Pooling for SARS-CoV-2 Control in Care Institutions
Background
Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection of these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources.
The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people.
Methods
A total of 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were individually tested using RT-PCR. Prevalence and quantification cycle (Cq) value distribution of positives was calculated. Besides, 26 pools of 20 samples and 14 pools of 5 samples were tested using RT-PCR as well (1 positive/pool). Pooling proof of concept was performed in two populations with 1.7% and 2% prevalence.
Results
Distribution of SARS-CoV-2 infection at Care Homes was uneven (0-60%). As the virus circulation global rate was low in our area (3.32%), the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on Cq values (5 and 2.85 cycles for pools of 20 and 5 samples, respectively).
Conclusions
A new screening system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Homes, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.
Figure 1
Figure 2
This is a list of supplementary files associated with this preprint. Click to download.
Additional file 1. SARS CoV-2 prevalence. Global prevalence is shown on the left. Stacked bar charts show Care Home prevalence obtained by individual testing for Care Homes with SARS-CoV-2 infections and without infection (prevalence zero). (HTML).
Additional file 2. Distribution of SARS-CoV-2 RT-PCR Cq value. Summary of the distribution of Cq values of Care Homes with more than 5 positives. It is shown for each detected target. Samples were tested individually. (HTML).
Additional file 3. Age Distribution. Distribution of age of Care Home residents and workers individually tested. (HTML).
Additional file 4. E gene amplification curves. Example of amplification curves (E gene) obtained for the same sample processed individually and in pools of 5 (P5) and 20 (P20) samples. Obtained Cq values were 26.20, 29.31 and 30.82 for the individual sample, P5 and P20, respectively. (png)
Additional file 5. N gene amplification curves. Example of amplification curves (N gene) obtained for the same sample processed individually and in pools of 5 (P5) and 20 (P20) samples. Obtained Cq values were 28.69, 31.99 and 33.26 for the individual sample, P5 and P20, respectively. (png)
Additional file 6. RdRP gene amplification curves. Example of amplification curves (RdRP gene) obtained for the same sample processed individually and in pools of 5 (P5) and 20 (P20) samples. Obtained Cq values were 28.80, 31.49, 31.79 for the individual sample, P5 and P20, respectively. (png)
Posted 23 Sep, 2020
Received 19 Aug, 2020
On 19 Aug, 2020
Received 28 Jul, 2020
On 27 Jul, 2020
Invitations sent on 24 Jul, 2020
On 24 Jul, 2020
On 14 Jul, 2020
On 14 Jul, 2020
On 13 Jul, 2020
On 13 Jul, 2020
Pooling for SARS-CoV-2 Control in Care Institutions
Posted 23 Sep, 2020
Received 19 Aug, 2020
On 19 Aug, 2020
Received 28 Jul, 2020
On 27 Jul, 2020
Invitations sent on 24 Jul, 2020
On 24 Jul, 2020
On 14 Jul, 2020
On 14 Jul, 2020
On 13 Jul, 2020
On 13 Jul, 2020
Background
Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection of these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources.
The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people.
Methods
A total of 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were individually tested using RT-PCR. Prevalence and quantification cycle (Cq) value distribution of positives was calculated. Besides, 26 pools of 20 samples and 14 pools of 5 samples were tested using RT-PCR as well (1 positive/pool). Pooling proof of concept was performed in two populations with 1.7% and 2% prevalence.
Results
Distribution of SARS-CoV-2 infection at Care Homes was uneven (0-60%). As the virus circulation global rate was low in our area (3.32%), the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on Cq values (5 and 2.85 cycles for pools of 20 and 5 samples, respectively).
Conclusions
A new screening system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Homes, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.
Figure 1
Figure 2