Comparative infectivity and pathogenesis of emerging SARS-CoV-2 variants in Syrian hamsters

Within one year after its emergence, more than 108 million people contracted SARS-CoV-2 and almost 2.4 million succumbed to COVID-19. New SARS-CoV-2 variants of concern (VoC) are emerging all over the world, with the threat of being more readily transmitted, being more virulent, or escaping naturally acquired and vaccine-induced immunity. At least three major prototypic VoC have been identified, i.e. the UK (B.1.1.7), South African (B.1.351) and Brazilian (B.1.1.28.1), variants. These are replacing formerly dominant strains and sparking new COVID-19 epidemics and new spikes in excess mortality. We studied the effect of infection with prototypic VoC from both B.1.1.7 and B.1.351 lineages in Syrian golden hamsters to assess their relative infectivity and pathogenicity in direct comparison to two basal SARS-CoV-2 strains isolated in early 2020. A very efficient infection of the lower respiratory tract of hamsters by these VoC is observed. In line with clinical evidence from patients infected with these VoC, no major differences in disease outcome were observed as compared to the original strains as was quantified by (i) histological scoring, (ii) micro-computed tomography, and (iii) analysis of the expression profiles of selected antiviral and pro-inflammatory cytokine genes. Noteworthy however, in hamsters infected with VoC B.1.1.7, a particularly strong elevation of proinflammatory cytokines was detected. Overall, we established relevant preclinical infection models that will be pivotal to assess the efficacy of current and future vaccine(s) (candidates) as well as therapeutics (small molecules and antibodies) against two important SARS-CoV-2 VoC.

Spatial interference between infectious hotspots: epidemic condensation and optimal windspeed

We discuss the effects of spatial interference between two infectious hotspots as a function of the mobility of individuals (wind speed) between the two and their relative degree of infectivity. As long as the upstream hotspot is less contagious than the downstream one, increasing the wind speed leads to a monotonic decrease of the infection peak in the downstream hotspot. Once the upstream hotspot becomes about between twice and five times more infectious than the downstream one, an optimal wind speed emerges, whereby a local minimum peak intensity is attained in the downstream hotspot, along with a local maximum beyond which the beneficial effect of the wind is restored. Since this nonmonotonic trend is reminiscent of the equation of state of nonideal fluids, we dub the above phenomena “epidemic condensation”. When the relative infectivity of the upstream hotspot exceeds about a factor five, the beneficial effect of the wind above the optimal speed is completely lost: any wind speed above the optimal one leads to a higher infection peak. It is also found that spatial correlation between the two hotspots decay much more slowly than their inverse distance. It is hoped that the above findings may offer a qualitative clue for optimal confinement policies between different cities and urban agglomerates.

Epidemiological parameters of COVID-19 and its implication for infectivity among patients in China, 1 January to 11 February 2020

Background The natural history of disease in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained obscure during the early pandemic. Aim Our objective was to estimate epidemiological parameters of coronavirus disease (COVID-19) and assess the relative infectivity of the incubation period. Methods We estimated the distributions of four epidemiological parameters of SARS-CoV-2 transmission using a large database of COVID-19 cases and potential transmission pairs of cases, and assessed their heterogeneity by demographics, epidemic phase and geographical region. We further calculated the time of peak infectivity and quantified the proportion of secondary infections during the incubation period. Results The median incubation period was 7.2 (95% confidence interval (CI): 6.9‒7.5) days. The median serial and generation intervals were similar, 4.7 (95% CI: 4.2‒5.3) and 4.6 (95% CI: 4.2‒5.1) days, respectively. Paediatric cases < 18 years had a longer incubation period than adult age groups (p = 0.007). The median incubation period increased from 4.4 days before 25 January to 11.5 days after 31 January (p < 0.001), whereas the median serial (generation) interval contracted from 5.9 (4.8) days before 25 January to 3.4 (3.7) days after. The median time from symptom onset to discharge was also shortened from 18.3 before 22 January to 14.1 days after. Peak infectivity occurred 1 day before symptom onset on average, and the incubation period accounted for 70% of transmission. Conclusion The high infectivity during the incubation period led to short generation and serial intervals, necessitating aggressive control measures such as early case finding and quarantine of close contacts.

