A novel coronavirus, SARS-CoV-2, was recently reported in the city of Wuhan, Hubei province, China, causing severe respiratory diseases as well as epidemic all around the China. The inflection point of confirmed cases didn’t occur until February 2020, with the first patient hospitalized on the 12 ^th of December 2019 ¹ . On 29 ^th February, 573 new confirmed cases of novel coronavirus infection were reported on the Chinese mainland, bringing the total to 78,630. There were 35 new fatalities reported daily, with the cumulative fatalities were up to 2761. Meanwhile, outside the Chinese mainland, more than 5000 cases have been confirmed in Asia, in places such as Japan, Singapore, Thailand and South Korea, in Europe, in places like Germany and France, and in the Americas. Consensus that the SARS-CoV-2 originated from bats has been reached ² . However, intermediate hosts are deemed as having mediated human infection via gradually adapting the mechanism of transcription and translation in the human body.

The exact putative parent of SARS-CoV-2 remains uncertain. Frequent contact between humans and swine could lead to a higher risk of cross-species transmission or virus recombination. For the sake of identifying intermediate host, relative synonymous codon usage (RSCU) analysis was applied to evaluate the potential diversity of species acting as reservoirs. Phylogenetic and homologous recombination analysis were also used to illuminate the correlated coronavirus hosting in the most possible host.

In China, the cumulative number of patients diagnosed as infected with SARS-CoV-2 is thought to over 100,000, with more than 2000 deaths. It is the most severe public health emergency since the outbreak of SARS 17 years ago ⁹ . Local residents were reined with anxiety and confused during the virus outbreak, although the Chinese government has taken substantial action to prevent and control the spread of the virus. However, multiple different messages could disrupt the attention of medical workers and science researchers. Current research about the origin of SARS-CoV-2 mostly focuses on wildlife, since the first case was thought to be highly associated with wild animals in Wuhan sea food market.

The origin of SARS-CoV-2 had caused great concern to the public. Natural variation was the dominant view holding by most scholars, believing that bats and other wild animals provide reservoirs for the virus. However, coronavirus from bats is unlikely to infect humans directly; one or two intermediate hosts may facilitate the homologous recombination, enabling the coronavirus to gradually adjust to the human genetic code, then survival and breeding successfully.

From our perspective, natural variation would be a more reasonable explanation for the origin of SARS-CoV-2. However, the wild animals in Wuhan seafood market should not accept all the liability, since there is evidence that patients with early infection didn’t have any contact with the market ⁹ . Some researchers ¹⁰ have also pointed out that the Wuhan seafood market is not the only area of origin, indicating that another creature may act as intermediate host apart from those animals being sold at the market. In our study, the captivity animal, Sus scrofa (swine) and Mus musculus (mice) were suspected to be critical hosts of SARS-CoV-2.

Our finding supports the theory of natural variation. Natural variation believes that people get infected because they eat or come into contact with intermediate hosts. SARS-CoV-2 was found to be 96% identical at the whole-genome level to the bat coronavirus ² . Other reports state that snakes, mink, and pangolins could be potential hosts for SARS-CoV-2 ¹¹ .

Either wild animals or reared livestock could serve as hosts. It has been reported that Wuhan seafood market may not be the only source of novel virus spreading globally because the earliest patient became ill on 1 December 2019 and had no epidemiological link to the seafood market or later cases. The official details about the first 41 hospitalized patients showed 13 of the 41 patients had no link to the marketplace at all ⁹ . One possible hypothesis is that the cross-species transmission has occurred in other places before the outbreak of Wuhan Huanan Seafood market.

Previous study into fatal swine acute diarrhea syndrome (SADS) revealed that SADS-related coronavirus was responsible for a large-scale outbreak of fatal disease in pigs in China ¹² . Here we discovered Porcine epidemic diarrhea virus (PEDV) periodicity burst in China ¹³ . Among one of the strains, H11-SD2017 showed closely affiliation with SARS-CoV-2 via implementing relative synonymous codon usage (RSCU) and phylogenetic analysis. Swine-to-human cross species transmission may explain why many patients with coronavirus disease-19 (COVID-19) not only suffer from severe respiratory diseases, but also diarrhea ⁹ .

In the past 10 years, PEDV has spread into most provinces with the swine industry in China. Hubei was the first region to be infected with PEDV strain CH/HBQX/10 in 2010; from then on, more and more provinces reported the presence of PEDV ¹³ . The spread of PEDV has gone beyond its initial geographical limitation. There were more than 300 PEDV strains clustered into pandemic, meaning the significant natural variation took place in the spread of PEDV in different regions. Further analysis among 21 strains of PEDV and coronavirus from varied species indicate that swine and mice could be other hosts of SARS-CoV-2 ( Figure 1A, Figure 2 and Figure 3).

RDP4 and Simplot analysis helped us better understand the homologous recombination of SARS-CoV-2 ( Table 1, Figure 4). It verified that not only porcine coronavirus, but also murine coronavirus, experienced recombination events. Therefore, we speculate that SARS-CoV-2 may originate from the bat firstly, undergoing a series of recombination events, with swine and mice playing critical role in mediating cross species transmission.

Pairwise analysis of distance also indicated that Mus musculus could be a possible host of SARS-CoV-2 ( Figure 1B). Previously, the Chinese Centers for Disease Control said that 33 of the samples were positive for the novel coronavirus nucleic acid. The positive samples were distributed among 22 stalls and a garbage truck in the Wuhan Huanan seafood market, so the outbreak is highly suspected to be related to the wildlife trade. But how could wild animal movement around the market lead to cross-infection with disparate species in different regions? One plausible phenomenon is that mice could be infected with SARS-CoV-2 firstly, transferring the infection to other wild species in the market. Thus, the role of mice in the market deserves more attention. In order to verify the exact intermediate host, mice and swine living around Wuhan should be collected for further proof test basing on Koch’s postulates

Eventually, the rear livestock should be deserved more notice apart from wild vertebrate creatures. To our knowledge, this is the first study to illustrate that swine and mice are the probable livestock reservoir for the SARS-CoV-2. Furthermore, the mice around the seafood market may also be involved in the cross transmission of the virus to some extent. All of those output based on the bioinformatics analysis, further identification of host should be verified from isolation and other experiments.