Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants

Population testing remains central to COVID-19 control and surveillance, with countries increasingly using antigen tests rather than molecular tests. Here we describe a SARS-CoV-2 variant that escapes N antigen tests due to multiple disruptive amino-acid substitutions in the N protein. By fitting a multistrain compartmental model to genomic and epidemiological data, we show that widespread antigen testing in the Italian region of Veneto favored the undetected spread of the antigen-escape variant compared to the rest of Italy. We highlight novel limitations of widespread antigen testing in the absence of molecular testing for diagnostic or confirmatory purposes. Notably, we find that genomic surveillance systems which rely on antigen population testing to identify samples for sequencing will bias detection of escape antigen test variants. Together, these findings highlight the importance of retaining molecular testing for surveillance purposes, including in contexts where the use of antigen tests is widespread.

Yellow fever in Asia-a risk analysis

BACKGROUND

There is concern about the risk of yellow fever (YF) establishment in Asia, owing to rising numbers of urban outbreaks in endemic countries and globalisation. Following an outbreak in Angola in 2016, YF cases were introduced into China. Prior to this, YF had never been recorded in Asia, despite climatic suitability and the presence of mosquitoes. An outbreak in Asia could result in widespread fatalities and huge economic impact. Therefore, quantifying the potential risk of YF outbreaks in Asia is a public health priority.

METHODS

Using international flight data and YF incidence estimates from 2016, we quantified the risk of YF introduction via air travel into Asia. In locations with evidence of a competent mosquito population, the potential for autochthonous YF transmission was estimated using a temperature-dependent model of the reproduction number and a branching process model assuming a negative binomial distribution.

RESULTS

In total, 25 cities across Asia were estimated to be at risk of receiving at least one YF viraemic traveller during 2016. At their average temperatures, we estimated the probability of autochthonous transmission to be <50% in all cities, which was primarily due to the limited number of estimated introductions that year.

CONCLUSION

Despite the rise in air travel, we found low support for travel patterns between YF endemic countries and Asia resulting in autochthonous transmission during 2016. This supports the historic absence of YF in Asia and suggests it could be due to a limited number of introductions in previous years. Future increases in travel volumes or YF incidence can increase the number of introductions and the risk of autochthonous transmission. Given the high proportion of asymptomatic or mild infections and the challenges of YF surveillance, our model can be used to estimate the introduction and outbreak risk and can provide useful information to surveillance systems.

Synchronization of coupled rotators: Josephson junction ladders and the locally coupled Kuramoto model

We show that the resistively shunted junction (RSJ) equations describing a ladder array of overdamped, critical-current disordered Josephson junctions that are current biased along the rungs of the ladder can be mapped onto a Kuramoto model with nearest neighbor, sinusoidal couplings. This result is obtained by an averaging method, in which the fast dynamics of the RSJ equations are integrated out, leaving the dynamics which describe the time scale over which neighboring junctions along the rungs of the ladder phase and frequency synchronize. We quantify the degree of frequency synchronization of the rung junctions by calculating the standard deviation of their time-averaged voltages, sigma(omega), and the phase synchronization is quantified by calculating the time average of the modulus of the Kuramoto order parameter, <|r|>. We test the results of our averaging process by comparing the values of sigma(omega) and <|r|> for the original RSJ equations and our averaged equations. We find excellent agreement for dc bias currents of I(B)/<I(c)> greater, similar 3, where <I(c)> is the average critical current of the rung junctions, and critical current disorders of up to 10%. We also study the effects of thermal noise on the synchronization properties of the overdamped ladder. Finally, we find that including the effects of junction capacitance can lead to a discontinuous synchronization transition as the strength of the coupling between neighboring junctions is smoothly varied.