Infection of SARS-CoV-2 in domestic dogs associated with owner viral load.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive pet owners are reported to be a risk factor for infection of their pets; however, the influence of the viral load and associated risks has not been fully established. This study aimed to assess potential association of viral load in owners with the presence of SARS-CoV-2 infection in their dogs. Of 20 SARS-CoV-2-positive pet owners from 13 families in Curitiba, Brazil, 5 of 22 (22.7%) dogs were positive for SARS-CoV-2. Viral presence was detected in oropharyngeal samples for 2 of 5 (40.0%) dogs at 8 and 9 days after the first positive sample. Detection of SARS-CoV-2 in these dogs was associated with higher viral loads in the owners and close owner contact. All 5 RT-qPCR-positive dogs had antibodies to at least one viral protein tested in the serological assay. Molecular detection of SARS-CoV-2 in dogs was statistically associated with clinical signs in owners such as cold, cough, or diarrhea (P = 0.039), number of positive persons in the household (P = 0.002), and higher viral load (P = 0.039). Such findings serve as a warning for risks of human to dog infection, mainly due to sharing beds and other close interactions without protection. In conclusion, people with coronavirus disease 2019 (COVID-19), particularly in households with multiple residents and high viral load, should take the same preventive measures when interacting with their dogs during self-isolation as they do with people.

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

ACE2 polymorphisms as potential players in COVID-19 outcome.

The clinical condition COVID-19, caused by SARS-CoV-2, was declared a pandemic by the WHO in March 2020. Currently, there are more than 5 million cases worldwide, and the pandemic has increased exponentially in many countries, with different incidences and death rates among regions/ethnicities and, intriguingly, between sexes. In addition to the many factors that can influence these discrepancies, we suggest a biological aspect, the genetic variation at the viral S protein receptor in human cells, ACE2 (angiotensin I-converting enzyme 2), which may contribute to the worse clinical outcome in males and in some regions worldwide. We performed exomics analysis in native and admixed South American populations, and we also conducted in silico genomics databank investigations in populations from other continents. Interestingly, at least ten polymorphisms in coding, noncoding and regulatory sites were found that can shed light on this issue and offer a plausible biological explanation for these epidemiological differences. In conclusion, there are ACE2 polymorphisms that could influence epidemiological discrepancies observed among ancestry and, moreover, between sexes.

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021.

Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

Bombali Ebolavirus in Mops condylurus Bats (Molossidae), Mozambique.

We detected Bombali ebolavirus RNA in 3 free-tailed bats (Mops condylurus, Molossidae) in Mozambique. Sequencing of the large protein gene revealed 98% identity with viruses previously detected in Sierra Leone, Kenya, and Guinea. Our findings further support the suspected role of Mops condylurus bats in maintaining Bombali ebolavirus.

First reported cases of SARS-CoV-2 infection in pets in São Paulo, Brazil.

Background and Aim: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the global coronavirus pandemic (COVID-19) in humans in 2019. Although SARS-CoV-2 infection is primarily asymptomatic and transitory in companion animals, the role of these animals in the life cycle of the virus remains unclear. This study aimed to survey the first SARS-CoV-2 infection cases in pets, including a dog and three cats in São Paulo, Brazil. Materials and Methods: We invited COVID-19-positive pet owners to participate in the survey and obtained nasal, oropharyngeal, and rectal swab samples from their pets. These samples were placed in vials and subjected to a real-time quantitative polymerase chain reaction. In addition, the owners answered an epidemiological questionnaire, and the pets underwent clinical examination and monitoring. Results: Out of 49 sampled pets, 3/19 (15.8%) cats and 1/30 (3.3%) dogs tested positive, with wide variations in viral loads. Despite the limitations of size and non-randomized sampling, our results showed that cats are more susceptible than dogs to SARS-CoV-2 infection, presenting a cat: dog ratio of 4.8: 1. Only one cat presented mild and transitory respiratory symptoms. Conclusion: Although SARS-CoV-2 infection was detected in pets in the largest South American city and the COVID-19 epicenter at the time, these first detected pet cases displayed either none or mild clinical signs.

The Genomic Profile Associated with Risk of Severe Forms of COVID-19 in Amazonian Native American Populations.

Genetic factors associated with COVID-19 disease outcomes are poorly understood. This study aimed to associate genetic variants in the SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, and ABO genes with the risk of severe forms of COVID-19 in Amazonian Native Americans, and to compare the frequencies with continental populations. The study population was composed of 64 Amerindians from the Amazon region of northern Brazil. The difference in frequencies between the populations was analyzed using Fisher's exact test, and the results were significant when p ≤ 0.05. We investigated 64 polymorphisms in 7 genes; we studied 47 genetic variants that were new or had impact predictions of high, moderate, or modifier. We identified 15 polymorphisms with moderate impact prediction in 4 genes (ABO, CXCR6, FYCO1, and SLC6A20). Among the variants analyzed, 18 showed significant differences in allele frequency in the NAM population when compared to others. We reported two new genetic variants with modifier impact in the Amazonian population that could be studied to validate the possible associations with COVID-19 outcomes. The genomic profile of Amazonian Native Americans may be associated with protection from severe forms of COVID-19. This work provides genomic data that may help forthcoming studies to improve COVID-19 outcomes.

