Patryk Aftanas's research while affiliated with Sunnybrook Health Sciences Centre and other places

... The detected variant has 76 residue substitutions (including 37 mutations related to non-human hosts). This study concluded potential evidence for SARS-CoV-2 evolution in white-tailed deer [250]. ...

... Previous studies have hypothesized that these deer may act as reservoirs and may play a role in driving the variation in SARS-CoV-2 strains (Du et al. 2022;Mallapaty 2022). Deer-to-human transmission of SARS-CoV-2 has been confirmed (Pickering et al. 2022), further emphasizing the need to study possible wildlife reservoirs, including WTD, to better understand the ecology of the virus. Therefore, surveillance of SARS-CoV-2 infections in WTD is a priority for proactive detection of possible reverse zoonosis, given the identification of multiple circulating lineages and detection rates as high as 40% in some studies (Chandler et al. 2021). ...

... As SARS-CoV-2 evolves, new variants of concern (VOCs) with immune escape potential and higher transmission rates have emerged 11,12 . We and others have demonstrated that sera from rst-generation vaccinated individuals retain some ability to neutralize VOCs such as Beta, Delta, and Omicron, albeit to lower levels compared to neutralization of ancestral SARS-CoV-2 [13][14][15] . Due to the rise of immune evasive SARS-CoV-2 Omicron VOC and its subvariants, updated mRNA vaccines have been authorized for use 7 . ...

... Evidence based on sequencing shows transmission to humans from mink in Europe, deer in Canada, and a cat in Thailand. (25,26,27,28) After the outbreaks of SARS-CoV-2 on mink farms in Denmark and Poland, novel variants found in mink subsequently appeared within the local human community. (25,29,30) Experimentally infected mink transmitted SARS-CoV-2 Omicron to other individuals by contact. ...

... Compared with ancestral COVID-19, the sera from individuals who received 3 doses of mRNA-1273 or BNT162b2 demonstrated lower neutralizing capacity on the Omicron variant. However, sera from individuals who infected with ancestral COVID-19 and subsequently vaccinated with 2 doses of BNT162b2 induced significantly higher neutralizing antibody titer against ancestral COVID-19 and all VOCs [224]. ...

... Although the animal reservoir of ancestral SARS-CoV-2 remains unknown, SARS-CoV-2 has close relatives in bats and an ancestral variant likely spilled over into humans via an intermediate animal host in a seafood market in Wuhan, China (Worobey et al., 2022). Although SARS-CoV-2-related coronaviruses from animals in the Wuhan market were not sampled, there have been several subsequent reports of SARS-CoV-2 transmission ('spillback') from humans to animals including in farmed mink (Oude Munnink et al., 2021) and wild white-tailed deer (Odocoileus virginianus) Kotwa et al., 2022). Consequently, transmission among potential animal reservoirs is a key feature of the past and future evolution of coronaviruses. ...

... Due to its significantly altered antigenicity, Omicron has demonstrated resistance against human antibodies generated as a result of infection with earlier variants [68,[93][94][95] as well as immunization [93][94][95][96][97][98]. This makes sense, considering that seven out of 17 SARS-CoV-2 RBD contact residues for binding ACE2 are mutated in Omicron (Fig. 2). ...

... Evidence from the available studies suggests that transmission on the DP was associated with close proximity [35] and potentially with common source exposure events [25,30]. More recent viral culture research reports significant amounts of infectious SARS-CoV-2 in the environment [45][46][47]. Although no live virus was found on cruise ships on fomites, a recent systematic review focusing on high-quality studies found that replication-competent SARS-CoV-2 was present on fomites [47]. ...

... Santarpia et al. (2020) attempted virus culture but, given the low concentrations found in collected samples, cultivation of virus was not successful. Kotwa et al. (2021) investigated viability of positive samples (Ct < 34 on PCR analysis) and found that none of the positive air samples yielded viable virus, however, viable virus was observed in 6 out of 36 surface samples cultured. Virus cultures done in samples collected at a COVID-19 University health care facility in Florida were negative (Lednicky et al., 2020a) but resulted positive the cultures done in samples collected at a hospital in Florida with viable viral concentrations between 6000 and 74,000 TCID50 m −3 (Median Tissue Culture Infectious Dose) (Lednicky et al., 2020b). ...

... In 2002, C. kroppenstedtii was first described in a retrospective case series of histologically proven granulomatous lobar mastitis in predominantly young Polynesian women, and accounted for 40% of isolates recovered from these patients [12]. Since then, C. kroppenstedtii has been reported in multiple case reports and case series associated with GM [14][15][16][17], typically in young parous women [18][19][20]. C. kroppenstedtii can be identified by whole genome sequencing, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), and 16S rRNA sequencing. MALDI-TOF MS has largely supplanted gene sequencing due to the higher cost, greater technical complexity, and prolonged turnaround time associated with gene sequencing [21,22]. ...