key: cord-0823865-zh7znaiq authors: Stange, M.; Wuerfel, E.; Peter, J. K.; Seth-Smith, H.; Roloff, T.; Gsponer, S.; Mari, A.; Cabrera Gil, B.; Lebrand, A.; Wegner, F.; Heininger, U.; Bielicki, J.; Tschudin Sutter, S.; Stadler, T.; Leuzinger, K.; Hirsch, H. H.; Ledergerber, M.; Fuchs, S.; Egli, A. title: SARS-CoV-2 in schools: genome analysis shows that concurrent cases in the second and third wave were often unconnected date: 2022-01-28 journal: nan DOI: 10.1101/2022.01.26.22269824 sha: 0dd3b40ae1dd1fe56e95e070f542833705fe9672 doc_id: 823865 cord_uid: zh7znaiq Background. The risk of SARS-CoV-2 (SCoV2) infection in schools and student households is typically assessed using classical epidemiology whereby transmission is based on time of symptom onset and contact tracing data. Using such methodologies may be imprecise regarding transmission events of different, simultaneous SCoV2 variants spreading with different rates and directions in a given population. We analysed with high resolution the transmission among different communities, social networks, and educational institutions and the extent of outbreaks using whole genome sequencing (WGS). Methods and Findings. We combined WGS and contact tracing spanning two pandemic waves from October 2020 to May 2021 in the Canton of Basel-City, Switzerland and performed an in-depth analysis of 235 cases relating to 22 educational institutions. We describe the caseload in educational institutions and the public health measures taken and delineate the WGS-supported outbreak surveillance. During the study period, 1,573 of 24,557 (6.4%) children and 410 of 3,726 (11%) staff members from educational institutions were reported SCoV2 positive. Thereof, WGS data from 83 children, 35 adult staff in 22 educational institutions and their 117 contacts (social network, families) was available and analysed. 353 contextual sequences from residents of the Canton of Basel-City sequenced through surveillance were identified to be related to cases in the educational institutions. In total, we identified 55 clusters and found that coinciding SCoV2-cases in individual educational institutions were mostly introduced from different sources such as social networks or the larger community. More transmission chains started in the community and were brought into the educational institutions than vice versa (31 vs. 13). Adolescents (12-19 years old) had the highest case prevalence over both waves compared to younger children or adults, especially for the emerging Alpha variant. Conclusions. Introduction of SCoV2 into schools accounts for most events and reflects transmission closely related to social activity, whereby teenagers and young adults contribute to significant parallel activity. Combining WGS with contact tracing is pivotal to properly inform authorities about SCoV2 infection clusters and transmission directions in educational settings and the effectiveness of enacted public health measures. The gathered data showing more clusters to seed in the community than vice versa as well as few subsequent in-school transmissions indicate that the agilely employed health measures for educational institutions helped to prevent outbreaks among staff and children. The clinical trial accession number is NCT04351503 (clinicaltrials.gov). During the first wave of the SARS-CoV-2 (SCoV2) pandemic in 2020, schools and day-care 66 centres for children were widely closed around the world as part of the extensive measures, 67 in order to reduce community-spread of the pandemic virus. In the following months, data 68 suggested that children were not the main drivers of the SCoV2 pandemic; although children 69 do get infected and transmit the virus, they are less susceptible to infection than adults [1-3] 70 and also at low risk of a severe clinical course [4] . On the other hand, negative side-effects of 71 the global lockdowns were found to be particularly pronounced in children and adolescents. 72 Children from socio-demographic less privileged families regularly suffered from educational 73 and psychological constraints because of the school closures [5, 6] . 74 In Switzerland, as in many other countries worldwide, the experiences from the strict lockdown 75 during the first wave of the pandemic led to a broad social agreement to avoid further school 76 closures during the ongoing pandemic with all possible efforts [7] [8] [9] . However, whether SCoV2 77 would circulate uncontrolled in schools and childcare facilities was controversially discussed 78 and difficult to address due to lack of experience with the new pandemic virus. Viewpoints 79 changed over time with the emergence of new data, more transmissible SCoV2 lineages, and 80 an increasingly vaccinated adult population. 