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Unravelling the modes of transmission of SARS-CoV-2 during a nursing home outbreak: looking beyond the church super-spread event

Abstract Background An outbreak of COVID-19 in a nursing home in the Netherlands, following an on-site church service held on March 8 th, 2020, triggered an investigation to unravel sources and chain(s) of transmission. Methods Epidemiological data were collected from registries and through a questionnaire among church attendees. Symptomatic residents and healthcare workers (HCWs) were tested for SARS-CoV-2 by RT-PCR and subjected to whole genome sequencing (WGS). Sequences from a selection of people from the same area were included as community reference. Results After the church service, 30 of 39 attendees (77%) developed symptoms; 14 were tested and were positive for COVID-19 (11 residents and 3 non-residents). In the following five weeks, 62 of 300 residents (21%) and 30 of 640 HCWs (5%) tested positive for COVID-19; 21 of 62 residents (34%) died. The outbreak was controlled through a cascade of measures. WGS of samples from residents and HCWs identified a diversity of sequence types, grouped into eight clusters. Seven resident church attendees all were infected with distinct viruses, four of which belonged to two larger clusters in the nursing home. Conclusions Although initial investigation suggested the church service as source of the outbreak, detailed analysis showed a more complex picture, most consistent with widespread regional circulation of the virus in the weeks before the outbreak, and multiple introductions into the nursing home before the visitor ban. The findings underscore the importance of careful outbreak investigations to understand SARS-CoV-2 transmission to develop evidence-based mitigation measures.


Introduction
In January 2020, the health authorities of China notified the World Health Organisation (WHO) of an outbreak of a severe acute respiratory syndrome caused by a SARS-like coronavirus (SARS-CoV-2).
Although initial control efforts were directed at containment, following the model of the first SARS outbreak in 2003, the virus continued to spread and the WHO declared the disease COVID-19 to be a pandemic on March 11 th , 2020. In the Netherlands, the first case of COVID-19 was diagnosed on February 27 th , in a Dutch national who had returned from the Lombardy region of Italy [1]. On March 16 th , the prime minister announced physical distancing measures, but a first pandemic wave occurred with 50.661 cases and 6118 deaths, particularly in elderly, by July 1 st .
Two COVID-19 outbreaks in long-term care skilled nursing facilities in Washington US showed the potential for rapid spread among residents of these types of facilities [2,3]. Nursing home residents are susceptible to severe COVID-19 outcomes as a consequence of their age and, in some cases, underlying health conditions. They accounted for 25% to 50% of the documented deaths due to COVID-19 in some countries [4]. The impact of COVID-19 in nursing homes is aggravated by delayed recognition due to atypical clinical presentation in elderly persons, and difficulties of implementing stringent control measures [5]. In addition, it was augmented by shortages of personal protection equipment (PPE) [6]. In view of the severe consequences, understanding how SARS-CoV-2 transmits in this population is crucial.
On March 15 th , the day when country-wide measures were announced following confirmation of widespread community-circulation of SARS-COV-2 in a neighbouring province [7,8], the local public health service was notified of a positive COVID-19 test result in a resident from a large nursing home A c c e p t e d M a n u s c r i p t 6 (300 beds), located on an island in the province South-Holland. The following week, more cases were confirmed among residents and health care workers (HCWs), triggering a cascade of infection control measures at the facility. Nursing home management was informed by church leaders on March 18 th that many church attendees from the local community had fallen ill, supposedly after a church service that had been held on March 8 th in the chapel of the nursing home facility. This raised the suspicion that the nursing home outbreak had been triggered by the church service. In this study, we aim to reconstruct the introduction and spread of SARS-CoV-2 in the nursing home, including the possible role of the church service, combining extensive diagnostic screening, epidemiological information and whole genome sequencing (WGS).

Sample collection and SARS-CoV-2 diagnostic testing
All residents and HCWs in the nursing home who developed respiratory symptoms since March 14 th (the day of the first suspected case) were tested for presence of SARS-CoV-2 RNA in throat and nose swabs by RT-PCR [9]. All residents and HCWs testing positive before April 15 th were included in the study. In addition, to be able to compare the sequences from nursing home patients with those circulating in the local community, a random selection of unrelated SARS-CoV-2 positive COVIDpatients living on the same island was included for sequence analysis. This selection was made based on postal codes, ensuring inclusion of patients from different parts of the island.

Data collection
The public health service contacted all SARS-CoV-2 positive residents and HCWs to perform contact tracing and to collect disease specific information. These data were supplemented with data from the nursing home organisation and included information such as date of onset of symptoms, testing date, unit (for residents and HCWs), hospitalisation, death, and attendance to the church service of A c c e p t e d M a n u s c r i p t 7 March 8 th . The nursing home organisation also provided a detailed timeline of the measures taken in order to mitigate the outbreak, and maps of the facility.
An online questionnaire was developed and forwarded to the non-residents who attended the church service by the reverend. The reverend also provided details on the church service. The questionnaire covered: age, gender, symptoms at day of the church service, recent travel abroad, contact with a COVID-19 patient, symptoms since church service, onset date of symptoms, perceived severity, hospitalisation, ICU admission, and testing for Sars-CoV-2. In addition, respondents were asked if they had any household member who had symptoms on the day of the church service, or developed symptoms or was hospitalised thereafter. Nursing home residents who attended the church service could not be included in the questionnaire, due to the severe impact of the outbreak in the nursing home, and because by the end of March many of them were too ill or passed away.
Their data were retrieved from the nursing home registry, similar to other SARS-CoV-2 positive nursing home residents.

