Characteristics of endemic human Coronavirus infections during times of COVID-19 pandemic / Características de las infecciones causadas por Corona virus humanos endémicos durante la pandemia COVID-19

Abstract Introduction : After the implementation of mitigation strategies during the COVID-19 pandemic, the incidence of respiratory viruses, including human coronaviruses (HCoV), experienced a significant decrease. The aim of this study is to characterize the epidemiology and clinical aspects of HCoV infections in ambulatory adults during COVID-19 pandemic times. Methods : descriptive, prospective, longitudinal study performed in a private hospital in La Plata, Buenos Aires, Argentina between November 2020 and October 2022; 458 outpatient adults with upper respiratory tract infections (URTI) were studied undergoing clinical and microbiological follow-up. Results : 44 (9.6%) subjects were positive by multiplex PCR for HCoV. 14 of them for 229E (31.8%), 13 for OC43 (29.5%), 11 for HKU-1 (25.1%) and 6 for NL63 (13.6%). A repeated PCR was positive for the same HCoV in 19 (57%) of 33 patients on day 3-5. No hospitalizations or deaths were reported. Discussion : Endemic HCoV caused a significant pro portion of URTI among outpatient adults during COVID- 19-related restrictions times. An alternating pattern of circulation between alfa-HCoV and beta-HCoV was observed.

Resumen Introducción : Tras la implementación de estrate gias de mitigación durante la pandemia de COVID-19, la incidencia de virus respiratorios, incluyendo los coronavirus humanos (HCoV), disminuyó significati vamente. El objetivo de este estudio es caracterizar la epidemiología y los aspectos clínicos de las infecciones por HCoV en adultos ambulatorios durante la pandemia de COVID-19. Métodos : estudio descriptivo, prospectivo, longitudi nal, realizado en un hospital privado de La Plata, Buenos Aires, Argentina, entre noviembre de 2020 y octubre de 2022. Se estudiaron 458 pacientes adultos ambulatorios con infecciones del tracto respiratorio superior (ITRS) bajo seguimiento clínico y microbiológico. Resultados : 44 (9.6%) sujetos fueron positivos por PCR multiplex para HCoV. Se detectaron 14 229E (31.8%), 13 OC43 (29.5%), 11 HKU-1 (25.1%) y 6 NL63 (13.6%). Una segunda PCR fue positiva para el mismo HCoV en 19 (57 %) de 33 pacientes en los días 3-5. No se reportaron hospitalizaciones ni muertes. Discusión : los HCoV endémicos causaron una pro porción significativa de ITRS entre pacientes adultos ambulatorios durante los tiempos de restricciones rela cionados con COVID-19. Se observó un patrón alternante de circulación entre alfa-HCoV y beta-HCoV.

Structure-function relationships among selected human coronaviruses-Supplementary data

Identifying the key proteins among different types of human disease-causing coronaviruses is essential for the molecular mechanism and thereby designing potential drug molecules. Eight selected proteins of seven types of disease-causing coronaviruses, viz.SARS-CoV-2 (severe acute respiratory syndrome coronavirus2), SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (middle east respiratory syndrome coronavirus), Human coronavirus OC43, Human coronavirus HKU1, Human coronavirus 229E and Human coronavirus NL63, were chosen for the comparison. Further, an attempt has been made to explore the most important host-pathogen interactions with a special focus on spike (RBD) protein region as this region deemed to be functionally most important. Epitope region was also identified which helps in the design of epitope-based vaccines. The structural comparison carried out among the seven types of human coronaviruses has revealed the molecular level details on the similarity among this series. This study has facilitated the identification of the important residues in the studied proteins which control the key functions such as viral replication and transmission. Thus, exploring the protein space in the family of coronaviruses, provide valuable insights into the molecular basis associated with the role of proteins and viral infections, which is expected to trigger the identification of the drug targets for coronaviruses infections, in a rational way.

Structure-function relationships among selected human coronaviruses-Supplementary data

Identifying the key proteins among different types of human disease-causing coronaviruses is essential for the molecular mechanism and thereby designing potential drug molecules. Eight selected proteins of seven types of disease-causing coronaviruses, viz.SARS-CoV-2 (severe acute respiratory syndrome coronavirus2), SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (middle east respiratory syndrome coronavirus), Human coronavirus OC43, Human coronavirus HKU1, Human coronavirus 229E and Human coronavirus NL63, were chosen for the comparison. Further, an attempt has been made to explore the most important host-pathogen interactions with a special focus on spike (RBD) protein region as this region deemed to be functionally most important. Epitope region was also identified which helps in the design of epitope-based vaccines. The structural comparison carried out among the seven types of human coronaviruses has revealed the molecular level details on the similarity among this series. This study has facilitated the identification of the important residues in the studied proteins which control the key functions such as viral replication and transmission. Thus, exploring the protein space in the family of coronaviruses, provide valuable insights into the molecular basis associated with the role of proteins and viral infections, which is expected to trigger the identification of the drug targets for coronaviruses infections, in a rational way.

Structure-function relationships among selected human coronaviruses

Identifying the key proteins among different types of human disease-causing coronaviruses is essential for the molecular mechanism and thereby designing potential drug molecules. Eight selected proteins of seven types of disease-causing coronaviruses, viz.SARS-CoV-2 (severe acute respiratory syndrome coronavirus2), SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (middle east respiratory syndrome coronavirus), Human coronavirus OC43, Human coronavirus HKU1, Human coronavirus 229E and Human coronavirus NL63, were chosen for the comparison. Further, an attempt has been made to explore the most important host-pathogen interactions with a special focus on spike (RBD) protein region as this region deemed to be functionally most important. Epitope region was also identified which helps in the design of epitope-based vaccines. The structural comparison carried out among the seven types of human coronaviruses has revealed the molecular level details on the similarity among this series. This study has facilitated the identification of the important residues in the studied proteins which control the key functions such as viral replication and transmission. Thus, exploring the protein space in the family of coronaviruses, provide valuable insights into the molecular basis associated with the role of proteins and viral infections, which is expected to trigger the identification of the drug targets for coronaviruses infections, in a rational way.

2019 Novel Coronavirus Disease Outbreak and Molecular Genetic Characteristics of Severe Acute Respiratory Syndrome-Coronavirus-2

The 2019 novel coronavirus disease (COVID-19) outbreaks that emerged in Wuhan city, Hubei province, have led to a formidable number of confirmed cases that resulted in >5,700 deaths globally, including 143 countries in all 6 continents. The World Health Organization declared a Public Health Emergency of International Concern with a very high level of global risk assessment. Severe acute respiratory syndrome (SARS)-coronavirus-2 (SARS-CoV-2), the agent of COVID-19, has >79% nucleotide sequence homology to SARS-CoV; therefore, both belong to the genus betacoronavirus and subgenus sarbecovirus. The S1 domains of the two appeared to share the cellular receptor ACE2, but revealed a much higher S1-ACE2 binding affinity. As seen in many other human coronaviruses, SARS-CoV-2 also shows respiratory infection, but the basic reproductive number (R₀) in transmission and the clinical latency are quite dissimilar from those of SARS- or MERS-CoVs. Many scientists infer that the time point of cross-barrier transfer from bats to mediate animals or to humans should be a rather recent event based on the full-length genome analyses obtained from the very first patients. Copy-choice polymerization, which often leads to a significant genome recombination rate in most coronaviruses, predicts the continued emergence of novel coronaviruses.

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