key: cord-0731404-gbskrqtm
authors: Sánchez-Morales, Lidia; Sánchez-Vizcaíno, José M.; Pérez-Sancho, Marta; Domínguez, Lucas; Barroso-Arévalo, Sandra
title: The Omicron (B.1.1.529) SARS-CoV-2 variant of concern also affects companion animals
date: 2022-04-13
journal: bioRxiv
DOI: 10.1101/2022.04.13.488132
sha: 5ddb7460f2524aa5400a9d08383d0a3cee9c24ad
doc_id: 731404
cord_uid: gbskrqtm

The recent emergence of the Omicron variant (B.1.1.529) has brought with it a large increase in the incidence of SARS-CoV-2 disease worldwide. However, there is hardly any data on the incidence of this new variant in companion animals. In this study, we have detected the presence of this new variant in domestic animals such as dogs and cats living with owners with COVID19 in Spain that have been sampled at the most optimal time for the detection of the disease. None of the RT-qPCR positive animals (10.13%) presented any clinical signs and the viral loads detected were very low. In addition, the shedding of viral RNA lasted a short period of time in the positive animals. Infection with the Omicron variant of concern (VOC) was confirmed by a specific RT-qPCR for the detection of this variant and by sequencing. These outcomes suggest a lower virulence of this variant in infected cats and dogs. This study demonstrates the transmission of this new variant from infected humans to domestic animals and highlights the importance of doing active surveillance as well as genomic research to detect the presence of VOCs or mutations associated with animal hosts.

The pandemic associated with the COronaVIrus Disease 2019 , produced by the 23 SARS-CoV-2 virus, has been active for almost two years now. From the beginning, 406 24 million cases have been confirmed in the world, with 6.09 million deaths according to the last 25 World Health Organization (WHO) report (World Health Organisation, 2022) . 26 The SARS-CoV-2 is an RNA virus whose organization is shared with other Beta 27 coronaviruses. The genome of this virus consists of 13 opening reading frames (ORFs) and 28 15 non-structural proteins (NSP). The ORFs, from 5' to 3', codify for replicase 29 (ORF1a/ORF1b), spike (S) protein, envelope (E) protein, membrane (M) protein, and 30 nucleocapsid (N) protein (Hu, Guo et al. 2021 , Raj 2020 Viralzone, 2022) . Due to these 31 genomic characteristics, this coronavirus has been suffering a great number of mutations, 32 mainly in the spike protein, which may have influenced the virus transmission rate, the protein have been related to increased viral antibody neutralization evasion capacity or higher 47 affinity between the spike/ACE receptor binding (Zou, Xia et al. 2021) , facilitating the virus 48 entry into the cell. Thus, this constellation of mutations appears to have influenced virus 49 transmissibility, severity, and immune evasion (CDC 2021 , He, Hong et al. 2021 , Araf, Akter 50 et al. 2022 ). These mutations have led to greater contagiousness than the previous variants as 51 well as different clinical signs, which consist of slight fever, myalgia, fatigue, and shortness 52 of breath. However, the most dangerous characteristic of this variant is its high rate of 53 immune escape even in previously immunized by natural infection and vaccinated people 54 (Meo, Meo et al. 2021) . Because of these characteristics, the Omicron variant has gained 55 great concern in public health worldwide. 56 In Spain, according to data published by the Ministry of Health, the cumulative incidence of 57 Shortly after the SARS-CoV-2 virus entered our lives, field studies on the incidence in 70 animals, as well as experimental studies, began to be carried out to learn about their role in 71 this new disease (Shi, Wen et al. 2020 (Suzuki, Yamasoba et al. 2022) . The conclusions 78 obtained by these studies were that, unlike other VOCs, Omicron is not able to efficiently 79 replicate in the lower respiratory tract of Syrian hamsters, which results in the detection of 80 lower viral loads and fewer pathology findings in the lungs of the experimentally infected 81 animals comparing with infection by other isolates (Abdelnabi, Foo et al. 2022 ). In addition, Platinum One-Step qRT-PCR kit (Invitrogen) according to the protocol described in (Sibai, 138 Wang et al. 2022).

Positive samples for RT-qPCR were subjected to attempts of viral isolation using the 140 previously described methods in (Gortázar, Barroso-Arévalo et al. 2021 ).

Whole-genome sequences were obtained from the two positive oropharyngeal swabs samples 143 with the higher viral loads based on Ct values (Ct of 32.45 and 30.01) by both "Diagnosis" 144 and "Omicron" RT-qPCRs, following the protocol described by (Paden, 2020) . Sequence 145 analysis was performed using the Sequencing Analysis software v.5.3.1(Applied 146 Biosystems), while SeqScape v.2.5 software (Applied Biosystems) was used for sequence 147 assembly using the SARS-CoV-2 isolate Wuhan-Hu-1, complete genome (GenBank 148 accession number: NC_045512) as a reference genome.

Phylogenetic analysis was performed using MEGA X software (Tamura, 1992) . Four 150 sequences were obtained from this study (Dog_ 8, Cat_19, Owner_1, and Owner_2, which 151 correspond with one dog, one cat, the dog's owner, and the owner of Cat_26, 27, and 28.