81 The widespread school closures had hampered the ability to collect data on the transmission 82 risk in these settings. Studies addressing the question of SCoV2 infection patterns in schools 83 and childcare facilities most often inferred infection clusters and attack rates based on date of 84 symptom onset or positive test result, and contact tracing. Those studies largely concluded 85 low contribution of schools to the overall dynamics of the epidemic, evidenced by few child-to-86 child transmissions [10] [11] [12] [13] and few child-to-household transmissions [14] . Transmission and 87 outbreaks that failed to be contained were shown to be due to insufficiently executed mitigation 88 measures [11] . Importantly, these studies were often conducted over a short time-frame of a 89 few weeks and primarily relied on counting numbers of SCoV2 infected students and staff 90 members in schools, assuming that concurrently occurring infections in schools equate to 91 contagion within the school. The directionality of transmission was deducted via the chronology 92 of onset of symptoms. However, this may be misleading, as cases may arise from 93 transmissions outside school premises. The diversification of SCoV2 into lineages [15] can be 94 discerned by the application of whole genome sequencing (WGS). WGS provides the highest 95 typing resolution and even allows the separation of single viral genotypes (variants) within and 96 between samples from infected individuals. Ultimately, this means that the above found child-97 to-child and child-to-household transmission events could be even less, if controlled for virus 98 identity of the infected persons. Further, studies that focussed on outbreak analyses in 99 educational settings using WGS did not consider the outbreaks in relation to infection events 100 in the larger community context [16] and hence could not draw conclusions about whether 101 genotypic variation in the observed outbreak was due to viral evolution or the simultaneous 102 introduction of similar variants from the community. A profound knowledge about the routes 103 and directions of transmission events between and within schools and communities would 104 allow adaptation of measurement concepts to reduce transmission events. 105 In this study, we address the question, whether clusters of SCoV2 infections in children and 106 adolescents within educational settings over two pandemic waves (October 2020 to May 2021) 107 were acquired in schools or childcare facilities, or if these could rather be traced back to 108 transmission events within the family, other social networks, or the broader community. We 109 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 further investigated the prevalence of detected SCoV2 lineages across different age groups. 110 Our work used a complementary approach combining detailed contact tracing data with WGS 111 of viral isolates to reconstruct the routes of transmission at high resolution. 112 Study design. In this observational retrospective epidemiological study, we describe SCoV2 114 transmission dynamics over a period of eight months from October 2020 to May 2021 within 115 educational institutions of the Canton of Basel-City, Switzerland. This time frame includes the 116 second and third SCoV2 local epidemic waves in Switzerland. The first wave is not included 117 in the study because schools were closed early during the first wave and testing capacities 118 were limited to symptomatic people, which led to an incalculable underestimation of the total 119 caseload among children [17, 18] . 120 All cases in schools and child care facilities were monitored by the Child and Adolescent Health 121 Services of Basel-City. Here, case clusters with suspected in-school transmission and contacts 122 were identified for WGS and subjected to a molecular epidemiological outbreak analysis. 123 Potential clusters of cases in schools were defined as four or more cases among students and 124 children and staff in the same educational group appearing within ten days between single 125 cases. We excluded cases that did not fit the definition of potential clusters. For not previously 126 sequenced samples via our surveillance program, the patients' nasopharyngeal swabs or 127 saliva samples were collected from the testing laboratories and sent to the University Hospital 128 of Basel for WGS and lineage typing. Two datasets were used for the subsequent analyses. 