SARS-CoV-2 sequencing and analysis
RT-PCR-positive samples of residents, HCWs and inhabitants of the same island, with a viral load below a Ct value of 32, were selected for sequencing using a SARS-CoV-2 specific amplicon-based Nanopore sequencing protocol as previously described [10]. The consensus genome was generated only including positions with a coverage >30 as described previously [11]. Sequences were compared to a reference database developed for the national COVID-19 response effort. Sequences were assigned to a transmission cluster when they had a maximum of 2 nucleotides difference [12]. For cluster A, it was not possible to apply the 2 nucleotides cutoff. The cluster contained both sequences from the nursing home and unrelated SARS-CoV-2 sequences from the same island, with up to 6 A c c e p t e d M a n u s c r i p t 8 nucleotides difference between sequences. Cluster A was therefore assigned as a regional cluster (as opposed to a possible transmission cluster).

Medical ethical clearance
Outbreak investigations of notifiable diseases such as COVID-19 are the legal tasks of the Public Health Service as described under the Public Health Act, and do not require separate medical ethical clearance.

Results
The nursing home is located in the South-West of the Netherlands in a small town on the rural island of Goeree-Overflakkee (260 square km with 50,000 inhabitants). It is a skilled nursing home facility with 300 beds, giving long and short term residential care, divided over five buildings with two to four stories. There are 146 long-term residential care/assisted living apartments, 24 short-term residential care apartments (medical rehabilitation), and 17 residential groups of 7 -8 residents    Table 2 for detailed timeline of infection prevention and control measures). Until April 14 th (study period), 62 of 300 residents (21%) and 30 of 640 HCWs (5%) tested positive for SARS-CoV-2, while 51 residents and 69 HCWs developed respiratory symptoms but tested negative (3 more residents and 12 more HCWs tested positive after the study period; 1 more resident died). The attack rate for residents who attended the church service was 85% (11/13) while for residents who did not attend it was 18% (51/287). Attendees did not differ from non-attendees with regard to age, mobility, or number of contacts with visitors.
The outbreak started in the first and second floor of the nursing home, with most affected units housing at least one resident who attended the church service (Figure 2a). Residents on the ground floor (residential groups) were mostly infected later. Some residential groups were more affected than others (ranging from 0 -7 of 8 residents affected). The air conditioning system did not recirculate used air.

Discussion
After the church service on March 8 th , 30 of 39 attendees (77%) developed symptoms or tested positive for COVID-19. Although the church service initially was thought to be the source of the outbreak in the nursing home, the genomic analysis showed a more complex picture. Residents who had attended the church service were infected with distinct viruses, and subsequent transmission M a n u s c r i p t 12 within the nursing home was limited. Analysis of sequence data from viruses from residents and HCWs suggested that there were at least 17 separate introductions, with limited within-home transmission. The data are most consistent with widespread regional circulation of the virus in the weeks before the outbreak, and multiple introductions through contacts between residents and visitors or HCWs before the visitor ban on March 17 th . The combination of extensive epidemiological data collection and whole genome sequencing, and comparison of sequences to a national reference database, allowed us to interpret transmission patterns in a unique way.
Based on this investigation it is not possible to assess exactly how many persons were infected at the church service, as only a minority of non-residents who attended the church service were tested for SARS-CoV-2. This was in line with the national guidance at the time, that recommended testing for persons with recent travel history or persons with severe respiratory disease. Religious gatherings have been linked to outbreaks of COVID-19 in South Korea, Singapore and the US [13][14][15]. Here, the high prevalence of respiratory symptoms in the community members who attended the church service does suggest that this was an amplifying event. However, finding considerable diversity of viruses in the affected nursing home residents who attended the church service showed that this was not a single superspreading event, and that multiple viruses were already present.
The nursing home where the epidemic took place is a large facility of 300 beds, with many volunteers and family caregivers, and many social activities and facilities. Being located on an island, with a homogenous religious background, the close social bonds facilitate frequent contacts between residents and non-residents. This may all have contributed to the multiple introductions and spread of SARS-CoV-2 within the nursing home (and within the island) in the week(s) before the visitor ban. Initial spread could stay unnoticed, probably due to people having mild complaints and not knowing that the virus was already present on the island. The first COVID-19 patient on the island was diagnosed on March 12 th , only 2 days before the first resident was tested positive. Before then, the nursing home was can make an essential contribution in this, by revealing transmission patterns that would otherwise remain concealed. In this case, epidemiological data would have pointed towards large scale within nursing home transmission following the church service, while WGS showed that the situation was more complex. Other COVID-19 studies have also shown the added value of whole genome sequencing in epidemiological investigations [8,12]. Furthermore, our findings show the possible implications if there are no measures in place to prevent introductions of the virus when there is extensive community transmission, but also the efficacy of stringent measures to control subsequent SARS-CoV-2 outbreaks in nursing homes, especially when implemented at an early stage.
As the measures have a huge social and mental impact and can last for many weeks, an ethical discussion, including opinions of residents, family, and HCWs, is needed to strengthen compliance and acceptance, for example during the second wave of SARS-CoV-2.