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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases of virus transmission between cats and humans. The objective of this study was to assess the prevalence of SARS-CoV-2 variant infection of cats in an urban setting. We investigated the prevalence of SARS-CoV-2 variant infections in domestic and community cats in the city of Pittsburgh ( n = 272). While no cats tested positive for SARS-CoV-2 viral RNA, 35 cats (12.86%) tested SARS-CoV-2-antibody-positive. Further, we compared a cat-specific experimental lateral flow assay (eLFA) and species-agnostic surrogate virus neutralization assay (sVNT) for SARS-CoV-2 antibody detection in cats ( n = 71). The eLFA demonstrated 100% specificity compared to sVNT. The eLFA also showed 100% sensitivity for sera with >90% inhibition and 63.63% sensitivity for sera with 40-89% inhibition in sVNT. Using a variant-specific pseudovirus neutralization assay (pVNT) and antigen cartography, we found the presence of antibodies to pre-Omicron and Omicron SARS-CoV-2 variants. Hence, this approach proves valuable in identifying cat exposure to different SARS-CoV-2 variants. Our results highlight the continued exposure of cats to SARS-CoV-2 and warrant coordinated surveillance efforts.

The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single-amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single- and multiple-amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Millions of individuals who have recovered from SARS-CoV-2 infection may be eligible to participate in convalescent plasma donor programs, yet the optimal window for donating high neutralizing titer convalescent plasma for COVID-19 immunotherapy remains unknown. Here we studied the response trajectories of antibodies directed to the SARS-CoV-2 surface spike glycoprotein and in vitro SARS-CoV-2 live virus neutralizing titers (VN) in 175 convalescent donors longitudinally sampled for up to 142 days post onset of symptoms (DPO). We observed robust IgM, IgG, and viral neutralization responses to SARS-CoV-2 that persist, in the aggregate, for at least 100 DPO. However, there is a notable decline in VN titers ≥160 for convalescent plasma therapy, starting 60 DPO. The results also show that individuals 30 years of age or younger have significantly lower VN, IgG and IgM antibody titers than those in the older age groups; and individuals with greater disease severity also have significantly higher IgM and IgG antibody titers. Taken together, these findings define the optimal window for donating convalescent plasma useful for immunotherapy of COVID-19 patients and reveal important predictors of an ideal plasma donor.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), believed to have originated from a bat species, can infect a wide range of non-human hosts. Bats are known to harbor hundreds of coronaviruses capable of spillover into human populations. Recent studies have shown a significant variation in the susceptibility among bat species to SARS-CoV-2 infection. We show that little brown bats (LBB) express angiotensin-converting enzyme 2 receptor and the transmembrane serine protease 2, which are accessible to and support SARS-CoV-2 binding. All-atom molecular dynamics (MD) simulations revealed that LBB ACE2 formed strong electrostatic interactions with the RBD similar to human and cat ACE2 proteins. In summary, LBBs, a widely distributed North American bat species, could be at risk of SARS-CoV-2 infection and potentially serve as a natural reservoir. Finally, our framework, combining in vitro and in silico methods, is a useful tool to assess the SARS-CoV-2 susceptibility of bats and other animal species. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, the causative agent of the COVID-19 pandemic, can infect a wide range of mammals. Since its spread in humans, secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. Understanding the extent of adaptation to these animal hosts is critical for assessing the threat that the spillback of animal-adapted SARS-CoV-2 into humans poses. We compare the genomic landscapes of SARS-CoV-2 isolated from animal species to that in humans, profiling the mutational biases indicative of potentially different selective pressures in animals. We focus on viral genomes isolated from mink (Neovison vison) and white-tailed deer (Odocoileus virginianus) for which multiple independent outbreaks driven by onward animal-to-animal transmission have been reported. We identify five candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V), and one in deer (NSP3a_L1035F), though they appear to confer a minimal advantage for human-to-human transmission. No considerable changes to the mutation rate or evolutionary trajectory of SARS-CoV-2 has resulted from circulation in mink and deer thus far. Our findings suggest that minimal adaptation was required for onward transmission in mink and deer following human-to-animal spillover, highlighting the 'generalist' nature of SARS-CoV-2 as a mammalian pathogen. Here, Tan et al. find that the rapid spread of SARS-CoV-2 in mink and deer required minimal adaptation, has only caused moderate changes to the evolutionary trajectory of the virus, and has not led to viral mutations that greatly improve human transmission thus far. [ABSTRACT FROM AUTHOR]

