Abstract In the wake of pandemics like COVID-19, which have zoonotic origins, the role of wildlife as reservoirs for emerging infectious diseases has garnered heightened attention. Migratory birds, traversing continents, represent a potent but under-researched vector for the spread of infectious diseases, including novel coronaviruses. This study delves into the genetic diversity and transmission dynamics of coronaviruses in migratory birds, presenting pivotal findings. From April 2019 to April 2023, we screened 5,263 migratory bird samples collected from Shanghai, China, identifying 372 coronavirus-positive samples belonging to five avian-related coronavirus subgenera and subsequently obtaining 120 complete genome sequences. To facilitate further research with a global perspective, the study curated all available 19,000 avian-associated CoVs and expanded the original 12 species to 16, including three novel coronavirus species identified in our study and one re-classified species from the public domain. The study illuminates the intricate genetic evolution and transmission dynamics of birds-related coronaviruses on a global scale. A notable aspect of our research is the identification of complex recombination patterns within the spike protein across different virus species and subgenera, highlighting migratory birds as a reservoir of coronavirus. Notably, the coronaviruses found in migratory birds, predominantly from the orders Anseriformes, Charadriiformes, and Pelecaniformes, with domestic ducks from Anseriformes playing a key role in bridging the transmission of coronaviruses between migratory and non-migratory birds. These findings reveal the genetic and recombination characteristics of coronaviruses in migratory birds, emphasizing the critical role of ecologically pivotal bird species in coronavirus transmission and genetic diversity shaping.
Table S1. Samples of the 55 animal species used in this study and the provinces and dates of collection. Table S2. The reads of virus under each family. Table S3. The reads of mammailan virus under each family. Table S4. Origin and accession number of viruses identified in this study. Table S5. Amino acid identity of rodents Arenavirus and representatives of other species. Table S6. The aa identities (%) of the predicted ORF1a and ORF1b between Rodent Arteriviruses and other known members of the family Arteriviridae (including a tentative member, WPDV). Table S7. The aa identities (%) between these hepaciviruses and other known rodent hepacivirus. Table S8. Amino acid identity (%)of rodents Hepatitis E and representatives of other Genotypes. Table S9. The aa identities (%) between these BtCoVs and other known members of the lineage-A beta-CoVs. Table S10. The aa identities (%) between these BtCoVs and other known members of alpha-CoVs. Table S11. Amino acid identity of rodents picornaviruses and representatives of other genera in P1, P2, and P3 regions. Table S12. Pairwise amino acid identities (%) of predicted gene products of RtAp-ParaV/NX2015 compared to other Jeilongvirus members. Table S13. Amino acid identity of rodents parvovirus and representatives of other genera. (XLSX 149 kb)
Abstract Background and study aims Multiple surgical approaches have been studied and accepted for the removal of highly downward migrated lumbar disc herniation (LDH). Here, we investigated the efficacy and safety of full-endoscopic foraminoplasty for highly downward migrated LDH. Patients and methods Thirty-seven patients with highly down-migrated LDH treated by the full-endoscopic foraminoplasty between January 2018 and January 2020 were retrospectively investigated. Clinical parameters were evaluated preoperatively and 1, 6, and 12 months postoperatively, using pre- and post-operative Oswestry Disability Index (ODI) scores for functional improvement, visual analog scale (VAS) for leg and back pain, and modified MacNab criteria for patients satisfactory. Results Thirty-seven patients with highly downward migrated LDH were successfully removed via the transforaminal full-endoscopic discectomy. The average VAS back and leg pain scores were significantly reduced from 7.41 ± 1.17 and 8.68 ± 1.06 before operation to 3.14 ± 0.89 and 2.70 ± 0.46 at postoperative 1 month, and 1.76 ± 0.59 and 0.92 ± 0.28 at postoperative 12 months, respectively ( P < 0.05). The average ODI scores were reduced from 92.86 ± 6.41 to 15.30 ± 4.43 at postoperative 1 month, and 9.81 ± 3.24 at postoperative 12 months ( P < 0.05). Based on the modifed MacNab criteria, 36 out of 37 patients (97.30%) were rated as excellent or good outcomes. Conclusion The full-endoscopic foraminoplasty can be used successfully for surgical removal of high grade down-migrated LDH, and it could serve as an efficient alternative technique for patients with highly downward migrated LDH.