Unfortunately, no positive sample for sequencing was available from the owner of Cat_19. In 153 the case of cats 26, 27, and 28, sequencing was not possible because of the low RNA loads of 154 the positive samples (Table 1) .

A total of 31 additional representative sequences were used for the analysis, including 156 sequences from cats and dogs, the reference genome from Wuhan, as well as variants of The SARS-CoV-2 B.1.529 (Omicron) variant, the last VOC detected, is nowadays highly 233 extended around the world. Concretely in Spain, epidemiological data from the Omicron-234 associated wave has evidenced that the transmission rate of this variant is quite superior to 235 other variants such as Beta or Delta. This fact has promoted the rapid spread of this variant, 236 being dominant since November 2021 (He, Hong et al. 2021) . One concern about this new 237 variant is its potential transmission to other species, in which it could evolve and acquire new 238 mutations that may be involved in higher virulence, among other fears. For this reason, it is 239 necessary to evaluate its capability to infect susceptible species. In this sense, pets such as 240 cats and dogs should be a major focus due to their close contact with humans.

In this study, we evidenced the detection of the Omicron SARS-CoV-2 variant in companion 242 animals, demonstrating that pets are susceptible to the infection with this strain. However, 243 according to the outcomes obtained by this work, there was a relatively low number of involved an active sampling. In all the cases, owners assured high contact with their pets. In (Hamer, Pauvolid-Correa et al. 2020, 262 Barroso-Arevalo, Barneto et al. 2021 ) and other variants (Barroso-Arevalo, Rivera et al. All these results may be explained by the fact that a higher affinity with the human cellular 271 receptor has been reported in the case of the Omicron variant compared to other variants (He, 272 Hong et al. 2021 , Zou, Xia et al. 2021 , Suzuki, Yamasoba et al. 2022 ). This could have led to 273 the displacement of the binding between the animal cell and the virus, maybe due to specific Fortunately, despite their higher susceptibility, the risk of high contact with an infected 292 human in this species is quite low, contrary to what is happening in the case of pets. These 293 aspects highlight the importance of the investigation of these new variants both in urban and 294 wild fauna (Vandegrift, Yon et al. 2022) .

From what we have observed in this study, it appears that the Omicron variant is less virulent 296 to pets than the previous variants as well as the original isolate. Although 10.13% of the 297 animals analyzed in this field study tested positive for RT-qPCR, low viral loads were 298 detected and none of the infected animals showed any symptomatology. This, together with 

The omicron (B.1.1.529) SARS-326

CoV-2 variant of concern does not readily infect Syrian hamsters

Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current 330 COVID-19 vaccines

First Detection of SARS-CoV-2 B.1.617.2 (Delta) Variant of 341

Concern in a Symptomatic Cat in Spain. Frontiers in Veterinary Science 9

National Center for Immunization and Respiratory Diseases (NCIRD), 344 Division of Viral Diseases, CDC COVID-19 Science Briefs

Omicron BA.2 (B.1.1.529.2): high potential to becoming the 346 next dominating variant. Research square, rs.3.rs-1362445

Detection 350 of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Europeen sur les maladies transmissibles

Omicron BA.2 lineage spreads in clusters and is 354 concentrated in Denmark

Complete Genome of SARS-CoV-2 Delta (AY.3) Variant Identified in a Dog in Kansas, 365 USA

Infection with SARS-CoV-2 variant B.1.1.7 detected in a group of dogs and cats 368 with suspected myocarditis

617.2) Variant of Concern in a Dog with Clinical Signs in Spain

SARS-CoV-2 B.1.1.7 variant of concern detected in a pet dog and 381 cat after exposure to a person with COVID-19, USA. Transboundary and emerging diseases

Isolations among Serially Tested Cats and Dogs in Households with

SARS-CoV-2 Omicron variant: 389 Characteristics and prevention

Characteristics of SARS-CoV-2 and COVID-391 19

Omicron SARS-CoV-2 new 393 variant: global prevalence and biological and clinical characteristics. European review for 394 medical and pharmacological sciences

Challenges of the Omicron 396 (B.1.1.529) Variant and Its Lineages: A Global Perspective

Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2. 400 Emerging infectious diseases

Analysis of non-structural proteins, NSPs of SARS-CoV-2 as targets for 402 computational drug designing

Characterization of the novel SARS-CoV-2 Omicron (B.1.1.529) 405 variant of concern and its global perspective

CoV-2 in a cat owned by a COVID-19-affected patient in Spain

Susceptibility of ferrets, cats, dogs, and other domesticated animals 414 to SARS-coronavirus 2

Journal of clinical virology: the official 418 publication of the Pan American Society for Clinical Virology

Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

Estimation of the number of nucleotide substitutions when there are strong 425 transition-transversion and G+C-content biases

Experimental infection of mink with 435

BA.1) variant leads to symptomatic disease with lung pathology and 436 transmission

Variantes de SARS-CoV-2 en España: Ómicron. 2021, 2022. Centro de Coordinación de 438

Possible host-adaptation of 441

SARS-CoV-2 due to improved ACE2 receptor binding in mink

World Health Organization. WHO Health Emergency Dashboard

This research was funded by the Institute of Health Carlos III (ISCIII), project "Estudio del 309 potencial impacto del COVID19 en mascotas y linces" (reference: COV20/01385) and the