Persistent COVID-19 symptoms among South Africans infected during SARS-CoV-2 Beta, Delta and Omicron variant waves

In a recent study posted to the medRxiv* preprint server, researchers longitudinally followed up hospitalized (H) and non-hospitalized (NH) coronavirus disease 2019 (COVID-19) patients six months after laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections to identify factors that increase the risk of post-COVID-19 condition (PCC) development in the South African (SA) population.

Study: A cohort study of Post COVID-19 Condition across the Beta, Delta and Omicron waves in South Africa: 6-month follow up of hospitalised and non-hospitalised participants. Image Credit: SWKStock/Shutterstock

Studies have reported developing PCC symptoms or persistent COVID-19 symptoms (PCS) such as dyspnea, fatigue, cough, arthromyalgia, headaches, pain in the chest, anxiety/depression, disturbed sleep, and cognitive decline, including memory loss and concentration difficulties among several individuals globally. The characterization of PCC risk factors could enable the early identification of individuals at risk and guide the management of such individuals.

About the study

In the present prospective cohort study, researchers identified and characterized PCC risk factors among H and NH COVID-19 patients in SA. They also evaluated the effects of COVID-19 severity, SARS-CoV-2 VOCs (variants of concern) such as Delta, Omicron, and Beta dominance, SARS-CoV-2 vaccinations, and human immunodeficiency virus (HIV) infections on PCC development risks.

The NICD (national institute for communicable diseases)-led study was conducted as part of an international-level study by the ISARIC (international severe acute respiratory and emerging infections consortium). The present study comprised 1,000 adult H and NH individuals infected with SARS-CoV-2 during the dominance of Beta and Delta VOC (between November 2020 and July 2021) and Omicron BA.1 sub-VOC (between December 2021 and February 2022) in South Africa. In addition, an NH cohort of individuals infected during Delta dominance (between August and November 2021) was enrolled in the study.

The team identified NH COVID-19 patients from the NMC-SS (national case line list) data and H individuals were identified based on the national daily hospital surveillance (DATCOV) data of those admitted in private and public hospitals across all SA provinces. Participants were randomly sampled with SARS-CoV-2-positive RT-PCR (reverse transcription polymerase chain reaction), or RAT (rapid antigen test) reports. They underwent telephonic assessment after one month (M1), three months (M2), and six months (M3) of discharge from the hospital or COVID-19.

Individuals were excluded if they were unavailable despite contacting them twice. Patients were assessed using the standardized CRF (case report form) questionnaire, ISARIC-developed protocol, and World Health Organization (WHO) COVID-19 clinical progression scale in terms of their QoL (quality of life) and COVID-19 severity. Negative binomial regression modeling was used to determine factors associated with ≥1 PCS at M3.


Out of 142,935 H and 273,429 NH initially eligible individuals, 10% (n=13,868) H and one percent (n=3,498) NH individuals were selected randomly for study enrollment. Of the individuals contacted, 24% (n=3,334) H and 39% (n=1,351) NH patients were enrolled. The average values for H and NH patients were 49 years and 37 years, respectively, and most H and NH patients were female. About 65% and 33% of H and NH individuals had comorbidities such as hypertension (HT), diabetes mellitus (DM), and obesity among H individuals, and HT, DM, and HIV among NH individuals.

The most frequent PCS in H patients at M3 were fatigue (F), breathlessness (B), concentration difficulties, headaches (H), and muscular pain, all of which were reduced in frequency between M1 and M3, especially between M1 and M2. In NH patients, the most frequent PCS at M3 were F, B, H, cough, nasal congestion, and smell loss, all of which showed lower frequency between M2 and M3. Among H and NH patients, 47% and 19% had ≥1 PCS at M3, respectively. Of H patients, 60%, 61%, and 19% infected during Beta, Delta, and Omicron dominance, respectively, had ≥1 PCS at M3.

Of H patients, 40% and 47% of those HIV-positive and HIV-negative experienced ≥1 PCS at M3, respectively. Of H patients, 33%, 17%, 16%, and 5.0% remained asymptomatic, were symptomatic until M2, were symptomatic until M3, developed novel symptoms at M2, and developed novel symptoms at M3, respectively. At M3, H patients reported QoL decreases of 38%, 24%, 16%, 13%, 12%, 8.0%, 8.0%, and 3.0% due to fatigue, disability, discomfort/pain, depression/anxiety, breathlessness, daily activities, mobility, and self-care, respectively; however, QoL improved from M1 to M3.

The adjusted incidence risk ratio (aIRR) values for patients 40 to 64 years of age and those aged above 65 years were 1.4 and 1.3, respectively, in comparison to those aged <40 years. The aIRR value for women compared to men was 1.2, and the values for White, Indian, and mixed races were 1.2, 1.3, 1.4, and 1.2, respectively, compared to Black individuals. Comorbidities increased PCS risks (aIRR 1.3), and so did one to three and ≥4 acute SARS-CoV-2 infection symptom presence with aIRR values of 1.3 and 1.6, respectively, compared to lack of such symptoms.

The aIRR values for NH symptomatic patients, H patients needing oxygen, H patients not needing oxygen, and intensive care unit (ICU)-admitted patients compared to asymptomatic NH patients were 2.3, 4.0, 6.0, and 5.8, respectively. PCC risks were lower (aIRR 0.5) for individuals SARS-CoV-2-positive during Omicron-dominance than those SARS-CoV-2-positive during Beta-dominance.

Overall, the study findings showed a high PCS prevalence among South Africans at M3, although the risks were lower among those infected during Omicron BA.1 dominance.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
  • Waasila Jassat et al. (2022). A cohort study of Post COVID-19 Condition across the Beta, Delta and Omicron waves in South Africa: 6-month follow up of hospitalised and non-hospitalised participants. medRxiv. doi:

Posted in: Medical Science News | Medical Research News | Disease/Infection News

Tags: Antigen, Anxiety, Coronavirus, Coronavirus Disease COVID-19, Cough, covid-19, Depression, Diabetes, Diabetes Mellitus, Disability, Dyspnea, Fatigue, Frequency, HIV, Hospital, Immunodeficiency, Intensive Care, Laboratory, Nasal Congestion, Obesity, Omicron, Oxygen, Pain, Polymerase, Polymerase Chain Reaction, Respiratory, SARS, SARS-CoV-2, Severe Acute Respiratory, Severe Acute Respiratory Syndrome, Sleep, Syndrome, Transcription, Virus

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Pooja Toshniwal Paharia

Dr. based clinical-radiological diagnosis and management of oral lesions and conditions and associated maxillofacial disorders.

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