129 Firstly, WGS data of SCoV2 isolates from all inhabitants of the canton of Basel-City were 130 combined with WGS and contact tracing data from case clusters to infer routes of transmission 131 in educational institutions for the respective study period. Secondly, WGS data from all 132 inhabitants of the canton of Basel-City with available age data were used to infer SCoV2 133 lineage-specific prevalence per age group, as well as the odds of certain SCoV2 lineages 134 affecting younger age groups more than adults. 135 Ethical statement. The study was approved by the local ethical committee (EKNZ number 136 2020-00769). All data was anonymized for the analysis of the transmission events. 137 Description of the school landscape in the Canton of Basel-City. In the Canton of Basel-138 City, children start compulsory education at the age of four years with two years of 139 kindergarten. This is followed by six years of primary school (children aged 6 to 12 years) and 140 three years of secondary school level I (children aged 12 to 15 years). This compulsory 141 education is followed by two to four years of secondary school level II (children aged 15 years 142 and older), which ranges from vocational education to college education and prepares for 143 tertiary education. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 General case management . The diagnostic laboratories notify each SCoV2 negative or 152 positive test result via the national, mandatory reporting system to the Department of Health 153 Basel-City as the official place of residence. were contacted by phone and were isolated for ten days. Isolation started from the day after 159 the onset of first symptoms or the date of sampling in asymptomatic patients. All individuals 160 tested positive by an antigen test were advised to confirm infection with a SCoV2 specific 161 nucleic acid amplification test (NAT) assay. All close contact persons (CCP) were also sent 162 into quarantine for ten days -beginning from the day of the last close contact to the IP. Close 163 contact outside of school and childcare facilities was defined as contact with less than 1.5 164 metres distance for more than 15 minutes without sufficient protective measures (e.g. wearing 165 of masks). CCP were advised to take a NAT assay during the ten-day quarantine. During the 166 isolation or quarantine, personal and clinical information was registered in the cantonal COVID 167 Care App-database. The health condition of all IPs and CCPs was monitored through a 168 smartphone app where questionnaires were filled out regarding the current severity or absence 169 of symptoms. Individuals without the app were followed-up by phone. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269824 doi: medRxiv preprint not specifically sequenced for this analysis were used as community or contextual sequences. 198 We could, in most instances, access meta information such as host sex, age, place of 199 residence and, travel history for the whole-genome sequenced samples originating from UHB, 200 whereas semi-public and public data retrieved from external sources such as GISAID or ENA 201 lack this information. Filtering data from UHB and additional samples by other providers from 202 ENA for those originating from the Canton of Basel-City residents only between 1 October 203 2020 to 31 May 2021 yielded 4,674 sequences that were subjected to analyses of transmission 204 direction (Table S2 ; 3,433 from UHB, 1,240 from ETHZ, 1 from HUG). A subset of 1,693 205 sequences contained information on age and were subjected to the analysis of lineage-specific 206 infections in children and adolescents (Table S2 ; 1,589 from UHB, 4 from ETHZ). 207 of the Canton of Basel-City. We calculated census-normalised ratios of sequenced and 209 reported cases in children in order to infer whether children and youth in different education 210 institutions were more at risk to be infected with certain viral lineages than adults. The ratios 211 were then scaled to 100,000 inhabitants. With the available metadata for this particular 212 analysis, we cannot know which educational institution the infected person visited, so we 213 inferred the educational institution using age as a proxy. We equated zero-to three-year-olds 214 to "childcare", four-to five-year-olds to "kindergarten" (i.e., mandatory pre-school); six-to 215 eleven-year-olds to "primary school", 12-to 15-year-olds to "secondary school Level I", and 216 16-to 19-year-olds to "secondary school Level II. People aged 20 or older were assigned as 217 "adults". Case numbers can be found in Table 2 . To quantify the risk of children in different institutions according to their age being infected with 225 a certain lineage, we applying logistic regression using age groups as co-variate and extracted 226 odds ratios and p-values for the exponential model coefficients. Confidence intervals are 227 calculated as exponential 2.5% and 97.5% confidence intervals from the fitted model (point 228 estimate of the coefficient +/-97.5% symmetric interval for a standard normal distribution x 229 standard error of the coefficient). 