Many paramyxoviruses are responsible for a variety of mild to severe human and animal diseases. Based on the novel discoveries over the past several decades, the family Paramyxoviridae infecting various hosts across the world includes 4 subfamilies, 17 classified genera and 78 species now. However, no systematic surveys of bat paramyxoviruses are available from the Chinese mainland. In this study, 13,064 samples from 54 bat species were collected and a comprehensive paramyxovirus survey was conducted. We obtained 94 new genome sequences distributed across paramyxoviruses from 22 bat species in seven provinces. Bayesian phylodynamic and phylogenetic analyses showed that there were four different lineages in the Jeilongvirus genus. Based on available data, results of host and region switches showed that the bat colony was partial to interior, whereas the rodent colony was exported, and the felines and hedgehogs were most likely the intermediate hosts from Scotophilus spp. rather than rodents. Based on the evolutionary trend, genus Jeilongvirus may have originated from Mus spp. in Australia, then transmitted to bats and rodents in Africa, Asia and Europe, and finally to bats and rodents in America.
Bat coronavirus RaTG13 shares about 96.2% nucleotide sequence identity with that of SARS-CoV-2 and uses human and Rhinolophus affinis (Ra) angiotensin-converting enzyme 2 (ACE2) as entry receptors. Whether there are bat species other than R. affinis susceptible to RaTG13 infection remains elusive. Here, we show that, among 18 different bat ACE2s tested, only RaACE2 is highly susceptible to transduction by RaTG13 S pseudovirions, indicating that the bat species harboring RaTG13 might be very limited. RaACE2 has seven polymorphic variants, RA-01 to RA-07, and they show different susceptibilities to RaTG13 S pseudovirions transduction. Sequence and mutagenesis analyses reveal that residues 34, 38, and 83 in RaACE2 might play critical roles in interaction with the RaTG13 S protein. Of note, RaACE2 polymorphisms have minimal effect on S proteins of SARS-CoV-2 and several SARS-CoV-2 related CoVs (SC2r-CoVs) including BANAL-20-52 and BANAL-20-236 in terms of binding, membrane fusion, and pseudovirus entry. Further mutagenesis analyses identify residues 501 and 505 in S proteins critical for the recognition of different RaACE2 variants and pangolin ACE2 (pACE2), indicating that RaTG13 might have not been well adapted to R. affinis bats. While single D501N and H505Y changes in RaTG13 S protein significantly enhance the infectivity and minimize the difference in susceptibility among different RaACE2 variants, an N501D substitution in SARS-CoV-2 S protein displays marked disparity in transduction efficiencies among RaACE2 variants with a significant reduction in infectivity on several RaACE2 variants. Finally, a T372A substitution in RaTG13 S protein not only significantly increases infectivity on all RaACE2 variants, but also markedly enhances entry on several bat ACE2s including R. sinicus YN, R. pearsonii, and R. ferrumeiqunum. However, the T372A mutant is about 4-fold more sensitive to neutralizing sera from mice immunized with BANAL-20-52 S, suggesting that the better immune evasion ability of T372 over A372 might contribute to the natural selective advantage of T372 over A372 among bat CoVs. Together, our study aids a better understanding of coronavirus entry, vaccine design, and evolution.
Abstract In the wake of pandemics like COVID-19, which have zoonotic origins, the role of wildlife as reservoirs for emerging infectious diseases has garnered heightened attention. Migratory birds, traversing continents, represent a potent but under-researched vector for the spread of infectious diseases, including novel coronaviruses. This study delves into the genetic diversity and cross-species transmission dynamics of coronaviruses in migratory birds, presenting pivotal findings. From April 2019 to April 2023, we screened 5,263 migratory bird samples collected from Shanghai, China, identifying 317 coronavirus-positive samples belonging to five avian-related coronavirus subgenera and subsequently obtaining 120 complete genome sequences. To facilitate further research with a global perspective, the study curated all currently available 19,000 avian-associated CoVs and expanded the original 12 species to the current 16 species, including three novel coronavirus species identified in our study and one re-classified species from the public domain. The study illuminates the intricate genetic evolution and cross-species transmission dynamics of birds-related coronaviruses on a global scale. A notable aspect of our research is the identification of complex recombination patterns within the spike protein across different virus species and subgenera, highlighting migratory birds as a reservoir of coronavirus. Notably, the coronaviruses found in migratory birds, predominantly from the orders Anseriformes, Charadriiformes, and Pelecaniformes, with domestic ducks from Anseriformes playing a key role in bridging the transmission of coronaviruses between migratory and non-migratory birds. These findings reveal the genetic and recombination characteristics of coronaviruses in migratory birds, emphasizing the critical role of ecologically pivotal bird species in coronavirus cross-species transmission and genetic diversity shaping.