The role of symptomatic presentation in influenza A transmission risk

SUMMARYComputer models can be useful in planning interventions against novel strains of influenza. However such models sometimes make unsubstantiated assumptions about the relative infectivity of asymptomatic and symptomatic cases, or conversely assume there is no impact at all. Using household-level data from known-index studies of virologically confirmed influenza A infection, the relationship between an individual's infectiousness and their symptoms was quantified using a discrete-generation transmission model and Bayesian Markov chain Monte Carlo methods. It was found that the presence of particular respiratory symptoms in an index case does not influence transmission probabilities, with the exception of child-to-child transmission where the donor has phlegm or a phlegmy cough.

Infectivity and reproduction of Scutellonema bradys on weeds and cultivated plant species

The nematode Scutellonema bradys is the main phytosanitary problem of yam (Dioscorea rotundata) in the Brazilian State of Bahia. Little is known about the host range of this nematode in Brazil, especially on weeds and plant species cultivated together with yam. This study aimed at evaluating different plant species to determine their host status to S. bradys and to study the relative infectivity of different stages of the nematode on selected host plants. Among the 48 evaluated plant species, 12 were infected by S. bradys. Yam was considered to be the only good host of the nematode, while Luffa algyptiaca, Momordica charantia, Heliotropium indicum, Vigna unguiculata, Cucurbita pepo, Abelmoschus esculentus, Sicana odorifera, Solanum lycopersicum and Ipomoea batatas were classified as bad hosts because of the relatively low reproduction factor as compared to yam. Crotalaria juncea and Cajanus cajan behaved as trap plants because large numbers of S. bradys penetrated their roots but populations decreased over time. Our results showed that juveniles are more infective than females and these are more infective than males on roots of five host plants. We also demonstrated that S. bradys prefers certain host plants as inferred by their lower reproduction on roots of these hosts. Penetration of juveniles tended to be spread over 16 days after inoculation, whereas for adults it was more concentrated at 8 days after inoculation. These results may be important to plan crop rotation schemes to control the yam nematode.

Interactions among co-infecting parasite species: a mechanism maintaining genetic variation in parasites?

Individuals of free-living organisms are often infected simultaneously by a community of parasites. If the co-infecting parasites interact, then this can add significantly to the diversity of host genotype×parasite genotype interactions. However, interactions between parasite species are usually not examined considering potential variation in interactions between different strain combinations of co-infecting parasites. Here, we examined the importance of interactions between strains of fish eye flukes Diplostomum spathaceum and Diplostomum gasterostei on their infectivity in naive fish hosts. We assessed the infection success of strains of both species in single-strain exposures and in co-exposures with a random strain of the other species. Parasite infection success did not consistently increase or decrease in the co-exposure treatment, but depended on the combinations of co-infecting parasite strains. This disrupted the relative infectivity of D. spathaceum strains observed in single-strain exposures. The infection success of D. gasterostei strains was independent of exposure type. These results suggest that interactions among parasite species may be strain specific and potentially promote maintenance of genetic polymorphism in parasite populations.

Investigation of the relative infectivity and pathogenicity of different hepatitis C virus genotypes in hemophiliacs

To assess the relative infectivity and pathogenicity of variants of hepatitis C virus (HCV) genotypes, the distribution of genotypes in hemophilic patients who had been treated with nonvirally inactivated factor concentrates or cryoprecipitates prepared from local blood donors was compared with those found in the respective blood donor populations. Genotype frequencies differed markedly in the four countries investigated (Scotland, Hungary, South Africa, and Thailand) but in each, the HCV genotype distributions in hemophiliacs and blood donors were similar. In addition, HCV genotypes in recipients of commercially manufactured concentrates were similar to those found in the US general population. These findings provide no evidence that HCV genotypes differ significantly from each other in replication rate, transmissibility, or infectivity.