Persistent SARS-CoV-2 antigen presence in multiple organs of a naturally infected cat from Brazil.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the disease coronavirus 2019 (COVID-19) in humans. SARS-CoV-2 has been identified in cats with or without clinical signs. Case presentation: We describe the pathological and molecular findings in a six-month-old asymptomatic cat with SARS-CoV-2 infection from Brazil, belonging to a human family with COVID-19 cases. The pool of nasopharynx and oropharynx swabs at day zero tested positive by RT-qPCR for SARS-CoV-2. No amplification resulted from molecular testing performed on days 7 and 14. The cat was hit by a car and died 43 days after the molecular diagnosis. Immunohistochemistry at post-mortem examination demonstrated nucleocapsid protein in samples from the lungs, kidneys, nasal conchae, trachea, intestine, brain and spleen. Conclusion: The present study has highlighted the possibility that viral antigens can be detected by immunohistochemistry in multiple organs six weeks after infection, although the same tissues tested negative by RT-PCR.

Investigation of astrovirus, coronavirus and paramyxovirus co-infections in bats in the western Indian Ocean.

Co-infections have a key role in virus transmission in wild reservoir hosts. We investigated the simultaneous presence of astroviruses, coronaviruses, and paramyxoviruses in bats from Madagascar, Mayotte, Mozambique, and Reunion Island. A total of 871 samples from 28 bat species representing 8 families were tested by polymerase chain reactions (PCRs) targeting the RNA-dependent RNA-polymerase genes. Overall, 2.4% of bats tested positive for the presence of at least two viruses, only on Madagascar and in Mozambique. Significant variation in the proportion of co-infections was detected among bat species, and some combinations of co-infection were more common than others. Our findings support that co-infections of the three targeted viruses occur in bats in the western Indian Ocean region, although further studies are needed to assess their epidemiological consequences.

First report of severe acute respiratory syndrome coronavirus 2 detection in two asymptomatic cats in the state of Pernambuco, Northeastern Brazil.

BACKGROUND AND AIM: Despite worldwide case reports, including Brazilian cases, no frequency study on infection of pets by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been conducted to date in Brazil. Accordingly, the present study was aimed to assess dogs and cats belonging to positive owners in Recife, Northeastern Brazil. MATERIALS AND METHODS: This was a longitudinal prospective study on dogs and cats in the city of Recife whose owners were in isolation at home due to a confirmed laboratory diagnosis of SARS-CoV-2 through reverse-transcriptase polymerase chain reaction (RT-qPCR). Oral and rectal swabs from the pets were tested for the presence of SARS-CoV-2-specific RNA by means of RT-qPCR. RESULTS: Among the pets tested, 0/16 dogs and 2/15 cats were positive for SARS-CoV-2. Interestingly, the two positive cats were owned by two unrelated asymptomatic veterinary students, which, therefore, post a warning to veterinarians worldwide. CONCLUSION: The findings herein indicate that cats may act as sentinels for human cases, particularly sharing households with asymptomatic human cases. Although with small sampling and convenient recruiting, the presence of infected cats by SARS-CoV-2 was most likely due to close cat-human contact with positive owners, posting a human-animal health threat when pets share the same bed and interact with owners without protection, particularly during owner self-isolation. Thus, infected owners should follow the same human preventive guidelines with their pets to avoid spreading infection.

High SARS-CoV-2 seroprevalence in persons experiencing homelessness and shelter workers from a day-shelter in São Paulo, Brazil.

Brazil presents one of the highest COVID-19 death tolls in the world. The initial SARS-CoV-2 epicenter was São Paulo city. As of 2019, the homeless population of São Paulo city was estimated at 24,344 individuals, the largest national homeless population. The present study aimed to concomitantly assess the molecular and serological prevalence and associated risk factors of SARS-CoV-2 infection in a homeless population and related shelter workers from a day-shelter. Serum samples, nasopharyngeal and oropharyngeal swabs of persons who are homeless and shelter workers collected from August 25th to 27th, 2020 were tested for the presence of anti-SARS-CoV-2 IgM and IgG antibodies by ELISA and SARS-CoV-2 RNA by RT-qPCR, respectively. All swab samples tested negative by RT-qPCR. Seropositivity of IgM and IgG was 5/203 (2.5%) and 111/203 (54.7%) in persons who are homeless, and 5/87 (5.7%) and 41/87 (47.1%) in shelter workers, respectively, with no statistical differences between groups. The high seroprevalence found herein indicates early environmental and urban spreading of SARS-CoV-2, associated with sociodemographic and economic vulnerability.

Natural Infection by SARS-CoV-2 in Companion Animals: A Review of Case Reports and Current Evidence of Their Role in the Epidemiology of COVID-19.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), is the causative infectious agent of the current pandemic. As researchers and health professionals are still learning the capabilities of this virus, public health concerns arise regarding the zoonotic potential of SARS-CoV-2. With millions of people detected with SARS-CoV-2 worldwide, reports of companion animals possibly infected with the virus started to emerge. Therefore, our aim is to review reported cases of animals naturally infected with SARS-CoV-2, particularly companion pets, shedding light on the role of these animals in the epidemiology of COVID-19.

Bat coronavirus phylogeography in the Western Indian Ocean.

Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and ß-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.