Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021.

When SARS-CoV-2 Omicron emerged in 2021, S gene target failure enabled differentiation between Omicron and the dominant Delta variant. In England, where S gene target surveillance (SGTS) was already established, this led to rapid identification (within ca 3 days of sample collection) of possible Omicron cases, alongside real-time surveillance and modelling of Omicron growth. SGTS was key to public health action (including case identification and incident management), and we share applied insights on how and when to use SGTS.

Modelling flock heterogeneity in the transmission of peste des petits ruminants virus and its impact on the effectiveness of vaccination for eradication.

Peste des petits ruminants (PPR) is an acute infectious disease of small ruminants targeted for global eradication by 2030. The Global Strategy for Control and Eradication (GSCE) recommends mass vaccination targeting 70% coverage of small ruminant populations in PPR-endemic regions. These small ruminant populations are diverse with heterogeneous mixing patterns that may influence PPR virus (PPRV) transmission dynamics. This paper evaluates the impact of heterogeneous mixing on (i) PPRV transmission and (ii) the likelihood of different vaccination strategies achieving PPRV elimination, including the GSCE recommended strategy. We develop models simulating heterogeneous transmission between hosts, including a metapopulation model of PPRV transmission between villages in lowland Ethiopia fitted to serological data. Our results demonstrate that although heterogeneous mixing of small ruminant populations increases the instability of PPRV transmission-increasing the chance of fadeout in the absence of intervention-a vaccination coverage of 70% may be insufficient to achieve elimination if high-risk populations are not targeted. Transmission may persist despite very high vaccination coverage (>90% small ruminants) if vaccination is biased towards more accessible but lower-risk populations such as sedentary small ruminant flocks. These results highlight the importance of characterizing small ruminant mobility patterns and identifying high-risk populations for vaccination and support a move towards targeted, risk-based vaccination programmes in the next phase of the PPRV eradication programme. Our modelling approach also illustrates a general framework for incorporating heterogeneous mixing patterns into models of directly transmitted infectious diseases where detailed contact data are limited. This study improves understanding of PPRV transmission and elimination in heterogeneous small ruminant populations and should be used to inform and optimize the design of PPRV vaccination programmes.