scholarly journals Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

2021 ◽  
Author(s):  
Hong Zhou ◽  
Jingkai Ji ◽  
Xing Chen ◽  
Yuhai Bi ◽  
Juan Li ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Yunnan Province ◽  
Gene Sequence ◽  
Southern China ◽  
Geographic Region ◽  
Spike Gene ◽  
Diarrhea Virus ◽  
Wildlife Species ◽  
Evolutionary Origins ◽  
Diarrhea Syndrome

SummaryAlthough a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.

scholarly journals Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from 2012 to 2018

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Fanfan Zhang ◽  
Suxian Luo ◽  
Jun Gu ◽  
Zhiquan Li ◽  
Kai Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Southern China ◽  
Genetic Relationships ◽  
Transmissible Gastroenteritis Virus ◽  
Prevalence Rates ◽  
Spike Gene ◽  
Diarrhea Virus ◽  
Severe Diarrhea ◽  
The Usa

Abstract Background In China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010. To investigate the prevalence and genetic evolution of diarrhea-associated viruses responsible for the outbreaks, a total of 2987 field diarrheal samples collected from 168 pig farms in five provinces in Southern China during 2012–2018 were tested. Results Porcine epidemic diarrhea virus (PEDV) was most frequently detected virus with prevalence rates between 50.21 and 62.10% in samples, and 96.43% (162/168) in premises, respectively. Porcine deltacoronavirus (PDCoV) was the second prevalent virus with prevalence rates ranging from 19.62 to 29.19% in samples, and 70.24% (118/168) in premises, respectively. Both transmissible gastroenteritis virus (TGEV) and porcine rotavirus (PoRV) were detected at low prevalence rates of < 3% in samples and 10.12% in premises. In this study, we identified a newly emerged swine acute diarrhea syndrome coronavirus (SADS-CoV) in diarrheal samples of piglets from Fujian province in Southern China, and the prevalence rate of SADS-CoV was 10.29% (7/68). Co-infections of these diarrhea-associated viruses were common. The most frequent co-infection was PEDV with PDCoV, with an average detection rate of 12.72% (380/2987, ranging from 8.26–17.33%). Phylogenetic analysis revealed that PEDVs circulating in Southern China during the last 7 years were clustered with the variant strains of PEDV in genotype IIa. The most frequent mutations were present in the collagenase equivalent (COE) and epitope regions of the spike gene of the PEDVs currently circulating in the field. Genetic relationships of PDCoVs were closely related with Chinese strains, other than those present in the USA, South Korea, Thailand and Lao’s public. Conclusions The findings of this study indicated that variant PEDV, PDCoV, and SADS-CoV were leading etiologic agents of porcine diarrhea, and either mono-infections or co-infections of pathogenic enteric CoVs were common in pigs in Southern China during 2012–2018. Thus, significant attention should be paid in order to effectively prevent and control porcine viral diarrhea.

Latest 30-m map of mature rubber plantations in Mainland Southeast Asia and Yunnan province of China: Spatial patterns and geographical characteristics

2021 ◽  
pp. 030913332098374
Author(s):  
Chiwei Xiao ◽  
Peng Li ◽  
Zhiming Feng ◽  
Yanzhao Yang ◽  
Zhen You ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Yunnan Province ◽  
Vegetation Index ◽  
Southern China ◽  
Landsat 8 ◽  
Rubber Plantations ◽  
National Differences ◽  
Northern Edge ◽  
The Tropics ◽  
Mainland Southeast Asia

