key: cord-0297086-qnicoci6
authors: Schenk, B.; Hoehl, S.; Rudych, O.; Kreutzer, E.; Menger, D.; Farmand, S.; Gebert, D.; Flohr, M.; Berger, F.; Wrobel, F.; Weigel, V.; Kortenbusch, M.; Berger, A.; Ciesek, S.
title: Longitudinal testing for SARS-CoV-2 RNA in day care centers in Hesse, Germany, during increased local incidence and with VOC Alpha as dominant variant: Results of the SAFE KiDS 2 and SAFE KiDS 3 study
date: 2021-07-03
journal: nan
DOI: 10.1101/2021.06.29.21259633
sha: c6a2f04f85864d3c132e15af0618a8dcb779f715
doc_id: 297086
cord_uid: qnicoci6

In the summer of 2020, we investigated the rate of inapparent shedding of SARS-CoV-2 in a representative sample of day care centers from Hesse, Germany, and found a low positivity rate during a period of low local community spread. To investigate the influence of a high local incidence setting, we conducted the SAFE KiDS 2 study. 577 children and 334 staff members of 47 daycare centers were tested for respiratory and gastrointestinal shedding of SARS-CoV-2, and three infections with SARS-CoV-2 in the infectious period were detected. We conclude that viral shedding occurred infrequently while the original "wild-type" variant was dominant. The more transmissible SARS-CoV-2 variant Alpha (B.1.1.7) became the dominant strain after the SAFE KiDS 2 was concluded. The SAFE KiDS 3 study investigated the impact of the Alpha variant of SARS-Co-2 on inapparent viral shedding in the day care setting. In this study, 756 children and 226 staff members from 46 day care centers provided self-collected saliva swabs, the so-called "Lollipop" swabs, which were tested by RT-PCR. In the four-week study period, none of the participants tested positive for SARS-CoV-2 RNA, demonstrating that inapparent shedding of SARS-CoV-2 in the day care setting was also rare during the dominance of the Alpha variant. The influence of the variant of concern Delta on day care centers has yet to be examined.

In the early pandemic of COVID-19, many countries closed day care centers as measure to 32 curb community spread of the virus. While children of kindergarten age rarely have severe 33 disease when infected with SARS-CoV-2 1-3 measures of public health, such as distancing and 34 wearing of masks, cannot be applied to the same extend in day care centers as in other 35 educational facilities. Nevertheless, a growing body of evidence suggested a limited role of 36 day care centers in community spread of wild type SARS-CoV-2 in Central Europe in 2020 and 37 early 2021 4-8 . However, some of these studies were conducted during low community 38 activity 4,5 , limiting the transferability to a setting with increased community spread. One of these 39 studies was the SAFE KiDS study, which we conducted in the summer of 2020 in 50 day care 40 centers in the state of Hesse, Germany 4 . In this 12-week longitudinal study, we neither 41 detected respiratory nor gastrointestinal shedding of SARS-CoV-2 in any of 825 children 42 attending day care, and only in two staff members. 43

But the arrival of the more transmissible variant of concern (VOC) Alpha (B.1.1.7) in Germany 44 in the beginning of 2021 9 had the potential of new transmission dynamics, which may also 45 influence inapparent viral shedding in day care centers 10,11 . This could also have an impact on 46 effective hygiene concepts of regular operation "under hygienic conditions". 47

To evaluate potential changes to the epidemiology of SARS-CoV-2 in the day care setting we 48 investigated the frequency of shedding of SARS CoV-2 in day care centers in Hesse, Germany, 49 in a second and third round of the SAFE KiDS study: SAFE KiDS 2 and SAFE KiDS 3, which 50 were conducted from January 18 th to February 11 th , 2021 at a high incidence setting (local 7-51 day incidence: 23.75 to 281.43 cases / 100,000 inhabitants) during the dominance of the 52 original wild type and from May 17 th to June 11 th , 2021 with the Alpha variant being the 53 dominant SARS-CoV-2 variant (local 7-day incidence: 4.73 to 124.61 cases / 100,000 54 inhabitants) in Germany, respectively. In both studies, children and staff members self-55 collected swabs at home that subsequently were tested by real time (RT)-PCR for SARS CoV-56 2. 57 58 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Frankfurt, Germany. Before proceeding to Real-time (RT)-PCR testing, samples were pooled 81 in a 10-sample group-testing mini-pool protocol, to preserve reagents while maintain high 82 diagnostic sensitivity 13 . For this purpose, the swabs were incubated and agitated in 1.8 ml 83 virus deactivating buffer for approximately three minutes to generate the archive tubes. After 84 incubation, swabs were squeezed and 10 swabs were pooled into one vial containing 2.7 ml 85 virus deactivating buffer, agitated and incubated for at least three minutes before being 86 removed and discarded. The archive tubes were stored at 4°C and the PCR pool was tested (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 3, 2021. of the study did not contribute to study design, data collection, data analysis, data 111 interpretation, or writing and submitting of the report for publication. 112 113 114 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 3, 2021. Study participants and sample distribution 117 47 day care centers participated in this four-week-study. 577 children (age range 5 months to 118 6 years of age; age median 4 years) and 334 staff members were enrolled and provided at 119 least one swab. 5,019 swabs (2,837 buccal mucosa (56.5 %) and 2,182 anal swabs (43.5 %)) 120

were tested in total. 837 swabs (36.6 %) were provided by staff and 3,182 swabs (63.4 %) 121

were provided by children. 122

Results of testing for SARS-CoV-2 by RT-PCR week of the study, no additional SARS-CoV-2 infections were identified with similar numbers 136 of participants. One infection was detected in a child via anal swab in each of the third and 137 fourth study week. All study participants who tested positive had always provided both swab 138 specimens on the day of PCR testing, which were also tested individually by PCR. In no case 139 were both swabs positive. 140