Background and Objectives: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), besides causing human infection, has been shown to naturally infect several susceptible animal species including large cats (tigers, lions, pumas, spotted leopards), dogs, cats, ferrets, gorillas and minks. Cats and minks are continuing to be the most reported species with SARS‐CoV‐2 infections among animals but it needs to be investigated further. Methods and Results: We report the detection of SARS‐CoV‐2 from a domestic cat that exhibited respiratory disease after being exposed to SARS‐CoV‐2 virus from humans in the same household. SARS‐CoV‐2 RNA was detected in two oropharyngeal swabs collected at two time points, 11 days apart; the first, when the cat was reported to be sick and the second, before euthanasia due to poor prognosis. The viral nucleic acid detected at two time points showed no genomic variation and resembled the clade GH circulating in humans in the United States. Clinical and pathological findings noted in this 16‐year‐old cat were consistent with respiratory and cardiac insufficiency. Conclusions: SARS‐CoV‐2 viral infection was likely an incidental clinical finding, as the virus was not detected in fixed lungs, heart, or kidney tissues. Only fresh lung tissue collected at necropsy showed the presence of viral nucleic acid, albeit at a very low level. Further research is needed to clarify the clinical course of SARS‐CoV‐2 in companion animals of advanced age and underlying cardiac disease. [ABSTRACT FROM AUTHOR]

The article presents a study that explores how lyophilized, thermostable Spike or receptor-binding domain immunogenic liposomes induce protective immunity against SARS-CoV-2 in mice. It mentions about the assessment of low-dose immunization with lyophilized nanoparticles decorated with recombinant SARS-CoV-2 antigens.

Ultraviolet germicidal irradiation (UVGI) is a highly effective means of inactivating many bacteria, viruses, and fungi. UVGI is an attractive viral mitigation strategy against coronaviruses, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the coronavirus disease-2019 (COVID-19) pandemic. This investigation measures the susceptibility of two human coronaviruses to inactivation by 254 nm UV-C radiation. Human coronavirus NL63 and SARS-CoV-2 were irradiated in a collimated, dual-beam, aqueous UV reactor. By measuring fluence and integrating it in real-time, this reactor accounts for the lamp output transients during UVGI exposures. The inactivation rate constants of a one-stage exponential decay model were determined to be 2.050 cm2/mJ and 2.098 cm2/mJ for the NL63 and SARS-CoV-2 viruses, respectively. The inactivation rate constant for SARS-CoV-2 is within 2% of that of NL63, indicating that in identical inactivation environments, very similar UV 254 nm deactivation susceptibilities for these two coronaviruses would be achieved. Given the inactivation rate constant obtained in this study, doses of 1.1 mJ/cm2, 2.2 mJ/cm2, and 3.3 mJ/cm2 would result in a 90%, 99%, and 99.9% inactivation of the SARS-CoV-2 virus, respectively. The inactivation rate constant obtained in this study is significantly higher than values reported from many 254 nm studies, which suggests greater UV susceptibility to the UV-C than what was believed. Overall, results from this study indicate that 254 nm UV-C is effective for inactivation of human coronaviruses, including SARS-CoV-2. • 254 nm UV-C effectively inactivates human coronaviruses, including SARS-CoV-2. • Inactivation rate constants for SARS-CoV-2 and NL63 are identical. • NL63 can be used as a suitable surrogate for SARS-CoV-2 for inactivation studies. • 254 nm UV-C could be effective against a broad range of coronaviruses. [ABSTRACT FROM AUTHOR]

The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2. • Validated two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes of SARS-CoV-2 and demonstrated the assay specificity against other common human coronavirus RNA targets. • Demonstrated the capability of the positive/negative classification using the RT-LAMP amplicon event rate electronically counted by the glass nanopore sensors. • With 127 clinical nasopharyngeal samples, the RT-LAMP coupled nanopore digital counting platform could detect SARS-CoV-2 with 98% diagnostic sensitivity and 92% diagnostic specificity. • With further miniaturization of the device, the platform could provide a rapid, sensitive, and specific point-of-care testing of SARS-CoV-2. [ABSTRACT FROM AUTHOR]