Knowledge of the location, area and extent of rubber plantations is a prerequisite for assessing their ecological and environmental impacts. Mainland Southeast Asia (MSEA) and Yunnan province (MSEA&YN) in China are globally important rubber-planting regions. Rubber cultivation in areas at moderate and low altitudes (<1000 m) within these regions has expanded rapidly in recent years. However, datasets of maps generated at a fine spatial resolution are still unavailable for MSEA&YN. Because of this, three relevant and important questions remain unanswered: what are the northernmost boundary for rubber production in these regions, what is the highest altitude at which rubber is produced, and how are the plantations distributed in (cross-) border regions? An approach of the phenology- and Landsat-based re-normalized vegetation index (RNVI), originally developed for Xishuangbanna in southern China, is used in this study to verify the feasibility of mapping mature rubber plantations in MSEA&YN using the Landsat 8 Operational Land Imager data products acquired from January to April, 2013 to 2018. Characteristics of the vertical and horizontal distributions of mature rubber plantations in MSEA&YN, as well as national differences especially in the (cross-) borders, were examined using the generated map. The results showed that the RNVI method, although tailored to the northern edge of the tropics, is useful for detecting mature rubber plantations in MSEA&YN. The latest map of mature rubber plantations indicated that they occupied a total area of 7.69 × 106 ha, accounting for 3.32% of the study area. Spatial analyses showed three typical features of the distribution: new plantations at higher (over 1000 m) and lower (below 200 m) elevations, more cultivation in the borderlands (over a half within 60 km buffers), and their northward movement (as far as 25°N). The results of this study have important implications for phenological methods verification in the tropics, and provide valuable information on mature rubber plantations in MSEA&YN.

scholarly journals Genomic Epidemiology of Antimalarial Drug Resistance in Plasmodium falciparum in Southern China

2021 ◽  
Vol 10 ◽  
Author(s):  
Fang Huang ◽  
Christopher G. Jacob ◽  
Shannon Takala-Harrison ◽  
Matthew Adams ◽  
Heng-Lin Yang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Plasmodium Falciparum ◽  
Southeast Asia ◽  
Yunnan Province ◽  
Southern China ◽  
Artemisinin Resistance ◽  
Hainan Island ◽  
Parasite Clearance ◽  
Maximum Likelihood Estimates ◽  
Candidate Snps

Emerging artemisinin resistance in Southeast Asia poses a significant risk to malaria control and eradication goals, including China’s plan to eliminate malaria nationwide by 2020. Plasmodium falciparum was endemic in China, especially in Southern China. Parasites from this region have shown decreased susceptibility to artemisinin and delayed parasite clearance after artemisinin treatment. Understanding the genetic basis of artemisinin resistance and identifying specific genetic loci associated with this phenotype is crucial for surveillance and containment of resistance. In this study, parasites were collected from clinical patients from Yunnan province and Hainan island. The parasites were genotyped using a P. falciparum-specific single nucleotide polymorphism (SNP) microarray. The SNP profiles examined included a total of 27 validated and candidate molecular markers of drug resistance. The structure of the parasite population was evaluated by principal component analysis by using the EIGENSOFT program, and ADMIXTURE was used to calculate maximum likelihood estimates for the substructure analysis. Parasites showed a high prevalence of resistance haplotypes of pfdhfr and pfdhps and moderate prevalence of pfcrt. There was no mutation identified on pfmdr1. Candidate SNPs on chromosomes 10, 13, and 14 that were associated with delayed parasite clearance showed a low prevalence of mutants. Parasites from Southern China were clustered and separated from those from Southeast Asia. Parasites from Yunnan province were substructured from parasites from Hainan island. This study provides evidence for a genomic population with drug resistance in Southern China and also illustrates the utility of SNP microarrays for large-scale parasite molecular epidemiology.

Two new species of the Rhopalopsole magnicerca group (Plecoptera: Leuctridae) from China

Zootaxa ◽  
2018 ◽  
Vol 4388 (3) ◽  
pp. 444
Author(s):  
RAORAO MO ◽  
GUOQUAN WANG ◽  
DING YANG ◽  
WEIHAI LI
Keyword(s):  
New Species ◽  
Yunnan Province ◽  
Southern China ◽  
Southwestern China ◽  
Autonomous Region ◽  
Two New Species

Two leuctrid species of the Rhopalopsole magnicerca group are described as new, R. brevicula sp. nov. and R. jizushana sp. nov. from the Guangxi Autonomous Region of southern China, bordering Vietnam and Yunnan Province of southwestern China, respectively. The new species are compared with related taxa. 

