Whole-Genome Characterization of SARS-CoV-2 Reveals Simultaneous Circulation of Three Variants and a Putative Recombination (20B/20H) in Pets, Brazzaville, Republic of the Congo

Abstract

Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a "One Health" approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.

Keywords: NGS; RT-qPCR; Republic of the Congo (RoC); SARS-CoV-2; cats; dogs; pets; serology.

Figure 1

Maps of Brazzaville (RoC) showing the distribution of households where cats (A) and dogs (B) were sampled. Red and black dots represent the pets that tested positive and negative, respectively, for SARS-CoV-2. The cat with a putative recombinant variant is highlighted with a blue circle. Map data source: www.arcgis.com accessed on 3 February 2022.

Figure 2

Pet’s enrolment outline.

Figure 3

Duration of SARS-CoV-2 detection in dogs and cats from COVID-19+ households in Congo. (A) Duration of detection in dogs and cats. (B) Comparative mean duration of detection in nasopharyngeal and rectal samples from pets. Black dot—negative result; red dot—positive result; blue line—nasopharyngeal sample; and yellow line—rectal sample.

Figure 4

Bayesian phylogenetic analysis of ten pets’ SARS-CoV-2 whole genome sequences. The tree included eighty SARS-CoV-2 sequences from Congolese people and the reference sequences of alpha, beta, delta, and omicron VOCs available on GISAID. Pet sequences are highlighted in violet.

Figure 5

Identity plot of a putative recombinant sequence from Cat-103.