The eight results obtained were forwarded to the relevant health authorities. Only in the first 141 three cases the detected SARS-CoV-2 infection was confirmed by independent testing of a 142 respiratory swab by the health department. In one case of gastrointestinal viral shedding, a 143 past infection was known; in three cases a past infection was suspected due to SARS-CoV-2 144 infections in the household of the study participant prior to the study. In none of the eight cases, 145

according to the health authorities, were further transmissions detected in the day care center 146 during the study period (see Table 1 ). However, the local health authorities determined that in 147 six of the eight cases other persons in the household were also infected with SARS-CoV-2. 148

Only in two cases no other SARS-CoV-2 infections were detected in the household. 149 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 3, 2021. ; https://doi.org/10.1101/2021.06.29.21259633 doi: medRxiv preprint Community activity of SARS-CoV-2 in Hesse during the study 150 Local 7-day incidence rates per 100,000 population ranged from 66.01 to 138.71 in the five 151

counties of study participants who tested positive for SARS-CoV-2. Overall, 7-day incidence 152 rates for all participating urban and rural counties ranged from 23.75 to 281.43. 153

Due to low viral load in all samples with a positive result for SARS-CoV-2, key mutations from 155 the "variants of concern" Alpha could not be successfully examined using a melt curve analysis. 156

In an alternative approach, we applied the S-gene-targeted PCR assay to test for a drop-out 157 of S-gene-detectability characteristic for the Alpha variant. Due to the high Ct values of the 158 samples, the assay was indeterminable for two samples, for six samples a S-gene drop-out 159 was not detected (meaning the S-gene was detected) (table 1), suggesting that the Alpha 160 variant was not present in these samples. 161 162 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Community activity of SARS-CoV-2 in Hesse during the study (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In the SAFE KiDS 2 study, conducted with the "dual swabs" method of testing for both 182 respiratory and gastrointestinal shedding during moderately high local incidence, SARS-CoV-183 2 was detected in seven out of 577 children (1.2 %) and in one out of 334 staff members 184 (0.3%). Only three of these cases had evidence of respiratory viral shedding. Out of these, 185 SARS-CoV-2 was detected in the buccal mucosa swab collected in the study in two children. 186

In one case, SARS-CoV-2 was detected in an anal swab with subsequent independent testing 187 by the local health department. The evaluation of a questionnaire at the end of both studies did not identify a case where our 211 protocol with "dual swab" testing or "Lollipop" testing failed to detect an infection. 212 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 3, 2021. Our study has limitations. This includes that study duration and material was not consistent in 225 all three rounds of the study, limiting comparability of results. All samples were collected 226 without observation by a medical professional, which may have influenced testing sensitivity. 227

Also, since study participation was on a voluntary basis, biases may have also effected the 228 results of the study. We only tested for inapparent shedding, but transmissions were not 229 examined as part of the study. 230

For the upcoming weeks of the pandemic, it can be assumed that the currently dominant virus 231 variant Alpha will be displaced by the VOC Delta. Whether the even more infectious variant 232 Delta 19 will influence transmission among children and thus the incidence of infection in day 233 care centers in the future has to be investigated in further studies. 234 235 236 237 238 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 3, 2021. ; https://doi.org/10.1101/2021.06.29.21259633 doi: medRxiv preprint

SARS-CoV-2 Infection in Children

Clinical manifestations 273 of children with COVID-19: A systematic review

Severe Acute Respiratory Syndrome Coronavirus 2 276 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review

Longitudinal testing for respiratory and 279 gastrointestinal shedding of SARS-CoV-2 in day care centres in Hesse

Prevalence of SARS-CoV-2 Infection in Children and 282

Their Parents in Southwest Germany

Renewed absence of SARS-CoV-2 infections 285 in the day care context in Berlin

COVID-19 Transmission in US Child Care 288

SARS-CoV-2 transmission among children 290 and staff in daycare centres during a nationwide lockdown in France: a cross-sectional

Bericht zu den Virusvarianten von SARS-CoV-2 in 294

SARS-CoV-2 variant B.1.1.7 susceptibility 298 and infectiousness of children and adults deduced from investigations of childcare centre 299 outbreaks

Studie-Berichte/KiTAStudie_04_2021.pdf?__blob=publicationFile

Kita Testung Koeln) Konzept. Version 1

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted July 3, 2021. ; https://doi.org/10.1101/2021.06.29.21259633 doi: medRxiv preprint All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted July 3, 2021. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted July 3, 2021. ; https://doi.org/10.1101/2021.06.29.21259633 doi: medRxiv preprint