South China Seafood Market is NOT the Birthplace of Coronavirus (COVID-19)

2020-02-22

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According to the official website of the Xishuangbanna Tropical Botanical Garden of the Chinese Academy of Sciences (CAS), CAS, in conjunction with South China Agricultural University and Beijing Brain Center, has collected genomic data of 93 new crown virus (COVID-19) samples shared globally in the GISAID EpiFluTM database covering 12 countries on four continents (as of February 12 (Day). The analysis of the whole genome data found that the new coronavirus (COVID-19) in the South China Seafood Market in Wuhan was introduced from other places.

In December 2019, a pneumonia (now known as COVID-19) caused by a new coronavirus (SARS-CoV-2) broke out in Wuhan, Hubei. The outbreak of the new coronavirus has been more than two months. The birthplace of the virus is of great significance for finding the source of the virus and determining the intermediate host, which would help to control the epidemic and avoid recurrence.

Xishuangbanna Tropical Botanical Garden of the Chinese Academy of Sciences, together with researchers from South China Agricultural University and Beijing Brain Center, collected genomic data from 93 new coronavirus samples shared by all areas of the world and shared in the GISAID EpiFluTM database covering 12 countries on four continents (as of 2 12th), trace the source of infection and spread path through the analysis of whole-genome data.

The study found that the 93 samples received contained 58 haplotypes, which can be grouped into five groups (Figure 1), including 3 ancient super-spreader haplotypes (H1, H3, and H13) and 2 new super-spreads. Haplotypes (H56 and mv2); the new coronavirus from the South China seafood market was introduced from other places, and spread rapidly outside the market. At the same time, the current spread of cases came from at least 3 routes. The new coronavirus had two significant population expansions before February 12 (December 8 and January 6 respectively).

New coronavirus was introduced into South China Seafood Market from elsewhere

Based on 120 mutation sites, 58 haplotypes (gene types) were obtained. The haplotype evolution relationship showed that the haplotypes H13 and H38 were relatively “old” haplotypes, and they passed an intermediate vector (mv1, possibly a The ancestral haplotype, which may be from an intermediate host or “patient zero”) to associate with bat coronavirus RaTG13 and to produce haplotype H1 from haplotype H3. The patient sample haplotypes associated with the South China seafood market are H1 and its derived haplotypes H2, H8-H12 (Figure 1, A), while a Wuhan sample haplotype H3 has nothing to do with the South China seafood market.

It can be seen that the new coronavirus in the South China seafood market was introduced from other places and spread rapidly outside the market. In addition, the inference based on the patient’s onset time record and population expansion time also confirmed the inference that the South China seafood market is not the source of the virus.

Traces of “old” haplotype H13 and H38 virus samples were found in patients from Shenzhen (the first case in Guangdong) and patients in Washington State (the first case in the United States). Their travel records indicate that they should have been infected during their visits to relatives in Wuhan from the end of December 2019 to early January 2020. H13 and H38 haplotypes were not detected in the existing Wuhan samples, probably because the existing samples were mainly collected from several designated hospitals, and the sample collection time was limited to December 24, 2019 and January 5, 2020. If these two haplotypes can be detected in early patients in other hospitals in Wuhan, it will be very helpful to find the source of the virus.

New coronavirus experienced two significant population expansions before February 12

According to the new coronavirus genome data, it was estimated that the population expansion before January occurred on December 8. This result suggests that the virus may have spread from person to person in early December and even in late November, and then accelerated human-to-human transmission in the South China seafood market (figure 2). The study estimates that the population expansion time before February is January 6th, which may be related to the New Year’s Day holiday. It should be noted that on this day, the National Center for Disease Control and Prevention issued a Level 2 emergency response. Early warnings at that time served as a warning, and public activity and travel were reduced. If the warnings at that time could attract wider attention, the number of cases spreading nationally and globally in mid-to-late January would be reduced. Researchers further confirmed that infection cases in the other nine provinces in China and 11 other countries were directly or indirectly imported from Wuhan.

Spread of cases from at least 3 routes

In order to be able to subdivide the source, the researchers divided 58 haplotypes into five groups (Figure 1), using the standard of 3 centers (old super communicators) haplotypes (H1, H3, and H13) and 2 new ones. Super communicator haplotype (H56 and mv2). This identified three sources of viruses in Guangdong and two sources of viruses in Chongqing and Taiwan. Among them, the Shenzhen family of Guangdong spread it from person to person early. There are more samples in Australia, France, Japan and the United States, and their patients have at least two sources of infection, especially the United States with five sources. Of great concern is the haplotype of H56, which is also the source of infection for patients in Australia, France, and the United States, as well as Taiwan. Patients in other countries have fewer samples and most of them have a single source. In addition to being imported from Wuhan or infected in Wuhan, some people may be infected in Guangdong, Singapore and other places.

New coronavirus genome has not undergone recombination

The researchers found that no recombination event occurred in the novel coronavirus genome, and 120 nucleotides (0.41% sequence length) were mutated between 93 genomes and evenly dispersed in 10 coding regions (χ2 = 1.958, df = 9, P = 0.99). 120 mutant nucleotides were associated with 119 amino acid codons, of which 79 codons (65.83%) changed the amino acid type, and 42 (53.17%) amino acid physicochemical properties were changed (Figure 3). It is unclear whether these amino acid types and changes in physicochemical properties will affect the activity of the new coronavirus, and other proteomics and structural biology professionals need to verify it.

This research was carried out by the researchers of the Biodiversity Research Group of the Banna Botanical Gardens Comprehensive Conservation Center using their expertise in the field of systems and evolution. This research mentions that the haplotype evolution relationship analysis method can be combined into epidemiological research. Sources of infection and precise directions of spread and spread can provide very important information.

Relevant research results have been submitted to the pre-release platform of scientific papers of the Chinese Academy of Sciences http://www.chinaxiv.org/abs/202002.00033, which can be used for reference by relevant departments of disease control and epidemic prevention, and accept the exchange and discussion of experts and scholars.

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