230 targeted resolution of suspected outbreaks in schools or childcare facilities, we analysed 235 232 high-quality SCoV2 genomes from 83 children and students (5.3% of 1,573 totally infected), 233 22 teachers and 13 educational caregivers (8.5% of totally infected staff), and 117 household 234 contacts. These were from four Kindertagestätten (childcare facilities), two Tagesstrukturen 235 (childcare facilities), one Kindergarten (i.e., pre-school), 13 primary schools, and two 236 secondary schools level I. The percentage of included children and students is low as most 237 cases did not fit our inclusion criteria (at least 5 clustered cases within 10 days) and due to a 238 lower success rate in sequencing due to potential pre-analytical issues with samples from 239 these cohorts. In contrast to the above-mentioned analysis, we know from contact-tracing, 240 which educational institutions were attended by each IP and which persons were CCPs. We 241 discerned the source of infection between (i) community-acquired (publicly-available 242 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269824 doi: medRxiv preprint contextual data on ENA (Table S2) from genomic surveillance from residents of the Canton of 243 Basel-City), (ii) social-network-acquired from known contacts, or (iii) school-acquired. 244 Transmission chains were defined as genomes that are connected by hierarchical clustering 245 to a seed consisting of a 0 single nucleotide polymorphism (SNP) distance cluster. In detail, a 246 three-step method was used to identify transmission chains. Firstly, sequences at 0 SNP 247 distance (including missing regions) were grouped to obtain strict, mutually-exclusive, clusters, 248 without applying a time window for cluster delimitation, as we were interested in the 249 progression of transmission chains. At this point, if a SNP difference occurred in a missing 250 region of an otherwise identical sequence, this was counted as a SNP difference of 1 and 251 hence, the sequence with the missing region was placed in a separate cluster. To overcome 252 this limitation and also to account for the fact that the virus can mutate within a transmission 253 chain the initial 0 SNP clusters were expanded by adding sequences at 1 SNP distance from 254 each member of the cluster in a second step. Finally, to avoid having too many clusters that 255 contain several overlapping sequences, the expanded clusters were merged using hierarchical 256 clustering based on the sequences belonging to each expanded cluster. Prevention and protection concepts in schools. Figure 1 provides a detailed description 277 of the adjustments of prevention and protection concepts during the study period. By the 278 beginning of the study period in fall 2020, SCoV2 testing was well established, with sufficient 279 testing capacities and easy access in testing centres and medical facilities throughout the city 280 ( Figure 1A) . Initially, low-threshold testing was recommended to all people aged 12 years and 281 older showing mild symptoms of respiratory disease. Testing of children younger than 12 years 282 was recommended only in case of fever and reduced general condition, persistent fever or 283 cough for more than three days, or mild symptoms after close contact with a confirmed SCoV2 284 infected patient. In schools and childcare facilities, general protection measurements included 285 intensive hand, object, and surface hygiene and frequent ventilation of (class) rooms 286 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269824 doi: medRxiv preprint ( Figure 1B) . Staff in all educational facilities and students attending schools beyond the 287 compulsory school system were required to keep 1.5 m distance to each other, as well as to 288 younger students and children. Mandatory use of face masks was introduced for staff and 289 students (aged 12 years and older) in secondary schools from the beginning of the second 290 wave in November 2020. 291 From October to December 2020, group quarantines of entire classes or educational groups 292 were only imposed if two or more SCoV2 positive cases appeared within ten days in the same 293 group and a connection between the cases could not be excluded. When a single case 294 appeared in a class or educational group, all involved families and staff were informed and 295 testing was recommended in case of symptoms. 