Baseline cohort profile: clinical and molecular characterisation of SARS-CoV-2 infected patients recruited into a longitudinal COVID-19 cohort study (COVGEN) in Malaysia

A COVID-19 patient cohort study (COVGEN) was established in Malaysia to investigate the association between viral genetic variants, host risk factors, and COVID-19 severity. The COVGEN study is prospective, longitudinal, multicentre study and was conducted in Cheras, Kuala Lumpur, at the COVID-19 Assessment Centre in Bandar Tun Razak, Hospital Canselor Tuanku Muhriz (HCTM), and UKM Medical Molecular Biology Institute (UMBI). Here, we report the baseline characteristics (demographic and clinical outcomes) of 2406 COVID-19 patients who enrolled in the cohort, as well as the molecular characteristics of the SARS-CoV-2 that were isolated from the participants. Serial collection of biospecimens including blood, urine and swab were collected from each participant on day 0 (recruitment), with follow-up visits at three, six- and 12-months. A questionnaire was developed to assess demographic and socioeconomic characteristics, comorbidities, medical history, COVID-19 infection history, vaccination status, clinical symptoms and post-COVID-19 symptoms. Laboratory assessment included complete blood count, lipid profile and renal function tests. Molecular characterisation of SARS-CoV-2 isolated from the acute COVID-19 patients were performed using next-gene sequencing. Chi-square tests and multinomial logistic regression analyses were performed to identify risk factors associated with COVID-19 outcomes. A total of 2406 participants were enrolled in this cohort. In Malay, risk factors that were associated with severe outcome (Covid category (CAT); CAT-3, CAT-4 and CAT-5), were older age, vaccine type, vaccination status and underlying comorbidities including hypertension, chronic kidney disease, cardiovascular disease and respiratory. In Chinese, homologous vaccine regimens had higher risk to having severe outcomes than heterologous vaccine regimens. In Indian, underlying comorbidities were associated with CAT-4 outcomes. Olfactory dysfunctions were associated with infection during Delta period while sore throat was associated with infection during Omicron period. In this study, comorbidities were associated with severe outcomes and mortality, whereas heterologous vaccine regimens were associated with non-severe outcomes. Distinct symptoms profiles were observed between Delta and Omicron infections. The high attrition rate highlighted a challenge in conducting longitudinal study in Malaysia. Nonetheless, this study provides a valuable resource for future research on COVID-19 disease.