positive association to severe COVID-19 (p = 0.048; adjusted OR = 16.704; 95% CI: 1.020 - 273.670).

CONCLUSION

To our knowledge, this is the first study addressing seroprevalence of HCoV IgG antibodies in Colombia and Latin America. Previous exposure to HCoV-NL63 could protect against severe COVID-19, whereas patients with underlying HCoV-NL63 and HCoVHKU1 coinfection could be hospitalized with severe signs of COVID-19.

The scientific publication of the Memórias do Instituto Oswaldo Cruz (1909-2020): a history of contribution to the biomedical sciences

BACKGROUND

The Memórias do Instituto Oswaldo Cruz (MIOC) is one of the first scientific journals created in Brazil and currently one of the most important biomedical journals in South America. Knowledge of the main themes disseminated over time and its main contributors can contribute towards a better understanding of its trajectory and future.

OBJECTIVES

Map the journal’s scientific publication between 1909 and 2020.

METHODS

Data from three scientific databases was combined, alongside bibliometrics and network analysis to analyse publication records between 1909 and 2020.

FINDINGS

Publications increased substantially since the 1980s. The main publishing organisations are Brazilian. Excluding Brazil, the main publishing countries are the USA, Argentina, and Colombia. During the entire investigated period, the main themes refer to Chagas disease, schistosomiasis, and Leishmaniasis. During some periods, publications followed disease outbreaks in Brazil (e.g., dengue fever and yellow fever).

MAIN CONCLUSIONS

Since its foundation in 1909, the MIOC has focused on infectious and parasitic diseases. The editorial changes implemented from the 1980s onwards led MIOC to a relevant growth concerning annual publications and its transformation into an important communication vehicle for researchers from several Brazilian organisations besides Fiocruz, as well as organisations from other countries, especially within Latin America.

COVID-19: Immunology and treatment options

The novel coronavirus SARS-CoV2 causes COVID-19, a pandemic threatening millions. As protective immunity does not exist in humans and the virus is capable of escaping innate immune responses, it can proliferate, unhindered, in primarily infected tissues. Subsequent cell death results in the release of virus particles and intracellular components to the extracellular space, which result in immune cell recruitment, the generation of immune complexes and associated damage. Infection of monocytes/macrophages and/or recruitment of uninfected immune cells can result in massive inflammatory responses later in the disease. Uncontrolled production of pro-inflammatory mediators contributes to ARDS and cytokine storm syndrome. Antiviral agents and immune modulating treatments are currently being trialled. Understanding immune evasion strategies of SARS-CoV2 and the resulting delayed massive immune response will result in the identification of biomarkers that predict outcomes as well as phenotype and disease stage specific treatments that will likely include both antiviral and immune modulating agents.

Prevalence and genetic diversity analysis of human coronaviruses among cross-border children

Background

More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted.

Methods

A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test.

Results

78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered.

Conclusions

The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.

Clinico-epidemiological characteristics of acute respiratory infections caused by coronavirus OC43, NL63 and 229E

Antecedentes y objetivos

Las infecciones respiratorias agudas son una entidad muy frecuente en la población general. La mayoría de ellas son debidas a infecciones víricas. Este estudio pretende precisar las características clínicas y epidemiológicas de los pacientes adultos con infección respiratoria por los coronavirus OC43, NL63 y 229E.

Pacientes y métodos

Entre enero del 2013 y febrero del 2014 se estudió prospectivamente a todos los pacientes con sospecha clínica de infección respiratoria mediante la toma de un frotis faríngeo y la realización de una reacción en cadena de la polimerasa en transcripción reversa en tiempo real en búsqueda de coronavirus.

Resultados

En 48 casos (7,0% de los 686 pacientes incluidos; 12,6% de los 381 en los que se detectó algún virus) se pudo demostrar la presencia de algún coronavirus. En 24 casos se trataba del OC43 (50%), en 14 del NL63 (29%) y en 10 del 229E (21%). La edad media fue de 54,5 años, con un ligero predominio de varones. Las presentaciones clínicas más frecuentes fueron el cuadro gripal inespecífico (43,7%), la neumonía (29,2%) y la agudización de enfermedad pulmonar obstructiva crónica (8,3%). El 52% de los pacientes precisaron ingreso hospitalario, en 2 ocasiones en cuidados intensivos. No se produjo ningún fallecimiento.

Conclusión

Las infecciones respiratorias agudas causadas por coronavirus inciden preferentemente en varones fumadores en la edad media de la vida, frecuentemente afectados de enfermedades previas. La sintomatología clínica mas frecuente ha sido el cuadro gripal inespecífico.

Clinico-epidemiological characteristics of acute respiratory infections caused by coronavirus OC43, NL63 and 229E

BACKGROUND AND OBJECTIVES

Acute respiratory infection is a very common condition in the general population. The majority of these infections are due to viruses. This study attempted to determine the clinical and epidemiological characteristics of adult patients with respiratory infection by the coronavirus OC43, NL63 and 229E.