296 In January 2021, when the new Alpha variant of concern reached the Canton of Basel- City, 297 contact tracing policies were intensified to slow down its spread. The mandatory use of face 298 masks was extended to the staff of primary schools. As evidence pointed towards increased 299 infections in children caused by the Alpha variant, face masks also became mandatory for 300 students of 5th and 6th grade in primary schools (children of 10 years and older is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. and decreased for staff. 334 The temporal change of relative proportions of teacher/student infections are shown in 335 Figure 2 . Interestingly, the distribution patterns changed around January 2021 with a higher 336 case load predominantly in younger age groups covering childcare facilities, kindergarten and 337 primary schools. In contrast, the distribution of cases among students versus staff in secondary 338 school was consistent and relatively low during the entire study period. 339 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269824 doi: medRxiv preprint facilities. Based on the contact tracing information available to the Department of Health 355 Basel-City, we sought data and samples from cases linked to 22 educational facilities, resulting 356 in sequencing data for 83 infected students (primary to secondary level) and children (below 357 primary level but in childcare), 35 staff, 117 household contacts, to compare to surveillance 358 data for residents of the Canton of Basel-City. Based on this data, we attempted to define 359 clusters of infections and to discern the source and direction of transmissions. 360 The cluster analysis identified another 353 contextual sequences from residents of the Canton 361 of Basel-City that were putatively connected to the school cases. Across this dataset, we 362 identified 55 clusters with a total of 566 cases and a size of two to 63 cases per cluster 363 (Figure 3) . The largest identified cluster (no. 37 in Figure 3 ) belongs to the Alpha variant and 364 contains samples from 8 January 2021 to 10 March 2021 with 63 cases. This particular cluster 365 consisted of seven students and two teachers, from two schools in the same city quarter, as 366 well as seven contacts identified via contact tracing, and 47 additionally identified contextual 367 sequences from the community. The earliest cases from January 2021 were contextual 368 samples and only later, in early February 2021, cases were traced in the school environment. 369 When focusing on individual schools (colour of symbols), we observed that temporally 370 clustered cases per school frequently belong to different transmission chains, e.g., schools A, 371 C, O, M and others (Figure 3 ). In addition, among the identified clusters, some contain cases 372 from different educational institutions, e.g., clusters no. 0 and no. 2 (Figure 3) , which were 373 likely caused by cross-institutional visits such as primary school in the morning and a childcare 374 facility in the afternoon. 375 In summary, taking the temporal succession of cases by sampling date in each cluster into 376 account, the following plausible transmission scenarios unfold: we putatively identified 19 377 community-to-school transmissions (chains that start with "x") without within-school 378 transmissions and 12 with subsequent in-school transmissions (Figure 3) ; ten school-to-379 community transmissions without within-school transmission and three with within-school 380 transmissions (5 of which showed the Alpha variant). In transmission clusters with in-school 381 transmissions, we putatively identified seven with teacher-to-student, three with teacher-to-382 teacher, seven with student-to-student, and five with student-to-teacher transmissions 383 (Figure 3) . 384 Most outbreaks, in terms of numbers of involved cases, occurred during the second wave with 385 the introduction of VOCs: here the Alpha variant had the largest impact. During the equally 386 long two time periods before and after that (second wave pre-VOC and third wave), 17 and 28 387 clusters or single cases were counted, respectively (Figure 3) . 388 We also identified 22 single cases (11 students, two teachers, one caregiver, eight contacts) 389 from 28 November 2020 to 5 May 2021 that did not cluster with any other sequence registered 390 in the Canton of Basel-City (Figure 3) . By the study-inclusion criteria only clustered cases 391 were subjected to contact tracing-informed molecular cluster identification. Hence the 392 identified single cases were either connected to cases that failed sequencing or were true 393 single cases. The lack of other related sequences in the community dataset indicates 394 successful mitigation of broader transmission. 