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The emergence of new SARS-CoV-2 variants and their rapid spread pose a threat to both human and animal health and may conceal unknown risks. This report describes an Italian human-to-cat outbreak of SARS-CoV-2 lineage B.1.1.7 (the Alpha variant) . On March 7th, 2021, approximately ten days after COVID-19 appeared in the family, the onset of respiratory signs in a cat by COVID-19-affected owners led to an in-depth diagnostic investigation, combining clinical and serological data with rt-qPCR-based virus detection and whole genome sequencing. The Alpha variant was confirmed first in the owners and a few days later in the cat that was then monitored weekly: the course was similar with one-week lag time in the cat. In addition, based on comparative analysis of genome sequences from our study and from 200 random Italian cases of Alpha variant, the familial cluster was confirmed. The temporal sequence along with the genomic data support a human-to-animal transmission. Such an event emphasizes the importance of studying the circulation and dynamics of SARS-CoV-2 variants in humans and animals to better understand and prevent potential spillover risks or unwarranted alerts involving our pet populations., Highlights • Respiratory signs in a household cat ten days after the appearance of COVID-19 in the family led to a thorough investigation. • The Alpha variant (B.1.1.7) was first detected in owners and one week later in the cat which showed a similar course. • A familial cluster was confirmed based on a comparative sequence analysis of the study subjects and 200 Italian random cases. • The temporal sequence together with the genomic data support human-to-animal transmission. • The human epidemic, the easy crossing of species barriers and the abundance of pets suggest monitoring for spillover risks.

Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission. This work was funded by Portuguese Foundation for Science and Technology (FCT; Research4COVID19 projects 198_596862267, 617_613735895, 186_596855206). FCT also financed the PhD grant to NP (SFRH/BD/136299/2018) and post-doc grant to VF (SFRH/BPD/114927/2016).

In 2018, a cluster of two cases of cryptococcosis occurred at the Queen Elizabeth University Hospital (QEUH) in Glasgow, Scotland (UK). It was postulated that these cases may have been linked to pigeon droppings found on the hospital site, given there have been previous reports of Cryptococcus neoformans associated with pigeon guano. Although some samples of pigeon guano taken from the site yielded culturable yeast from genera related to Cryptococcus, they have since been classified as Naganishia or Papiliotrema spp., and no isolates of C. neoformans were recovered from either the guano or subsequent widespread air sampling. In an attempt to further elucidate any possible shared source of the clinical isolates, we used whole-genome sequencing and phylogenetic analysis to examine the relationship of the two Cryptococcus isolates from the QEUH cases, along with two isolates from sporadic cases treated at a different Glasgow hospital earlier in 2018. Our work demonstrated that these four clinical isolates were not clonally related; while all isolates were from the VNI global lineage and of the same mating type (MATα), the genotypes of the two QEUH isolates were separated by 1885 base changes and belonged to different sub-lineages, recently described as the intercontinental sub-clades VNIa-93 and VNIa-5. In contrast, one of the two sporadic 2018 clinical isolates was determined to belong to the VNIb sub-lineage and the other classified as a VNIV/VNI hybrid. Our work demonstrated that the two 2018 QEUH isolates and the two prior C. neoformans clinical isolates were all genetically distinct. It was not possible to determine whether the QEUH genotypes stemmed from independent sources or from the same source, i.e. pigeons carrying different genotypes, but it should be noted that whilst members of allied genera within the Tremellomycetes were isolated from the hospital environment, there were no environmental isolations of C. neoformans.

A novel RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the ongoing outbreak of coronavirus disease 2019 (COVID-19). Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19. However, due to extensive sampling bias and existence of infection clusters during the epidemic spread, direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation. In this study, we first present robust estimator for the time to the most recent common ancestor (TMRCA) and the mutation rate, and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2. The mutation rate is inferred to be 8.69 × 10-4 per site per year with a 95% confidence interval (CI) of [8.61 × 10-4, 8.77 × 10-4], and the TMRCA of the samples inferred to be Nov 28, 2019 with a 95% CI of [Oct 20, 2019, Dec 9, 2019]. The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market. We further demonstrate that genetic polymorphism patterns, including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters, are similar to those caused by evolutionary forces such as natural selection. Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2. Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.

