Clinical profiles at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period using a machine learning approach

Abstract

Background: The clinical manifestations of COVID-19 disease, caused by the SARS-CoV-2 virus, define a large spectrum of symptoms that are mainly dependent on the human host conditions. In Costa Rica, almost 319 000 cases have been reported during the first third of 2021, contrasting to the 590 000 fully vaccinated people. In the pre-vaccination period (the year 2020), this country accumulated 169 321 cases and 2185 deaths. Methods: To describe the clinical presentations at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period, we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles among 18 974 records of positive cases. Profiles were compared based on symptoms, risk factors, viral load, and genomic features of the SARS-CoV-2 sequence. Results: A total of seven COVID-19 clinical profiles were identified, which were characterized by a specific composition of symptoms. In the comparison between clusters, a lower viral load was found for the asymptomatic group, while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters. No other distribution patterns were found for age, sex, vital status, and hospitalization. Conclusion: During the pre-vaccination time in Costa Rica, the clinical manifestations at the time of diagnosis of COVID-19 were described in seven profiles. The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile, rather they are present in all the groups, including asymptomatic cases. In further analyses, these results will be compared against the profiles of cases during the vaccination period.

Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica

“…Nevertheless, this benefit could be no strong enough with the introductions of other lineages such as the lineages A.2.5, A.2.5.1 and, A.2.5.2 (with high frequency in Central America) which were predominant during 2021, and later with the arrival of the alpha and gamma variants. In addition, our previous work demonstrated that the clinical manifestations of COVID-19 in Costa Rican cases were independent of the SARS-CoV-2 lineages, including no differences for the lineage B.1.1.389 and the mutation S:T1117I (Molina-Mora, González, et al, 2021). COVID-19 disease, as an infection disease, depends not only on the viral agent (SARS-CoV-2 genotype), but also on the host conditions (genetics and risk factors) and the environment (social behavior) (Molina-Mora, González, et al, 2021;Tsui, Deng, & Pan, 2020).…”

“…In addition, our previous work demonstrated that the clinical manifestations of COVID-19 in Costa Rican cases were independent of the SARS-CoV-2 lineages, including no differences for the lineage B.1.1.389 and the mutation S:T1117I (Molina-Mora, González, et al, 2021). COVID-19 disease, as an infection disease, depends not only on the viral agent (SARS-CoV-2 genotype), but also on the host conditions (genetics and risk factors) and the environment (social behavior) (Molina-Mora, González, et al, 2021;Tsui, Deng, & Pan, 2020). Thus, this work represents another piece to understand the dynamics of the COVID-19 pandemic in Costa Rica, in this case focused on the virus.…”

“…The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, has been detected in more than 181 million people worldwide and more than 365 000 cases in Costa Rica (with at least 4650 deaths) until June 30 th , 2021. As part of the epidemiological surveillance of the pandemic in Costa Rica, we have studied both genomic features of the virus and clinical and demographic patterns among diagnosed patients Molina-Mora, González, et al, 2021).…”

“…This local genotype, now classified as a Costa Rican PANGOLIN lineage B.1.1.389, reached up to 30% of cases in this country by December 2020 . Furthermore, this lineage was distributed among all the distinct clusters or clinical profiles from Costa Rican cases of COVID-19, as we analyzed using machine learning (Molina-Mora, González, et al, 2021). For other geographic locations, other lineages carrying the mutation S:T1117I have been reported but, unlike Costa Rica, with a frequency <1% (https://www.gisaid.org/).…”

Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica

“…The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, has been detected in more than 181 million people worldwide and more than 365,000 cases in Costa Rica (with at least 4650 deaths) until June 30th, 2021. As part of the epidemiological surveillance of the pandemic in Costa Rica, we have studied both genomic features of the virus and clinical and demographic patterns among diagnosed patients ( Molina-Mora et al, 2021a ; Molina-Mora et al, 2021b ).…”