395 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 observed in adults (Figure 4A-D, Figure S1 ). demonstrates that during the second wave, before the occurrence of the Alpha variant, 414 adjusted for their proportion of the population of the Canton of Basel-City, youths aged 16 to 415 19 years were more infected than adults ( Figure 4B) . During the third wave, driven by the 416 Alpha variant, children aged 12 to 19 years were most affected ( Figure 4D ). Over both 417 epidemic waves the Alpha variant had the highest prevalence among children of school age 418 (aged 6 to 19 years) when compared to other age groups ( Figure 4A) . In terms of the odds to 419 be infected with a certain lineage compared to adults, during the entire study period, children 420 in the primary level and younger had 3 to 4 times the odds (p < 0.03) of an adult to be infected 421 with the Alpha variant and only 0.3 times the odds (p = 0.027) to be infected with B.1.177 422 ( Table 3, Table S3 ). During the first study period (second wave pre-VOCs, October to 423 December 2020) children aged 0 to 3 years old had 9 times (p=0.02) the odds of an adult 424 getting B.1.258 ( Table 3, Table S4 ). Yet during this time the diversity of SCoV2 lineages (N = 425 57) and hence viral competition for hosts was large ( differences in odds to be infected with a specific SCoV2 variant among age groups were found 432 ( Table 3, Table S6 ). 433 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10. 1101 /2022 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 Only the most prevalent lineages are shown here; the complete figures for the entire study period and 459 the subperiods can be found in Figures S1-S4 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 The observational investigation of transmission clusters in school settings showed that more 478 transmission chains started in the community and were brought into the educational institutions 479 than vice versa (31 vs. 13). Also, we observed fewer transmission chains resulting in in-school 480 than outside-school transmissions (15 vs. 29), independent of the source. When in-school 481 transmission occurred, staff commenced transmission chains to children more often than the 482 other way around (7 vs. 5 ). These findings support previous studies relying on contact tracing 483 data only, which also found a low rate of in-school transmissions, especially in younger 484 children [10] [11] [12] 35, 36] . Our results add more granularity and the fact that the community 485 largely seeded infection events within schools, which is important when evaluating protective 486 measures. Staff-to-staff and student-to-student transmissions were 3 vs. 7, which is 487 comparable to a study conducted in the UK where only about 10% of assumed transmission 488 events were between students themselves [13] . This is remarkable taking into account that 489 more than six times more students than teachers attend school, and given that especially 490 young children interact closer to each other and are less conscious of hygienic measures. This 491 observation may be biased by the higher test frequency and therefore higher detection rate in 492 adults compared to children during the study period. The recommendation to test differed for 493 children and adults, resulting in a higher threshold to test children especially below the age of 494 6 years old. However, the discrepancy might have been balanced out to a certain extent since 495 children were symptomatic more often due to several other viruses spreading in childcare 496 facilities and schools. Children therefore met test criteria frequently despite the high threshold 497 imposed. Notably, wearing face masks was mandatory as of 5th grade for children, but not for 498 children in the lower grades. We expected to observe shifts in the distribution of cases in 499 childcare facilities and in the primary school level towards a higher proportion of affected 500 students after January 2021. This shift is concomitant to the establishment of the Alpha variant 501 in the Canton of Basel-City and the implementation of the mandatory use of face masks among 502 staff in childcare facilities, kindergarten and primary school, as well as students of 5th and 6th 503 grade in primary school. We hypothesize that the few transmissions among staff can be 504 attributed to the implemented health measures, i.e., wearing of masks, distances, hygiene, 505 and free testing even for mildly symptomatic individuals. Yet although transmission in schools 506 were low, most lineage-specific SCoV2 prevalences were higher in children than in adults in 507 both epidemic waves particularly in 12-to 19-year-olds, meaning adolescents had a higher 508 relative case burden. Our analysis yielded an age-dependent infectiousness for the Alpha 509 variant, with younger children being more likely to be infected than adults. Contrasting 510 evidence is found in the current literature, from no differential affection of children and adults 511 [37] to preliminary not yet peer-reviewed findings that support higher case burden the younger 512 the children are [38] . 