Eurosurveillance - Volume 27, Issue 10, 10 March 2022

Human mobility was considerably reduced during the COVID-19 pandemic. To support disease surveillance, it is important to understand the effect of mobility on transmission.

We compared the role of mobility during the first and second COVID-19 wave in Switzerland by studying the link between daily travel distances and the effective reproduction number (Rt) of SARS-CoV-2.

We used aggregated mobile phone data from a representative panel survey of the Swiss population to measure human mobility. We estimated the effects of reductions in daily travel distance on Rt via a regression model. We compared mobility effects between the first (2 March–7 April 2020) and second wave (1 October–10 December 2020).

Daily travel distances decreased by 73% in the first and by 44% in the second wave (relative to February 2020). For a 1% reduction in average daily travel distance, Rt was estimated to decline by 0.73% (95% credible interval (CrI): 0.34–1.03) in the first wave and by 1.04% (95% CrI: 0.66–1.42) in the second wave. The estimated mobility effects were similar in both waves for all modes of transport, travel purposes and sociodemographic subgroups but differed for movement radius.

Mobility was associated with SARS-CoV-2 Rt during the first two epidemic waves in Switzerland. The relative effect of mobility was similar in both waves, but smaller mobility reductions in the second wave corresponded to smaller overall reductions in Rt. Mobility data from mobile phones have a continued potential to support real-time surveillance of COVID-19.

Throughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.

Here, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.

We developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69–70 and ORF1a Δ3675–3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.

Based on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69–70 was 0.34 (95% confidence interval (CI): 0.30–0.39) and based on ORF1a Δ3675–3677 was 0.53 (95% CI: 0.49–0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38–0.61).

Digital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.

The Delta variant of SARS-CoV-2 had become predominant globally by November 2021.

We evaluated transmission dynamics and epidemiological characteristics of the Delta variant in an outbreak in southern China.

Data on confirmed COVID-19 cases and their close contacts were retrospectively collected from the outbreak that occurred in Guangdong, China in May and June 2021. Key epidemiological parameters, temporal trend of viral loads and secondary attack rates were estimated. We also evaluated the association of vaccination with viral load and transmission.

We identified 167 patients infected with the Delta variant in the Guangdong outbreak. Mean estimates of latent and incubation period were 3.9 days and 5.8 days, respectively. Relatively higher viral load was observed in infections with Delta than in infections with wild-type SARS-CoV-2. Secondary attack rate among close contacts of cases with Delta was 1.4%, and 73.1% (95% credible interval (CrI): 32.9–91.4) of the transmissions occurred before onset. Index cases without vaccination (adjusted odds ratio (aOR): 2.84; 95% CI: 1.19–8.45) or with an incomplete vaccination series (aOR: 6.02; 95% CI: 2.45–18.16) were more likely to transmit infection to their contacts than those who had received the complete primary vaccination series.

Patients infected with the Delta variant had more rapid symptom onset compared with the wild type. The time-varying serial interval should be accounted for in estimation of reproduction numbers. The higher viral load and higher risk of pre-symptomatic transmission indicated the challenges in control of infections with the Delta variant.