Publisher : Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
Ref : http://www.xtbg.cas.cn/xwzx/kydt/202002/t20200220_5502619.html
English Translation : Gan Yung Chyan
/ KUCINTA SETIA
Image courtesy : Xishuangbanna Tropical Botanical Garden
In December 2019, novel coronavirus 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. To be certain if Huanan Seafood Market is the only source of the outbreak, the birthplace of the virus is of great significance for finding the source of the virus and determining the intermediate host to control the epidemic and avoid recurrence is crucial.
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 SARS-CoV-2 samples shared by all areas of the world in the GISAID EpiFluTM database covering 12 countries on four continents (as of 12 February 2020) and traced the source of infection and spread path through the analysis of whole genome data.
The study has found that the 93 samples received contain 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 include H56 and mv2; covi from the Huanan Seafood Market is introduced from other places, and spread rapidly outside the market; at the same time, the current spread of cases comes from at least 3 routes. SARS-CoV-2 has two significant population expansions before 12 February 2020 (8 December 2019 and 6 January 2020 respectively).
SARS-CoV-2 in Huanan Seafood Market is introduced from other places
Based on 120 mutation sites, 58 haplotypes (gene types) are obtained. The haplotype evolution relationship shows that the haplotypes H13 and H38 are relatively "old" haplotypes, and passes an intermediate vector (mv1, possibly an ancestral haplotype, which may be from an intermediate host or "patient zero"). They are associated with bat coronavirus RaTG13, and haplotype H1 is derived from haplotype H3. The patient sample haplotypes associated with the Huanan 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 Huanan Seafood Market. It can be seen that the covi in the Huanan Seafood Market is introduced from other places and spreads rapidly outside the market. In addition, the inference based on the patient's onset time record and population expansion time also confirms the inference that the Huanan Seafood Market is not the source of the virus.
Traces of "old" haplotype H13 and H38 virus samples are found in patients from Shenzhen (the first case in Guangdong) and 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 are not detected in the existing Wuhan samples, probably because the existing samples were mainly collected from several designated hospitals, and the sample collection time is limited to 24 December 2019 and 5 January 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.
COVID-19 experienced two significant outbreak expansions before 12 February 2020
According to the SARS-CoV-2 genome data, it was estimated that the outbreak expansion before January occurred on 8 December 2019. 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 Huanan Seafood Market (figure 2). The study estimates that the outbreak expansion time before February is 6 January 2020, that 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 have been reduced. Researchers further confirmed that infection cases in other nine provinces and 11 other countries in China were basically 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 have divided 58 haplotypes into five groups (Figure 1), using the criteria of 3 centers (ancient super communicators) haplotypes (H1, H3, and H13) and 2 new Super communicator haplotype (H56 and mv2). There are three sources of viruses identified in Guangdong and two sources of viruses identified in Chongqing and Taiwan. Among them, the virus family in Shenzhen spread 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 includes five sources. Of great concern is the haplotype of H56, which is also the source of infection for patients in Australia, France, the United States and 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.
No recombination of SARS-CoV-2 genome
The researchers have found that no recombination event has occurred in the novel coronavirus genome, and 120 nucleotides (0.41% sequence length) are mutated between 93 genomes and evenly dispersed in 10 coding regions (χ2 = 1.958, df = 9, P = 0.99). 120 mutant nucleotides are 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. The platform accepts the exchange and discussion of experts and scholars.
Figure 1. Evolutionary relationship and geographical distribution of 58 haplotypes of SARS-CoV-2 (A, B), possible evolutionary relationships between the haplotypes (C), and possible transmission and spread routes of SARS-CoV-2 (D) . The data in circles A and B are the number of samples.
Figure 2. Sample collection time of the new coronavirus haplotype. The sample in the red circle is confirmed to be related to the Huanan Seafood Market; the sample in the blue circle is confirmed to have nothing to do with the seafood market.
Figure 3. The distribution of 120 mutation sites in 8 coding regions. Statistical types include substitutions or substitutions (upper left corner), codon positions 1-3 (upper right corner), synonymous or non-synonymous mutations (lower left corner), and amino acid properties (lower right corner).
Back : China researchers : Wuhan Huanan Seafood Market is not the origin of COVID-19, by Gan Yung Chyan,
https://staygate.blogspot.com/2020/02/china-researchers-wuhan-huanan-seafood.html
Further Ref :
Chinese Academy of Sciences admits seafood market is not the origin of COVID-19. Human-to-human virus transmission begins in November 2019, Reported by Zhu Yin, Edited by Ming Xuan, New Tang Dynasty Television,https://www.ntdtv.com/b5/2020/02/22/a102783383.html
New study further proves Wuhan seafood market not the source of COVID-19, Ecns.cn http://www.ecns.cn/news/sci-tech/2020-02-23/detail-ifztvsqr0576579.shtml
COVID-19 | SARS-CoV-2 Coronavirus Portal
https://globalbiodefense.com/novel-coronavirus-covid-19-portal/
StayGate's Notes:
In layman terms, covi is in use for the virus SARS-CoV-2 in COVID-19 while covid is in short for the contagious disease scientifically known as COVID-19.