513 Importantly, we were able to demonstrate that suspected clusters with temporally co-occurring 514 cases were often caused by simultaneous introductions and sometimes transmissions of 515 different SCoV2 variants. Our study is unique in the sense that WGS data allowed us to prove 516 at highest resolution that many co-occurring cases were not connected. Previous studies on 517 school outbreaks assumed viral transmission when several cases co-occurred in a classroom 518 or childcare group within a certain time frame. In fact, we noted that during the second wave 519 before the occurrence of VOCs, almost all apparent school clusters could be unravelled to 520 stem from the random simultaneous appearance of different virus variants in the same 521 classroom. These findings also influenced public health decisions and measures in the Canton 522 of Basel-City, for instance challenging the assumptions previously leading to group 523 quarantines. 524 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. This study bears important limitations caused by missing data due to unsequenced cases. We 542 found 22 single cases which had -derived from contact tracing -been related to clusters in 543 schools or childcare facilities, for which we failed to detect other school or community cases 544 despite our extensive SCoV2 database for the Canton of Basel-City. Some of these might 545 indeed be "single cases" within the Canton of Basel-City and might have been imported from 546 other cantons or countries. However, particularly after the establishment of VOCs, WGS more 547 often failed because of pre-analytical quality or low viral load in the collected sample. This was 548 probably due to changes in contact tracing policies, now advising also asymptomatic contact 549 persons, as well as people with mild symptoms to undergo testing. Another important aspect 550 is the sampling bias due to changing recommendations. We tried to sequence as many cases 551 as possible to generate a comprehensive picture. 552 The SCoV2 pandemic is highly dynamic and therefore scientific results are in many ways 553 short-lived. After completion of this study, the Delta variant (B. of apparent infection clusters in schools and childcare facilities. It will be interesting to repeat 558 the analyses depicted in this study including and comparing the wave caused by the more 559 infectious Delta variant and the Omicron wave that is to come, especially since NAT pool-560 testing was established in the primary level as of June 2021. 561 Analysing SCoV2 case clusters with WGS, this study shows that in the Canton of Basel-City 563 from October 2020 to May 2021 cases of apparent transmission clusters in schools or 564 childcare facilities were often not connected, but caused by different SCoV2 variants 565 introduced from the community. In-school transmissions were infrequent and often involved 566 adults. Our findings confirm that schools and childcare facilities were not hotspots for SCoV2 567 transmission during the Alpha wave and mostly reflected contagion in the community. During 568 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269824 doi: medRxiv preprint both waves, teenagers had higher caseloads than younger children or adults, which may be 569 due to different behaviours. With the establishment of the Alpha variant as of January 2021, 570 children were more likely to be infected than adults. Our data add additional arguments to the 571 effectiveness of health measures, such as mandatory face masks and low testing thresholds. 572 Acknowledgements 573 SARS-CoV-2 genome assemblies were performed at sciCORE (http://scicore.unibas.ch/) 574 scientific computing centre at University of Basel, the support from the sciCORE team for the 575 analysis is greatly appreciated. We also thank Daniel Walther from the development team of 576 the Swiss Pathogen Surveillance Platform (www.spsp.ch), all authors who have shared their 577 genomic data on ENA, and Gilles Dutilh from Clinical Trial Unit of the Department Clinical 578 Research, University of Basel. 