Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands

Abstract

Background Individuals with intellectual and developmental disabilities (IDD) living in congregated settings have increased risk of COVID-19 infection and mortality. Little is known about variant B.1.1.519 with spike mutation T478K, dominant in Mexico. We describe a linked SARS-CoV-2 B.1.1.519 outbreak in three IDD facilities in the Netherlands. Methods Following notification of the index, subsequent cases were identified through serial PCR group testing. Positive specimens were submitted for whole-genome-sequencing. Clinical information was gathered through interviews with staff members of the three facilities. Results Attack rate (AR) in clients of the index facility was 92% (23/25), total AR in clients 45% (33/73) and in staff members 24% (8/34). 55% (18/33) of client cases were asymptomatic, versus 25% (2/8) of staff members. Five client cases (15%) were hospitalized, two died (6%). Sequencing yielded the same specific B.1.1.519 genotype in all three facilities. No significant difference in median viral load was established comparing the B.1.1.519 variant with other circulating variants. The index of the linked outbreak reported no travel history or link to suspected or confirmed cases suggesting regional surveillance. Observed peak regional prevalence of B.1.1.519 during the outbreak supports this. Conclusion AR, morbidity and mortality prior to control measures taking effect were high, probably related to the specific characteristics of the IDD setting and its clients. We assessed no evidence for intrinsic contributing properties of variant B.1.1.519. Our study argues for enhanced infection prevention protocols in the IDD setting, and prioritization of this group for vaccination against COVID-19.

Pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska

“…The functional significance of B.1.1.519 harboring these mutations in S is unclear. In a study from the Netherlands, there was no evidence of increased viral load conferred by B.1.1.519 23 .…”

“…Unfortunately, the necessary data to draw conclusions about the clinical impacts of B.1.1.519 in Alaska, as shown in the Mexico-City study, were not available. Another study, from the Netherlands, describes a cluster of cases associated with B.1.1.519, demonstrating a high within-facility attack rate 23 . Interestingly, that same study did not find differences in B.1.1.519 viral loads compared with other variants, and sample size limited conclusions about disease severity.…”

Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska

“…P681H also occurs in B.1.1.7 (Alpha) and has a weak ability to increase proteolytic cleavage of S1/S2 in vitro (Lubinskiet et al, 2021). The functional significance of B.1.1.519 harboring these mutations in S is unclear and in a study from the Netherlands there was no evidence of increased viral load conferred by B.1.1.519 (Gorgels et al, 2022).…”

“…Unfortunately, we lacked the availability of the necessary data for Alaska to draw conclusions about the clinical impacts of B.1.1.519 in Alaska as shown in the Mexico-City study. Another study, from the Netherlands, describes a cluster of cases associated with B.1.1.519 demonstrating a high within facility attack rate (Gorgels et al, 2022). Interestingly, that same study did not find differences in B.1.1.519 viral loads compared with other variants, and sample size limited conclusions about disease severity.…”

“…Interestingly, based on the regression of total AA changes over time, which exhibited an increase at a steady rate, B.1.1.519 genomes had fewer total AA changes across the genome than predicted (Figure 3A) but aligned with the number of spike protein AA changes (Figure 3B). (Gorgels et al, 2022). Interestingly, that same study did not find differences in B.1.1.519 viral loads compared with other variants, and sample size limited conclusions about disease severity.…”