Rapid longitudinal SARS-CoV-2 intra-host emergence of novel haplotypes regardless of immune deficiencies

On February 2020, the municipality of Vo’, a small town near Padua (Italy), was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. The entire population was swab tested in two sequential surveys. Here we report the analysis of the viral genomes, which revealed that the unique ancestor haplotype introduced in Vo’ belongs to lineage B and, more specifically, to the subtype found at the end of January 2020 in two Chinese tourists visiting Rome and other Italian cities, carrying mutations G11083T and G26144T. The sequences, obtained for 87 samples, allowed us to investigate viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo’. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptoms severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype, carried by an index case. The lockdown extinguished both viral spread and the emergence of new variants, confirming the efficiency of this containment strategy. The information gathered from household was used to reconstructs possible transmission events.

Change in Pediatric Health Care Spending and Drug Utilization during the COVID-19 Pandemic

Objective: To evaluate how the restrictive measures implemented during the SARS-CoV-2 pandemic have influenced the incidence of the most common children’s diseases and the consumption of medications in 2020 compared to 2019. Methods: We involved all family pediatricians of the local health authority of Latina, from which we requested data of monthly visits in 2019 and 2020 for six common diseases disseminated through droplets and contact, and the territorial and integrative pharmaceutical unit of the area, from which we requested data of the net expenditure regarding the most commonly used drugs at pediatric age. Results: There was significant reduction in the incidence of the evaluated diseases and in the consumption of investigated drugs between 2019 and 2020 in the months when the restrictive measures were in place, with an attenuation of this effect during the months of the gradual loosening of those measures. Conclusion: Nonpharmaceutical intervention measures have caused changes in the diffusion of common pediatric diseases. We believe that the implementation of a reasonable containment strategy, even outside of the pandemic, could positively influence the epidemiology of infectious and allergic diseases in children, and healthcare system spending.

Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction

When a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading lineages, as was the case for the Danish Cluster-5 mink variant (belonging to the B.1.1.298 lineage), the British B.1.1.7 lineage, and the South African B.1.351 lineage of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.

Slow pace of vaccinations drives Australia lockdowns

Significance The rapid spread of the Delta variant has exposed serious shortcomings in Australia’s containment strategy, which has been forced to rely on economically disruptive lockdowns because of the slow pace of vaccinations. Impacts The economy is expected to contract by 0.7% in the current quarter if lockdowns are prolonged. Confused pandemic policies have eroded trust in government, with a federal election due within nine months. Public support for vaccination is climbing but still lags in the 18-29 age group.

Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction

When a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading sub- types, as was the case for the Danish Cluster-5 mink, the British B.1.1.7, and the South African 501Y.V2 variants of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.