PATIENTS AND METHODS

Between January 2013 and February 2014, we prospectively studied all patients with suspected clinical respiratory infection by taking throat swabs and performing a reverse transcription polymerase chain reaction in search of coronavirus.

RESULTS

In 48 cases (7.0% of the 686 enrolled patients; 12.6% of the 381 in whom a virus was detected) the presence of a coronavirus demonstrated. In 24 cases, the virus was OC43 (50%); in 14 cases, the virus was NL63 (29%); and in 10 cases, the virus was 229E (21%). The mean age was 54.5 years, with a slight predominance of men. The most common clinical presentations were nonspecific influenza symptoms (43.7%), pneumonia (29.2%) and chronic obstructive pulmonary disease exacerbation (8.3%). Fifty-two percent of the patients required hospitalization, and 2 patients required intensive care. There were no deaths.

CONCLUSION

Acute respiratory infections caused by coronavirus mainly affect middle-aged male smokers, who are often affected by previous diseases. The most common clinical picture has been nonspecific influenza symptoms.

Stability of infectious human coronavirus NL63

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Optimal protocol for freeze-drying that allows safe and effective preservation of HCoV-NL63 infectious material was developed.

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Lyophilized virus preparations can be stored either at ambient temperature or at +4 °C. In the latter case samples may be stored for at least two months.

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HCoV-NL63 virions are exquisitely stable in liquid media and can be stored also without preservatives at ambient temperature for up to 14 days.

The human coronavirus NL63 was identified in 2004 and subsequent studies showed its worldwide distribution. Infection with this pathogen is associated with upper and lower respiratory tract diseases of mild to moderate severity. Furthermore, HCoV-NL63 is the main cause of croup in children. Within this study an optimal protocol for freeze-drying that allows safe and effective preservation of HCoV-NL63 infectious material was developed. Lyophilized virus preparations can be stored either at ambient temperature or at +4 °C. In the latter case samples may be stored for at least two months. Surprisingly, conducted analysis showed that HCoV-NL63 virions are exquisitely stable in liquid media and can be stored also without preservatives at ambient temperature for up to 14 days.

Epidemiological and clinical features of human coronavirus infections among different subsets of patients

BACKGROUND

Epidemiological and clinical data of human coronaviruses (HCoVs) infections are restricted to span 1-3 years at most. We conducted a comprehensive 9-year study on HCoVs by analyzing 1137 respiratory samples from four subsets of patients (asymptomatic, general community, with comorbidities, and hospitalized) in São Paulo, Brazil.

METHODS

A pan-coronavirus RT-PCR screening assay was performed, followed by species-specific real-time RT-PCR monoplex assays.

RESULTS

Human coronaviruses were detected in 88 of 1137 (7.7%) of the samples. The most frequently detected HCoV species were NL63 (50.0%) and OC43 (27.3%). Patients with comorbidities presented the highest risk of acquiring coronavirus infection (odds ratio=4.17; 95% confidence interval=1.9-9.3), and children with heart diseases revealed a significant HCoV infection presence. Dyspnea was more associated with HCoV-229E infections (66.6%), and cyanosis was reported only in HCoV-OC43 infections. There were interseasonal differences in the detection frequencies, with HCoV-229E being predominant in the year 2004 (61.5%) and HCoV-NL63 (70.8%) in 2008.

CONCLUSIONS

Our data provide a novel insight into the epidemiology and clinical knowledge of HCoVs among different subsets of patients, revealing that these viruses may cause more than mild respiratory tract disease.

Human coronavirus ocurrence in different populations of Sao Paulo: A comprehensive nine-year study using a pancoronavirus RT-PCR assay

Human coronaviruses (HCoVs) are considered one of the most common respiratory viruses associated with respiratory tract illnesses. An emergent human coronavirus was identified as the causal agent of an epidemic of severe acute respiratory syndrome (SARS) during 2002–2003. The severity of the disease combined with its rapid spread requires the continuous surveillance of coronaviruses in worldwide populations. Epidemiological and clinical data of HCoVs infectious in the Brazilian population are scarce and restricted to one or two groups of patients. Our study aimed to investigate retrospectively the presence of HCoVs in different populations of São Paulo presenting acute respiratory tract infections (ARIs) during the years of 2001–2010. A pancoronavirus RT-PCR was performed in this study. Coronaviruses were detected in 126 (11.5%) of 1,087 specimens. Peaks detection frequency was observed during 2002–2004 and 2008–2009, with the highest detection in 2008. The prevalence of HCoVs was higher among children with heart diseases (24.6%), patients under stem cell transplantation program (24.3%) and renal transplanted patients (20.2%). Coryza, cough and fever were the most common symptoms at presentation of positive cases and wheezing, a lower respiratory tract infection symptom was reported by 12% of the total, and 27% of high at-risk patients. HCoVs may have an important role among patients with underlying conditions and transplanted ones.