Ref : http://www.xtbg.cas.cn/xwzx/kydt/202002/t20200220_5502619.html
English Translation : Gan Yung Chyan
/ KUCINTA SETIA
Image courtesy : Xishuangbanna Tropical Botanical Garden
In December 2019, novel coronavirus 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. To be certain if Huanan Seafood Market is the only source of the outbreak, the birthplace of the virus is of great significance for finding the source of the virus and determining the intermediate host to control the epidemic and avoid recurrence is crucial.
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 SARS-CoV-2 samples shared by all areas of the world in the GISAID EpiFluTM database covering 12 countries on four continents (as of 12 February 2020) and traced the source of infection and spread path through the analysis of whole genome data.
The study has found that the 93 samples received contain 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 include H56 and mv2; covi from the Huanan Seafood Market is introduced from other places, and spread rapidly outside the market; at the same time, the current spread of cases comes from at least 3 routes. SARS-CoV-2 has two significant population expansions before 12 February 2020 (8 December 2019 and 6 January 2020 respectively).
SARS-CoV-2 in Huanan Seafood Market is introduced from other places
Based on 120 mutation sites, 58 haplotypes (gene types) are obtained. The haplotype evolution relationship shows that the haplotypes H13 and H38 are relatively "old" haplotypes, and passes an intermediate vector (mv1, possibly an ancestral haplotype, which may be from an intermediate host or "patient zero"). They are associated with bat coronavirus RaTG13, and haplotype H1 is derived from haplotype H3. The patient sample haplotypes associated with the Huanan 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 Huanan Seafood Market. It can be seen that the covi in the Huanan Seafood Market is introduced from other places and spreads rapidly outside the market. In addition, the inference based on the patient's onset time record and population expansion time also confirms the inference that the Huanan Seafood Market is not the source of the virus.
Traces of "old" haplotype H13 and H38 virus samples are found in patients from Shenzhen (the first case in Guangdong) and 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 are not detected in the existing Wuhan samples, probably because the existing samples were mainly collected from several designated hospitals, and the sample collection time is limited to 24 December 2019 and 5 January 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.
COVID-19 experienced two significant outbreak expansions before 12 February 2020
According to the SARS-CoV-2 genome data, it was estimated that the outbreak expansion before January occurred on 8 December 2019. 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 Huanan Seafood Market (figure 2). The study estimates that the outbreak expansion time before February is 6 January 2020, that 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 have been reduced. Researchers further confirmed that infection cases in other nine provinces and 11 other countries in China were basically 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 have divided 58 haplotypes into five groups (Figure 1), using the criteria of 3 centers (ancient super communicators) haplotypes (H1, H3, and H13) and 2 new Super communicator haplotype (H56 and mv2). There are three sources of viruses identified in Guangdong and two sources of viruses identified in Chongqing and Taiwan. Among them, the virus family in Shenzhen spread 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 includes five sources. Of great concern is the haplotype of H56, which is also the source of infection for patients in Australia, France, the United States and 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.
No recombination of SARS-CoV-2 genome
The researchers have found that no recombination event has occurred in the novel coronavirus genome, and 120 nucleotides (0.41% sequence length) are mutated between 93 genomes and evenly dispersed in 10 coding regions (χ2 = 1.958, df = 9, P = 0.99). 120 mutant nucleotides are 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. The platform accepts the exchange and discussion of experts and scholars.
Figure 1. Evolutionary relationship and geographical distribution of 58 haplotypes of SARS-CoV-2 (A, B), possible evolutionary relationships between the haplotypes (C), and possible transmission and spread routes of SARS-CoV-2 (D) . The data in circles A and B are the number of samples.
Figure 2. Sample collection time of the new coronavirus haplotype. The sample in the red circle is confirmed to be related to the Huanan Seafood Market; the sample in the blue circle is confirmed to have nothing to do with the seafood market.
Figure 3. The distribution of 120 mutation sites in 8 coding regions. Statistical types include substitutions or substitutions (upper left corner), codon positions 1-3 (upper right corner), synonymous or non-synonymous mutations (lower left corner), and amino acid properties (lower right corner).
Back : China researchers : Wuhan Huanan Seafood Market is not the origin of COVID-19, by Gan Yung Chyan,
https://staygate.blogspot.com/2020/02/china-researchers-wuhan-huanan-seafood.html
Further Ref :
Chinese Academy of Sciences admits seafood market is not the origin of COVID-19. Human-to-human virus transmission begins in November 2019, Reported by Zhu Yin, Edited by Ming Xuan, New Tang Dynasty Television,https://www.ntdtv.com/b5/2020/02/22/a102783383.html
New study further proves Wuhan seafood market not the source of COVID-19, Ecns.cn http://www.ecns.cn/news/sci-tech/2020-02-23/detail-ifztvsqr0576579.shtml
COVID-19 | SARS-CoV-2 Coronavirus Portal
https://globalbiodefense.com/novel-coronavirus-covid-19-portal/
StayGate's Notes:
In layman terms, covi is in use for the virus SARS-CoV-2 in COVID-19 while covid is in short for the contagious disease scientifically known as COVID-19.
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