Characterizing features of outbreak duration for novel SARS-CoV-2 variants of concern

Characterizing the dynamics of epidemic trajectories is critical to understanding the potential impacts of emerging outbreaks and to designing appropriate mitigation strategies. As the COVID-19 pandemic evolves, however, the emergence of SARS-CoV-2 variants of concern has complicated our ability to assess in real-time the potential effects of imminent outbreaks, such as those presently caused by the Omicron variant. Here, we report that SARS-CoV-2 outbreaks across regions exhibit strain-specific times from onset to peak, specifically for Delta and Omicron variants. Our findings may facilitate real-time identification of peak medical demand and may help fine-tune ongoing and future outbreak mitigation deployment efforts.

Risk evaluation at municipality level of a COVID-19 outbreak incorporating relevant geographic data: the study case of Galicia

The COVID-19 pandemic was an inevitable outcome of a globalized world in which a highly infective disease is able to reach every country in a matter of weeks. While lockdowns and strong mobility restrictions have proven to be efficient to contain the exponential transmission of the virus, its pervasiveness has made it impossible for economies to maintain this kind of measures in time. Understanding precisely how the spread of the virus occurs from a territorial perspective is crucial not only to prevent further infections but also to help with policy design regarding human mobility. From the large spatial differences in the behavior of the virus spread we can unveil which areas have been more vulnerable to it and why, and with this information try to assess the risk that each community has to suffer a future outbreak of infection. In this work we have analyzed the geographical distribution of the cumulative incidence during the first wave of the pandemic in the region of Galicia (north western part of Spain), and developed a mathematical approach that assigns a risk factor for each of the different municipalities that compose the region. This risk factor is independent of the actual evolution of the pandemic and incorporates geographic and demographic information. The comparison with empirical information from the first pandemic wave demonstrates the validity of the method. Our results can potentially be used to design appropriate preventive policies that help to contain the virus.

The Epidemic Risk of Dengue Fever in Japan: Climate Change and Seasonality

Dengue fever is a leading cause of illness and death in the tropics and subtropics, and the disease has become a threat to many nonendemic countries where the competent vectors such as Aedes albopictus and Aedes aegypti are abundant. The dengue epidemic in Tokyo, 2014, poses the critical importance to accurately model and predict the outbreak risk of dengue fever in nonendemic regions. Using climatological datasets and traveler volumes in Japan, where dengue was not seen for 70 years by 2014, we investigated the outbreak risk of dengue in 47 prefectures, employing the temperature-dependent basic reproduction number and a branching process model. Our results show that the effective reproduction number varies largely by season and by prefecture, and, moreover, the probability of outbreak if an untraced case is imported varies greatly with the calendar time of importation and location of destination. Combining the seasonally varying outbreak risk with time-dependent traveler volume data, the unconditional outbreak risk was calculated, illustrating different outbreak risks between southern coastal areas and northern tourist cities. As the main finding, the large travel volume with nonnegligible risk of outbreak explains the reason why a summer outbreak in Tokyo, 2014, was observed. Prefectures at high risk of future outbreak would be Tokyo again, Kanagawa or Osaka, and highly populated prefectures with large number of travelers.

Landscape Political Ecology: Rural-Urban Pattern of COVID-19 in Nigeria

The socio-ecological and political properties of rural and urban landscapes have been argued to produce the differentials in rural-urban health. However, the mechanism of the COVID-19 pattern in this socio-political-ecological perspective has not been understood in Africa. The study used spatial techniques to explore the pattern of urbanization-COVID-19 nexus in Nigeria. It has been argued that three elements (demographic dynamics, infrastructure or governance) typify the socio-political-ecological landscape of urban places. They shape the spread of infectious diseases. We explored the extent to which these factors predict the COVID-19 pattern in Nigeria. The study used data from Nigeria’s Centre for Diseases Control and the National Bureau of Statistics. The results indicate that more urban states in Nigeria tend to have higher COVID-19 cases than rural states. The COVID-19 pattern is best predicted by population dynamics more than other elements. The result indicates demographic attributes are more critical to surges in COVID-19 cases in Nigeria. Places with higher populations and densities will tend to have more spread of the virus than places with lesser populations and densities. Therefore, in a future outbreak, places of high densities should be given more attention to prevent further spread.

Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife

Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.

