Pooling for SARS-CoV-2 control in care institutions

Area of Science:

• Epidemiology
• Infectious Disease Control
• Public Health

Background:

• Care home residents and workers are at high risk for SARS-CoV-2 infection due to high mortality rates.
• Presymptomatic individuals play a significant role in transmission, making early detection crucial for outbreak control.
• Pooling strategies offer a method to conserve resources for SARS-CoV-2 testing.

Purpose of the Study:

• To determine the prevalence of SARS-CoV-2 in institutionalized individuals in Galicia, Spain, during the pandemic.
• To assess the performance of a reverse transcription-polymerase chain reaction (RT-PCR) pooling strategy for screening institutionalized populations.
• To evaluate the feasibility of pooling strategies for ongoing surveillance and outbreak prevention in care homes.

Main Methods:

• Conducted RT-PCR on 25,386 individual nasopharyngeal swab samples from care home residents and staff in Galicia (March-May 2020).
• Analyzed the distribution of SARS-CoV-2 prevalence and quantification cycle (Cq) values.
• Tested 26 pools of 20 samples and 14 pools of 5 samples, with one positive sample per pool, to demonstrate proof of concept in populations with 1.7% and 2% prevalence.

Main Results:

• Observed uneven distribution of SARS-CoV-2 infection across care homes, ranging from 0% to 60%.
• Demonstrated that pooling samples in low-prevalence clusters resulted in minimal average increases in Cq values (5 cycles for pools of 20, 2.85 cycles for pools of 5).
• Confirmed the effectiveness of pooling strategies for SARS-CoV-2 detection with resource preservation, even at low prevalence rates.

Conclusions:

• A new screening system is necessary for small clusters to ensure protection, moving beyond individual testing.
• The proposed pooling strategy for care homes, after achieving zero prevalence, can facilitate successive testing rounds for transmission control while conserving testing resources.
• Scaling this pooling method can help manage larger outbreaks, prevent viral circulation, and maintain the operational status of facilities.