See the published version of this preprint at BMC Infectious Diseases.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
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Research article
Benito Regueiro Garcia
Galicia Sur Health Research Institute (IIS Galicia Sur)
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4009-7922
License:
This work is licensed under a CC BY 4.0 License. Read Full License
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.
Keywords
SARS-CoV-2, pooling, detection, care homes, low prevalence, transmission control
Figure 1
Figure 2
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.html
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).
- Additionalfile2.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).
- Additionalfile3.html
Additional file 3. Age Distribution. Distribution of age of Care Home residents and workers individually tested. (HTML).
- additionalfile4.png
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)
- Additionalfile5.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)
- Additionalfile6.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)
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CURRENT STATUS: Published
View the published article at BMC Infectious Diseases.
Version 2
Posted 23 Sep, 2020
No community comments so far
Editorial decision: Accept
On 23 Sep, 2020
Editor assigned
On 21 Sep, 2020
Submission checks complete
On 20 Sep, 2020
Editor invited
On 20 Sep, 2020
No comments provided
Review #2 received
Received 19 Aug, 2020
Editorial decision: Major revision
On 19 Aug, 2020
Review #1 received
Received 28 Jul, 2020
Reviewer #2 agreed
On 27 Jul, 2020
Reviewers invited
Invitations sent on 24 Jul, 2020
Reviewer #1 agreed
On 24 Jul, 2020
First submitted
On 14 Jul, 2020
Editor assigned
On 14 Jul, 2020
Submission checks complete
On 13 Jul, 2020
Editor invited
On 13 Jul, 2020
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Subject Areas
Infectious Diseases
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See the published version of this preprint at BMC Infectious Diseases.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Benito Regueiro Garcia
Galicia Sur Health Research Institute (IIS Galicia Sur)
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4009-7922
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Infectious Diseases.
Version 2
Posted 23 Sep, 2020
No community comments so far
Editorial decision: Accept
On 23 Sep, 2020
Editor assigned
On 21 Sep, 2020
Submission checks complete
On 20 Sep, 2020
Editor invited
On 20 Sep, 2020
No comments provided
Review #2 received
Received 19 Aug, 2020
Editorial decision: Major revision
On 19 Aug, 2020
Review #1 received
Received 28 Jul, 2020
Reviewer #2 agreed
On 27 Jul, 2020
Reviewers invited
Invitations sent on 24 Jul, 2020
Reviewer #1 agreed
On 24 Jul, 2020
First submitted
On 14 Jul, 2020
Editor assigned
On 14 Jul, 2020
Submission checks complete
On 13 Jul, 2020
Editor invited
On 13 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Infectious Diseases
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Infectious Diseases.
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.
- Additionalfile1.html
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).
- Additionalfile2.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).
- Additionalfile3.html
Additional file 3. Age Distribution. Distribution of age of Care Home residents and workers individually tested. (HTML).
- additionalfile4.png
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)
- Additionalfile5.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)
- Additionalfile6.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)
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