Abstract Carbon emissions from fossil energy not only cause a lot of extreme weathers, but also global warming. Accurately forecasting of electricity demand can promote the development of the renewable energy, which is vital to achieving the goal of carbon peak and carbon neutrality. In this paper, a nonlinear interval grey model based on genetic algorithm and BP neural network optimization (BPGA-IGM (1,1)) is proposed to predict electricity consumption. Firstly, based on the forecast of China's energy consumption and China's coal consumption, the reliability and superiority of the BPGA-IGM (1,1) model have been verified. Then, the model and other competing models are applied to forecast Shanghai's electricity consumption. The empirical results show that the model designed in this paper could obtain more accurate and reliable prediction results. According to the empirical results, Shanghai's electricity consumption continues to rise to a higher level of no less than 1978.19 million kWh by 2025. On the basis of this issue, several suggestions have been offered.
Abstract Emerging infectious diseases significantly threaten global public health and socioeconomic security. The majority of emerging infectious disease outbreaks are caused by zoonotic/vector-borne viruses. Bats and rodents are the two most important reservoir hosts of many zoonotic viruses that can cross species barriers to infect humans, whereas mosquitos and ticks are well-established major vectors of many arboviral diseases. Moreover, some emerging zoonotic diseases require a vector to spread or are intrinsically vector-borne and zoonotically transmitted. In this study, we present a newly upgraded database of zoonotic and vector-borne viruses designated ZOVER (http://www.mgc.ac.cn/ZOVER). It incorporates two previously released databases, DBatVir and DRodVir, for bat- and rodent-associated viruses, respectively, and further collects up-to-date knowledge on mosquito- and tick-associated viruses to establish a comprehensive online resource for zoonotic and vector-borne viruses. Additionally, it integrates a set of online visualization tools for convenient comparative analyses to facilitate the discovery of potential patterns of virome diversity and ecological characteristics between/within different viral hosts/vectors. The ZOVER database will be a valuable resource for virologists, zoologists and epidemiologists to better understand the diversity and dynamics of zoonotic and vector-borne viruses and conduct effective surveillance to monitor potential interspecies spillover for efficient prevention and control of future emerging zoonotic diseases.
Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens, resulting in severe economic losses in the poultry industry. This study aimed to monitor and isolate the molecular identity of IBV in broiler flocks with respiratory symptoms in eight provinces of China. In total, 910 samples (oropharyngeal and cloacal mixed swabs) from broiler flocks showed IBV positive rates of 17.6% (160/910) using PCR assay. Phylogenetic analysis of the complete S1 genes of 160 IBV isolates was performed and revealed that QX-type (GI-19), TW-type (GI-7), 4/91-type (GI-13), HN08-type (GI-22),TC07-2-type (GVI-1), and LDT3-type (GI-28) exhibited IBV positive rates of 58.15, 25, 8.12, 1.86, 5.62, and 1.25%. In addition, recombination analyses revealed that the four newly IBV isolates presented different recombination patterns. The CK/CH/JS/YC10-3 isolate likely originated from recombination events between strain YX10 (QX-type) and strain TW2575-98 (TW-type), the pathogenicity of which was assessed, comparing it with strain GZ14 (TW-type) and strain CK/CH/GD/JR07-7 (QX-type). The complete S1 gene data from these isolates indicate that IBV has consistently evolved through genetic recombination or mutation, more likely changing the viral pathogenicity and leading to larger outbreaks in chick populations, in China.
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