We report three clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19) between January and February 2020 in Shanghai, China. Investigators interviewed suspected COVID-19 cases to collect epidemiological information, including demographic characteristics, illness onset, hospital visits, close contacts, activities’ trajectories between 14 days before illness onset and isolation, and exposure histories. Respiratory specimens of suspected cases were collected and tested for SARS-CoV-2 by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assay. The interval between the onset of illness in the primary case and the last contact of the secondary case with the primary case in our report was 1 to 7 days. In Cluster 1 (five cases), illness onset in the five secondary cases was 2 to 5 days after the last contact with the primary case. In Cluster 2 (five cases) and Cluster 3 (four cases), the illness onset in secondary cases occurred prior to or on the same day as the onset in the primary cases. The study provides empirical evidence for transmission of COVID-19 during the incubation period and indicates that pre-symptomatic person-to-person transmission can occur following sufficient exposure to confirmed COVID-19 cases. The potential pre-symptomatic person-to-person transmission puts forward higher requirements for prevention and control measures.

Coronavirus disease 2019 (COVID-19) is now a pandemic. The Korean government has declared a red alert, which is the highest level of the national infectious disease alert system, and the World Health Organization has similarly declared its highest-level pandemic alert (phase 6). The spread of COVID-19 is an unprecedented worldwide public health problem that governments and individuals must work to overcome. Recently, an infection cluster arose in a call center in Seoul. To support call center companies, the Korean Ministry of Employment and Labor has proposed covering the costs of installing partitions and air purifiers, providing hand sanitizers, and supplying masks to prevent droplet and aerosol infections. Air purifiers are expected to be installed on the floor with the exhaust outlets at a higher level, such as the level of the desks or breathing zones of workers. When a worker coughs or releases droplets near a colleague's respiratory system, the droplets may spread throughout the call center via air flow from air purifier. In this fashion, a single infected person can give rise to an infection cluster. Attempts to prevent infection must not lead to new infections, and the installation of air purifiers may cause new problems. Therefore, using air purifiers to control the spread of COVID-19 should be approached with caution.

Raccoons (Procyon lotor) are a successful urban adapter species that carry numerous pathogens of public health and veterinary significance. One such pathogen is the zoonotic roundworm Baylisascaris procyonis, the larval stage of which can cause disease in >150 species of birds and mammals including humans. This thesis investigated the ecology and epidemiology of B. procyonis in Ontario. Knowing that the larval stage of the parasite can cause neurological disease in a wide variety of host species, I performed a retrospective analysis of causes of morbidity and mortality in Ontario rodents and lagomorphs to determine the impact of this parasite in the province. The most common diagnosis across all species was encephalitis consistent with neural larval migrans, and the odds of this diagnosis were significantly greater for groundhogs (Marmota monax) than other species investigated. After establishing the parasite as a common cause of mortality, I performed a literature review to identify knowledge gaps and inconsistencies regarding host and environmental risk factors associated with B. procyonis in raccoons. Using a data set of 1539 raccoons submitted to the Canadian Wildlife Health Cooperative between 2013 and 2016, I investigated the influence of host factors, human population size, and predominate human land use type on B. procyonis infection in raccoons, finding previously reported associations and several interactions between variables. I then used spatial, temporal, and spatio-temporal scan statistics to identify regions and time periods with high or low clusters of infection prevalence, identifying a spatial and space-time cluster that included a portion of the greater Toronto area. With this knowledge, I performed an additional risk factor analysis using raccoons submitted to the Canadian Wildlife Health Cooperative from Toronto examining specific environmental factors and their association with infection prevalence. Many identified relationships were non-linear or involved interactions with host factors, emphasizing the complexity of host-pathogen-environment relationships. This thesis adds to the current understanding of the ecology of B. procyonis, particularly with respect to the influence of environmental factors on infection. It also demonstrates an approach to investigating environmental factors at multiple scales which can be applied to other host pathogen systems. 2021-09