579 The author(s) received no specific funding for this work. 581 The study was conducted according to good laboratory practice and in accordance with the 583 Declaration of Helsinki and national and institutional standards. The study was assessed and 584 approved by the local ethical committee (Ethikkommission Nordwest und Zentralschweiz, 585 www.eknz.ch; ID number: 2020-00769). No signature was required according to the ethical 586 assessment. All data from study participants (pediatric and adult patients) were reported in an 587 anonymous fashion. The clinical trial accession number is NCT04351503 (clinicaltrials.gov). 588 589 . CC-BY 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted January 28, 2022. ; https://doi.org/10. 1101 /2022 591 Susceptibility to SARS-CoV-2 Infection Among Children and Adolescents Compared 592 With Adults: A Systematic Review and Meta-analysis The role of children in 595 transmission of SARS-CoV-2: A rapid review SARS-CoV-2 in children: spectrum of disease, transmission and 599 immunopathological underpinnings Why is COVID-19 less severe in children? A review of the 602 proposed mechanisms underlying the age-related difference in severity of SARS-CoV-603 2 infections Reopening Primary Schools during the Pandemic Challenges for Child Mental Health Raised by School Closure and 609 Home Confinement During the COVID-19 Pandemic COVID-612 19 and schools. Guidelines of the French Pediatric Society. Archives de Pédiatrie: 613 organe officiel de la Societe francaise de pediatrie Closing schools is not evidence based 616 and harms children COVID-19 Guidance for Safe Schools and 618 Promotion of In-Person Learning CoV-2 in children aged 0 to 19 years in childcare facilities and schools after their 623 reopening in 626 Transmission of SARS-CoV-2 in Australian educational settings: a prospective cohort 627 study. The Lancet Child & adolescent Secondary 630 transmission of COVID-19 in preschool and school settings in northern Italy after their 631 reopening in September 2020: a population-based study Europeen sur les maladies transmissibles = European communicable disease bulletin SARS-CoV-2 infection 635 and transmission in educational settings: a prospective, cross-sectional analysis of 636 infection clusters and outbreaks in England. The Lancet Infectious diseases Transmission 639 Dynamics of COVID-19 Outbreaks Associated with Child Care Facilities -Salt Lake 640 A dynamic 643 nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. 644 Outbreak Associated with SARS-CoV-2 B.1.617.2 (Delta) Variant in an Elementary 647 School 650 Epidemiology and precision of SARS-CoV-2 detection following lockdown and 651 relaxation measures 654 Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence 655 Amidst Community-Acquired Respiratory Viruses. The Journal of infectious diseases CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant 659 linked to a mass gathering event Improving the 662 quality and workflow of bacterial genome sequencing and analysis: paving the way for 663 a Switzerland-wide molecular epidemiological surveillance platform R: A language and environment for statistical computing Python reference manual. Centrum voor Wiskunde en 669 Informatica Amsterdam Functions to Make Surveys Processing 671 Easier Tidy Messy Data. 2021 Elegant Graphics for Data Analysis Create Pivot Tables. R package version 1.5.2. 2021. Available: 676 Simple Data Frames Additional Themes, Theme Components and Utilities for 679 'ggplot2. 2020. 680 29. Kassambara A. ggpubr: "ggplot2" Based Publication Ready Plots. 681 30. The pandas development team Interactive Web-Based Data Visualization with R, plotly, and shiny. 683 Chapman and Hall/CRC SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning 686 of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic 687 Screening and Whole Genome Sequencing. Microorganisms . 2021. 688 CoV-2 vaccine Alpha and Delta variant breakthrough infections are rare and mild, but 691 happen relative early after vaccination Low SARS-CoV-2 697 Transmission in Elementary Schools -Salt Lake County MMWR Morbidity and mortality weekly report On the Effect of Age on the Transmission The Journal of infectious 702 diseases The Alpha 704 Variant (B.1.1.7) of SARS-CoV-2 in Children: First Experience from 3544 Nucleic Acid 705 Amplification Tests in a Cohort of Children in Germany Increased Transmissibility of SARS-CoV-2 Alpha Variant (B.1.1.7) in Children: 709 Three Large Primary School Outbreaks Revealed by Whole Genome Sequencing in 710 the Netherlands. PREPRINT (Version 1) available at Research Square Face masks effectively 713 limit the probability of SARS-CoV-2 transmission