A review of the non-lyctine powder-post beetles of Yunnan (China) with a new genus and new species (Coleoptera: Bostrichidae)

Zootaxa ◽  
2022 ◽  
Vol 5091 (4) ◽  
pp. 501-545
Author(s):  
YI-FENG ZHANG ◽  
LING-ZENG MENG ◽  
ROGER A. BEAVER
Keyword(s):  
New Species ◽  
Southeast Asia ◽  
Yunnan Province ◽  
New Genus ◽  
Southwest China ◽  
Geological History ◽  
Yunnan Region ◽  
Palearctic Region ◽  
History Of ◽  
First Time

The powder post beetles (Coleoptera: Bostrichidae) (except Lyctinae) of Yunnan Province in Southwest China are reviewed for the first time. Keys to twenty-six genera and fifty-two species from the Yunnan region are provided. One new genus and seven new species are described: Dinoderus (Dinoderastes) hongheensis sp. nov., Dinoderus (Dinoderastes) nanxiheensis sp. nov., Gracilenta yingjiangensis gen. nov., sp. nov., Calonistes vittatus sp. nov., Calophagus colombiana sp. nov., Xylodrypta guochuanii sp. nov. and Xylodrypta zhenghei sp. nov.. Fourteen species are recorded in China for the first time. The bostrichid fauna of Yunnan is compared with those of the neighbouring bio-geographically related Southeast Asian and Himalayan regions. The fauna has a close affinity with that of tropical Southeast Asia and a much weaker relationship with the Palearctic region. The differences with the Himalayas may reflect the separate evolutionary and complex geological history of the two areas.

scholarly journals A NEW SPECIES OF THE Pareas hamptoni COMPLEX (SQUAMATA, SERPENTES, PAREIDAE) FROM THE GOLDEN TRIANGLE

2020 ◽  
pp. 174-193
Author(s):  
Li Ding ◽  
Zening Chen ◽  
Chatmongkon Suwannapoom ◽  
Tan Van Nguyen ◽  
Nikolay A. Poyarkov ◽  
...  
Keyword(s):  
New Species ◽  
Yunnan Province ◽  
Southern China ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Molecular Data ◽  
Lower Number ◽  
Actual Distribution ◽  
Golden Triangle ◽  
Morphological And Molecular Data

An investigation of the taxonomic status of Pareas hamptoni (Hampton's Slug snake) based on morphological and molecular data revealed a new distinct species from the Golden Triangle region (comprising parts of southern China, and adjacent Laos and Thailand). The new species is shown to be a sister species to P. hamptoni but can be separated from the latter by having 3–5 dorsal scale rows at midbody slightly keeled (vs 5–9 scales strongly keeled); a lower number of ventrals, 170–188 (vs 185–195); and a lower number of subcaudals, 67–91 (vs 91–99). The new species is currently known from northwestern Thailand, northern Laos, and the southern part of Yunnan Province in China at elevations of 1,160–2,280 m a.s.l. We suggest that the new species to be considered of Least Concern (LC) in the IUCN‘s Red List categories. Problems of taxonomy and actual distribution of the P. hamptoni complex are briefly discussed; our results show P. hamptoni is now reliably known only from Myanmar and Vietnam, but its occurrence in Yunnan Province of China is likely.

δ-tocotrienol induce nasopharyngeal carcinoma apoptosis and Growth arrest in the CNE1 cells

2021 ◽  
Author(s):  
Junjun Shen ◽  
Tao Yang ◽  
Yiping Tang ◽  
Tianyi Guo ◽  
Ting Guo ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Middle East ◽  
Southeast Asia ◽  
Incidence Rate ◽  
North Africa ◽  
Southern China ◽  
Growth Arrest ◽  
The Arctic ◽  
High Incidence ◽  
High Incidence Rate

Nasopharyngeal carcinoma has a notably high incidence rate in Southern China, Southeast Asia, North Africa, Middle East, and the Arctic. δ-tocotrienol is abundant in cereal and has some health benefits....

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