The future of SARS-CoV-2 in animals: what will be the role of animals in COVID-19 epidemiology? (preprint)

Animals are common hosts for many coronaviruses where bats and rodents are commonly regarded as primary reservoirs. The unquestionable emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a yet unknown animal host - in addition with reports of further anthropogenic spread and sustained transmission in mustelids, captive felids, and domestic dogs and cats owned by people previously tested as SARS-CoV-2-positive, rise some concerns about possible continuous maintenance of the virus in nature and domestic species. In this review, we discussed the current data about coronaviruses in domestic and farming animals, recombination events, animal species susceptibility, virus-cell receptor interactions, and clinical signs of most relevant Coronaviridae members of each genera. Also, we present what is known about SARS-CoV-2 in animals and what will be the potential role of those species in COVID-19 epidemiology. Apparently, the virus can infect pets on some occasions, where cats look to be more susceptible than dogs. Thus, pet infection by sick owners is not only likely but expected given the numerous opportunities for spill-over during a massive outbreak. Regarded to farm animals, attention should be focused on breeding species of the Mustelidae family since they are those that have been shown to be more susceptible in experimental infections and have also effectively exhibited animal-to-human transmission. Other intensively bred species such as poultry, swine, horses and ruminants seem to present little or no epidemiological risk so far. The continuous monitoring of SARS-CoV-2 in animals in close contact with people with COVID-19 may be a key in the understanding of this emergent disease and the animal’s role in epidemiology in the future. It is possible that some species will serve as important reservoirs and source of infection of COVID-19 for humans making it re-emergent in the future, as is theoretically proposed for the origin of SARS-CoV-2.

Global disparities in SARS-CoV-2 genomic surveillance (preprint)

Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness. One-Sentence SummarySocioeconomic inequalities impacted the SARS-CoV-2 genomic surveillance, and undermined the global pandemic preparedness.

Levels of SARS-CoV-2 Lineage P.1 Neutralization by Antibodies Elicited after Natural Infection and Vaccination (preprint)

Background: A new SARS-CoV-2 lineage, named P.1 (20J/501Y.V3), has recently been detected in Brazil. Mutations accrued by the P.1 lineage include amino acid changes in the receptor-binding domain of the spike protein that also are reported in variants of concern in the United Kingdom (B.1.1.7) and South Africa (B.1.325).Methods: We isolated two P.1-containing specimens from nasopharyngeal and bronchoalveolar lavage samples of patients of Manaus, Brazil. We measured neutralization of the P.1 virus after incubation with the plasma of 19 COVID-19 convalescent blood donors and recipients of the chemically-inactivated CoronaVac vaccine and compared these results to neutralization of a SARS-CoV-2 B-lineage previously circulating in Brazil.Findings: The immune plasma of COVID-19 convalescent blood donors had 6-fold less neutralizing capacity against the P.1 than against the B-lineage. Moreover, five months after booster immunization with CoronaVac, plasma from vaccinated individuals failed to efficiently neutralize P.1 lineage isolates.Interpretation: These data indicate that the P.1 lineage may escape from neutralizing antibodies generated in response to polyclonal stimulation against previously circulating variants of SARS-CoV-2.Funding: São Paulo Research Foundation, MCTI/FINEP, Medical Research Council, National Council for Scientific and Technological Development, National Institutes of Health.Conflict of Interest: M.S.D. is a consultant for Inbios, Vir Biotechnology, NGMBiopharmaceuticals, and Carnival Corporation, and on the Scientific Advisory Boards of Moderna and Immunome. The Diamond laboratory has received funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions.Ethical Approval: All procedures followed the ethical standards of the responsible committee on humanexperimentation and approved by the ethics committees from the University of Campinas, Brazil (Approval number CONEP 4.021.484 for plasma collection of blood donors, CAEE32078620.4.0000.5404 and 30227920.9.0000.5404 for the sampling of vaccinated and viral genome sequencing, respectively). All patient data were anonymized before study inclusion.Informed consent was obtained from all subjects for being included in the study.