From Entry to Outbreak in a High School Setting: Clinical and Wastewater Surveillance of a Rare SARS-CoV-2 Variant

Abstract

In December 2021, an outbreak of the SARS-CoV-2 B.1.640.2 variant, potentially originating from Cameroon, was investigated among schoolchildren in Germany. The index case, an adult who had recently returned from a three-week stay in the Republic of Congo, introduced the variant into a school setting via their children, resulting in subsequent transmission within the school and ultimately to a hospital ward. Whole-genome sequencing of viral samples identified both B.1.640.1 and B.1.640.2 lineages. This outbreak highlights the unpredictable nature of emerging SARS-CoV-2 variants and emphasizes the importance of early detection and containment to mitigate transmission to high-risk populations. Notably, wastewater surveillance detected the variant during the study peri-od, reinforcing the utility of wastewater-based epidemiology as a complementary tool for the early warning and containment of novel variants. These findings underline the critical need for timely research and adherence to quarantine measures to enhance outbreak control efforts.

Keywords: SARS-CoV-2; outbreak investigation; wastewater.

Figure 1

(A) Schematic overview of the SARS-CoV-2 spike protein (blue) and locations of selected protein domains such as N-terminal domain (NTD, orange), receptor binding domain (RBD, red), subdomains 1 and 2 (SD1, SD2, gray), and the S1/S2 cleavage site (yellow) (adapted from https://covdb.stanford.edu/. Last accessed: 17 February 2022). (B,C) Protein alignment of the sequences resulting from the SARS-CoV-2 B.1.640.1 outbreak in a secondary school. Horizontal gray lines correspond to the consensus sequence of each patient (GISAID database accession numbers given) and the SARS-CoV-2 Wuhan-Hu-1 (NC_045512.2) reference sequence, respectively. Amino acid exchanges are depicted in pink. (B) Alignment of about 268 amino acids covering the RBD of the SARS-CoV-2 spike protein (red dashed line). (C) Alignment of about 275 amino acids covering the SD2 and part of the C-terminus of the protein (gray dashed line).

Figure 2

Phylogenetic tree based on partial SARS-CoV-2 spike gene RBD sequences (nucleotides 963 to 1737) from 14 infected schoolchildren and their relatives (GISAID database accession numbers given). Five epidemiologically unlinked isolates were included as references: EPI_ISL_3115625 (Alpha), EPI_ISL_1282471 (Beta), EPI_ISL_1849483 (Gamma), EPI_ISL_8038881 (Delta), and NC_045512.2 (SARS-CoV-2 Wuhan-HU-1). The tree is drawn to scale, with branch lengths representing the number of substitutions per site. Codon positions included are first, with 258 amino acid positions in the final dataset.

Figure 3

This picture provides a timeline and transmission pathway of the SARS-CoV-2 B.1.640.2 variant outbreak across multiple settings, including family units, a hospital, a high school, a primary school, kindergarten, and a retirement home. The outbreak originated on 26 November 2021 and was traced back to an individual returning from the Republic of Congo. Circles represent confirmed cases, with larger circles indicating clusters of infections. Transmission links between family members and within institutional settings are shown, demonstrating how the virus spreads through close contacts in schools, a healthcare setting, and a family network. Preventive measures and Christmas holidays achieved containment.

Figure 4

Transmission timeline and pathway of SARS-CoV-2 infections across different biotopes from 26 November 2021 to early January 2022. The diagram illustrates the spread of COVID-19 from an index family through various environments, including a retirement home, hospital, high school, and primary school. Circles represent infected individuals in each setting, with arrows indicating transmission pathways among family members and within institutional environments. Key nodes include the initial infection of a healthcare worker and subsequent spread to patients in the hospital, as well as secondary transmissions within a high school class and primary school.