Outbreak 1: residential care facility 1
Outbreak 1 occurred in a residential care facility which houses 25 clients. Each client had their own room with private sanitation. Two had Down syndrome. A full range of infection prevention measures to manage the risk related to Covid-19 transmission had been implemented, including the use of medical face masks by staff members. Staff comprised 15 members who all worked before and during the outbreak.
Four clients tested positive on 16 February, 2021 after multiple clients reported symptoms. One case had visited the care farm for daytime activities on 12 February, probably being the index for outbreak 2. Source tracing revealed a family member of one client as a putative source. This individual reported onset of symptoms on 5 February and tested positive on 9 February.
Outbreak control measures
Following identification of these four cases, additional control measures to prevent further transmission were implemented. Individual room isolation was mandated for all clients, a visitor ban was declared, temperature was monitored twice daily for all clients, and staff members were instructed to change PPE equipment every three hours while working on the location. PPE consisted of FFP2/N95 face masks, gloves, goggles and gown.
The first group testing session, comprising the 21 hitherto untested clients, was performed on 18 February and resulted in 15 cases positive for SARS-CoV-2. Of these, 14 reported no symptoms on the day of testing, but four developed symptoms over subsequent days. All staff members were tested as well, one of whom tested positive. Four staff members and two clients tested positive the days after.
A second group testing session was performed on 25 February on the four remaining clients and staff members who had tested negative before yielding two new client cases. A third group testing session was conducted on 4 March yielding no new cases.
Outbreak 2: a care farm
Outbreak 2 appeared in a care farm which offers daycare activities for 35 clients. All daycare clients live at residential care facilities or at home with their families. The care farm employs 10 staff members. Activities take place in groups of 8 clients at most, physical distance between clients and staff members is maintained and supervised during activities, and the use of non-medical face masks is mandatory for clients and staff members.
As mentioned earlier, a client from outbreak 1 had visited the care farm on 12 February. This client, who had a chronic cough but no other symptoms, tested positive on 16 February. One other day care farm client developed symptoms on 14 February and also tested positive on 16 February. This case inhabits residential care facility 2, probably being the index for outbreak 3.
Outbreak control measures
Following notification of these two cases, the care farm closed its daycare activities on 17 February. Two exposed clients tested positive on 18 February. Three clients and two staff members developed symptoms and tested positive in the following days.
Group testing was performed on all clients and staff members on 20 February, yielding one client case. On 26 February, a second round of group testing on all staff members and 14 clients revealed one more positive client. No further group testing sessions were carried out.
Outbreak 3: residential care facility 2
Outbreak 3 occurred in residential care facility 2 which houses 15 clients. The residential setting and implemented infection prevention measures were similar as described in outbreak 1. Staff comprised 9 members who all worked before and during the outbreak.
The client case, that had visited the care farm case, reported symptoms from 14 February and was immediately put into isolation, followed by a positive test on 16 February.
Outbreak control measures
Similar outbreak prevention measures were implemented as in outbreak 1. Staff members were tested yielding one asymptomatic case on 20 February. Group testing on clients, performed on 22 February, yielded two cases. Restraints were lifted for all clients who tested negative. No further group testing sessions were carried out.
Figure 1 shows a probable schematic reconstruction and figure 2 shows a chronological reconstruction of the three outbreaks. In outbreak 1 an attack rate (AR) of 92% was observed among clients. In outbreak 2 and outbreak 3 the AR was 24% and 14% respectively. Client cases were asymptomatic in 55% (18/33) of cases versus 25% (2/8) in staff members. Among client cases, 5 were hospitalized and two died (case mortality rate 6%). During the one-month follow-up 5 additional cases among family members of clients and staff members were identified and epidemiologically linked to the outbreaks.
The cycle threshold (Ct) of the RT-PCR test of one of the pre-symptomatic clients who tested positive on 18 February was 8. This client suffered from diabetes mellitus and obesity and was hospitalized later. Because of the high viral load, the sample obtained from this subject was selected for SARS-CoV-2 sequence analysis. The SARS-CoV-2 genotype in this patient belonged to the B.1.1.519 lineage. Subsequently, sequencing was performed on samples from all clients and staff members from all outbreaks and the family member suspected of being the putative source.
Of the 42 samples obtained, 36 were successfully sequenced. Thirty-five isolates belonged to the B.1.1.519 lineage (32 sequences being identical, while 3 sequences harbored one additional mutation), whereas one SARS-CoV-2 isolate from a client of outbreak 2, belonged to the B.1.177.40 lineage (Figure 3). These findings linked all outbreaks and indicated that a family member was the index of the linked outbreak. The index was subsequently contacted and reported no travel history or link to other confirmed or suspected cases.
Viral load analysis
Since the B1.1.519 lineage harbors a few mutations of interest in the spike protein including the T478K mutation (Figure S1) and the P681H mutation as established in several other lineages, including the B.1.1.7 variant , we studied whether samples harboring this genotype contained higher viral loads compared to isolates belonging to the B.1.1.7 or other variants. To exclude the effect of other mutations in the receptor-binding domain in isolates belonging to the B.1.1.7 lineage or other variants, we removed any isolates harboring a mutation that leads to an amino acid change between positions 319 and 541 in the spike protein from the analysis. A significant difference was only determined when comparing median Ct values of samples harboring the B.1.1.7 variant with other variants (18 versus 19, p<0.001) (figure 4).
Regional prevalence circulating genotypes
Since the second week of 2021, SARS-CoV-2 sequencing has been performed on a weekly base to monitor the prevalence of circulating genotypes in the region of South-Limburg, as part of the national surveillance program. All SARS-CoV-2-positive cases belonging to the reported outbreaks in this study were detected in week 7 and 8, which coincides with peak prevalence of B.1.1.519 in the community (6% for week 7 and 5% for week 8) (Figure 5). Before week 7, B.1.1.519 isolates had not been detected in the region of South-Limburg. Furthermore, the prevalence of B.1.1.519 declined gradually during week 8, after eventually disappearing in week 9. There was a strong increase in the prevalence of the B.1.1.7 lineage from week 6 (21%), over week 7 (40%) to week 8 (65%).