SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa

By Shanet Susan AlexReviewed by Danielle Ellis, B.Sc.Mar 18 2022

In a recent study published in The Lancet Infectious Diseases, researchers conducted a prospective household cohort study of coronavirus disease 2019 (COVID-19), influenza, and respiratory syncytial virus community burden, viral interaction, and transmission dynamics, called PHIRST-C study in South Africa.

Background

South Africa has been hit by three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) waves by August 2021, the second of which was attributed by the Beta variant and the third to Delta. Investigations to measure the SARS-CoV-2 symptomatic fraction, burden of asymptomatic infections, reinfection frequency, and duration of SARS-CoV-2 viral shedding have mainly been conducted in specific settings or associated with outbreak studies in Africa.

However, comprehensive community investigations on COVID-19 asymptomatic infections, burden, and transmission consisting of the SARS-CoV-2 Delta and Beta variants from Africa remain scarce.

About the study

The present PHIRST-C study conducted in South Africa from 2020-21 was based on a previously performed PHIRST study at the same South African sites from 2016 to 2018. 

In this study, the scientists evaluated COVID-19 transmission and burden in two South African communities: one urban and one rural. The team performed a prospective cohort analysis of the households in Klerksdorp, North West province (urban location) and Agincourt, Mpumalanga province (rural region) in South Africa between July 2020 and August 2021. While the households for the rural area were chosen randomly using the health and socio-demographic surveillance system (HDSS), global positioning system (GPS) coordinates were used for those from the urban site. 

Households with more than two members were eligible if at least 75% of the members agreed to participate in the study. A total of 643 household members from 114 households in the rural area and 557 members from 108 households in the urban area were included in the study. Household members' midturbinate nasal swabs were procured two times a week, regardless of symptoms, and were analyzed for SARS-CoV-2 using real-time reverse transcription-polymerase chain reaction (RT-rtPCR). Every two months, serum was taken and analyzed for anti-SARS-CoV-2 antibodies.

The main outcomes of the PHIRST-C study were: 1) the cumulative incidence of COVID-19, 2) reinfection frequency, 3) symptomatic fraction, 4) viral ribonucleic acid (RNA) shedding duration, and 5) household cumulative infection risk (HCIR).

Results

The results show that of the 115,759 nasal specimens procured from 1200 household members, 1976 were COVID-19-positive according to the RT-rtPCR analysis. Based on the combined data from RT-rtPCR and serology analyses, 749 of the 1200 people had at least one COVID-19 episode, and 87 of those 749 were SARS-CoV-2-reinfected. Further, the average infectious episode lasted 11.6 days.

Among the 662 RT-rtPCR-confirmed COVID-19 cases, 97 were symptomatic and experienced at least one symptom. The RT-rtPCR or serology tests showed that 200 of the 222 households contained at least one COVID-19-positive person. The overall HCIR was 23.9%; in symptomatic index patients, the HCIR was 23.3%, while for asymptomatic index episodes, it was 23.9%.

Index case younger than five years and age 40–59 years, low minimum cycle threshold (Ct) value of the index case, household contact aged between 5–18 years, index case female gender, and infection with Delta or Beta variant were all linked to higher HCIR in multivariable analysis. When infected with SAR-CoV-2, people living with human immunodeficiency virus (HIV) who were virally unsuppressed were more prone to developing symptomatic disease and shed SARS-CoV-2 for longer than people without HIV. Vaccination uptake was poor in both the urban and rural sites, with just 57 of 1200 people completely immunized at the end of the study.

Conclusions

The study findings imply that control efforts aimed at symptomatic SARS-CoV-2 patients had a narrow scope as index case symptom status had no effect on HCIR, and 565 COVID-19 cases were asymptomatic in this study. Increased household transmission of the SARS-CoV-2 Delta and Beta variants was probably a driving factor in subsequent waves of COVID-19 in South Africa, with over 60% of people infected by the completion of the research.

Furthermore, there was increased reinfection, acquisition, and attack rates in teenagers and extended SARS-CoV-2 shedding in HIV-positive adults who have not been virally suppressed. These data imply that the immunization of adolescents and people living with HIV who were virally unsuppressed is crucial to mitigating the COVID-19 community spread.