The risk for a new COVID-19 wave and how it depends on R 0 , the current immunity level and current restrictions

The COVID-19 pandemic has hit different regions differently. The current disease-induced immunity level î in a region approximately equals the cumulative fraction infected, which primarily depends on two factors: (i) the initial potential for COVID-19 in the region ( R 0 ), and (ii) the preventive measures put in place. Using a mathematical model including heterogeneities owing to age, social activity and susceptibility, and allowing for time-varying preventive measures, the risk for a new epidemic wave and its doubling time are investigated. Focus lies on quantifying the minimal overall effect of preventive measures p Min needed to prevent a future outbreak. It is shown that î plays a more influential roll than when immunity is obtained from vaccination. Secondly, by comparing regions with different R 0 and î it is shown that regions with lower R 0 and low î may need higher preventive measures ( p Min ) compared with regions having higher R 0 but also higher î , even when such immunity levels are far from herd immunity. Our results are illustrated on different regions but these comparisons contain lots of uncertainty due to simplistic model assumptions and insufficient data fitting, and should accordingly be interpreted with caution.

Characterisation of Staphylococcus argenteus carried by healthy Royal Marines: a molecular epidemiology case-study

Objectives: During a prospective study of S. aureus carriage in Royal Marines (RM) recruits, six S. argenteus strains were identified in four recruits undertaking military training together. As S. argenteus sepsis leads to mortality similar to S. aureus, we determined the potential for person-to-person transmission, to evaluate future outbreak risk. Methods: We used whole-genome sequencing to characterise S. argenteus and investigate phylogenetic relationships between isolates. Participant colonisation with S. aureus and skin and soft tissue infection acquisition were recorded. Results: All six S. argenteus strains were spa-type t5078, ST2250. Strains were detected in 4/40 recruits in the same troop (training cohort) in weeks 1, 6 or 15 of training. No mec, tsst or LukPV genes were detected. We identified differences of 10-35 core SNPs between S. argenteus from different recruits. In two recruits, two S. argenteus strains were isolated; these could be distinguished by 3 and 15 core SNPs in each case. S. argenteus was not identified in any one of the other 21 participating troops (1,012 recruits). Conclusions: The identification of S. argenteus within a single troop from the total recruit population supports a common source for transmission, supported by SNP analysis. The high number of SNPs between some isolates may indicate a common source of diverse isolates or a high level of S. argenteus mutation in carriage. S. argenteus ST2250 is a newly recognised lineage; a better understanding of the frequency of genetic changes during transmission and transition from asymptomatic carriage to disease is required.

Physically distant but socially close? Changes in non-physical intergenerational contacts at the onset of the COVID-19 pandemic among older people in France, Italy and Spain

Physical distancing is intended to mitigate the spread of the SARS-CoV-2 virus. However, the impact of a decrease in face-to-face contacts on non-physical social contacts of older people remains unclear. In particular, we focus on intergenerational contacts that are especially relevant for older people’s mental health. Our analyses rely on an online quota sampling survey conducted in France, Italy and Spain during April 14–24, 2020. We considered the subsample of individuals aged 50 + (N = 4207). We calculated post-stratification weights based on official statistics and used logistic regressions to analyze how changes in intergenerational contacts differed by socioeconomic factors and to what extent non-physical contacts (via phone, social media, etc.) have compensated the reduction in face-to-face contacts. Finally, the change in digital devices’ use has been explored as a consequence of both decreased physical intergenerational contacts (PIC) and increased non-physical intergenerational contacts (NPIC). We found that about 50% of older people have increased their NPIC during the first lockdown. Younger individuals, those with medium level of education, and those economically better off displayed higher probabilities of increased NPIC as compared to their counterparts. NPIC increased especially for individuals whose face-to-face contacts decreased, particularly so if this happened with respect to contacts with children. A large share of older people has increased their use of video calls and instant messages, while only some increased the use of social media. These findings are relevant to understand how intergenerational contacts changed during the pandemic and may be central to better plan future outbreak responses.

Eco-Environmental Aspects of COVID-19 Pandemic and Potential Control Strategies

A new coronavirus-strain from a zoonotic reservoir (probably bat)—termed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—has recently claimed more than two million deaths worldwide. Consequently, a burst of scientific reports on epidemiology, symptoms, and diagnosis came out. However, a comprehensive understanding of eco-environmental aspects that may contribute to coronavirus disease 2019 (COVID-19) spread is still missing, and we therefore aim to focus here on these aspects. In addition to human–human direct SARS-CoV-2 transmission, eco-environmental sources, such as air aerosols, different public use objects, hospital wastes, livestock/pet animals, municipal wastes, ventilation facilities, soil and groundwater potentially contribute to SARS-CoV-2 transmission. Further, high temperature and humidity were found to limit the spread of COVID-19. Although the COVID-19 pandemic led to decrease air and noise pollution during the period of lockdown, increased use of masks and gloves is threatening the environment by water and soil pollutions. COVID-19 badly impacted all the socio-economic groups in different capacities, where women, slum dwellers, and the people lacking social protections are the most vulnerable. Finally, sustainable strategies, waste management, biodiversity reclaim, eco-friendly lifestyle, improved health infrastructure and public awareness, were proposed to minimize the COVID-19 impact on our society and environment. These strategies will seemingly be equally effective against any future outbreak.