African swine fever virus (ASFV), the aetiological agent of African swine fever (ASF), causes lethal haemorrhagic fever in domestic pigs with high mortality and morbidity and has devastating consequences on the global swine industry. On-site rapid and sensitive detection of ASFV is key to the timely implementation of control. In this study, we developed a rapid, sensitive and instrument-free ASFV detection method based on CRISPR/Cas12a technology and lateral flow detection (named CRISPR/Cas12a-LFD). The limit of detection of CRISPR/ Cas12a-LFD is 20 copies of ASFV genomic DNA per reaction, and the detection process can be completed in an hour. The assay showed no cross-reactivity with other swine DNA viruses, and has 100% agreement with real-time PCR detection of ASFV in 149 clinical samples. Overall, the CRISPR/Cas12a-LFD method provides a novel alternative for the portable, simple, sensitive, and specific detection of ASFV and may contribute to the prevention and control of ASF outbreaks.

BackgroundPraziquantel has been used as first-line drug for chemotherapy of schistosomiasis since 1984. Besides praziquantel, artemether and artesunate have also been used for the control of this infectious disease since late 1990s. In this article, we conducted a systematic review and meta-analysis to evaluate the antischistosomal efficacy of different medication strategies including monotherapy or combination therapies of these drugs.ResultsA number of 52 trials from 38 articles published in peer-reviewed journals before July 2011 were selected for analysis after searching the following literature databases: the Cochrane Library, PubMed/Medline, ISI Web of Science, Chinese Biomedicine Literature Database, and China National Knowledge Infrastructure. Our meta-analyses showed that a dosage of 30-60 mg/kg praziquantel compared with placebo produced a protection rate of about 76% (95% CI: 67%-83%) for treating human schistosomiasis, which varied from 70% to 76% with no significant differences among the subspecies S. haematobium, S. japonicum or S. mansoni. Protection rates were higher when praziquantel doses were elevated, as concluded from the nRCTs results: the protection rate of praziquantel at 40 mg/kg was 52% (95% CI: 49%-55%), and it increased to 91% (95% CI: 88%-92%) when the dosages were elevated to 60/80/100 mg/kg divided two or more doses. Multiple doses of artemether or artesunate over 1- or 2-week intervals resulted in protection rates of 65% to 97% for preventing schistosomiasis, and increased doses and shorter medication intervals improved their efficacies. Praziquantel and artemisinin derivatives (artemether or artesunate) in combination resulted in a higher protection rate of 84% (95% CI: 64%-91%) than praziquantel monotherapy for treatment. praziquantel and artesunate in combination had a great protection rate of 96% (95% CI: 78%-99%) for preventing schistosomes infection.ConclusionsAccording to the results, praziquantel remains effective in schistosomiasis treatment, and multiple doses would improve its efficacy; meanwhile, praziquantel is also a good drug for preventing acute schistosomiasis morbidity. It's better to use multiple doses of artemether or artesunate with 1- or 2-week intervals for prevention against schistosome infection. Praziquantel and artemether or artesunate in combination perform better in treatment than praziquantel monotherapy, and they are especially suitable for treating the patients with repeated exposure to infected water.

Genetic variation of the human immunodeficiency virus type-1 (HIV-1) has been studied almost exclusively by the analysis of subgenomic segments ranging from 2% to 30% of the genome. Accordingly, in the current databases only very limited sequences encompassing the full-length HIV-1 genome have been reported, most of them deriving from B-clade HIV-1 isolates that were expanded in CD4 positive continuous celllines.1 However, in the light of recent findings describing that a significant fraction, perhaps more than 10%, of HIV-1 strains represent intersubtype mosaics,2,3 both, the genetic characterization of different variants of HIV-1 and the preparation of future vaccine trials would be facilitated by more complete sequencing of multiple full-length HIV-1 genomes.4HIV vaccine formulations may need to be tailored to the local strains circulating within a country or a geographical region.5 The expert group of the joint United Nations Program on AIDS4 recently identified Yunnan, a southwestern province of China as a region, in which the HIV epidemic is starting to gain speed, reminding to the situation in Thailand 10 years ago. In this province, drug abuse is the predominant factor of HIV-1 transmission (90%). Within this relatively isolated rural community, the incidence of HIV infections varied from 0.6% up to 30.1% in different counties.6,7 Molecular epidemiological studies showed that the first epidemic in this region was initiated by subtype B strains imported from Thailand in the late 80s by drug trafficking.8,9 With time, a shift occurred towards Thai-B(B') genotypes and the former predominant prototype B strains (90% in 1990) were taken over by Thai-B' variants (90% in 1996).10,n Although a second epidemic was imported by Indian IDUs carrying subtype C strains in the early 1990s12,13 and despite a few incidences caused by subtype E,14 subtype B' strains still represent the predominant virus in Yunnan. The homogenous seed virus transmitted among the local population recommended this area as a potential site for future safety and efficacy vaccine trials.10,11In order to gain deeper insight into the epidemiological situation of this area, sequence information encompassing a full-length HIV-1 genome from a representative primary isolate, would be highly desirable. Accordingly, PBMCs from an asymptomatic IDU (patient RL42), which has been demonstrated by C2V3 genotyping to be infected by a representative virus strain, were prepared. Phenotypical characterization by co-cultivation of the virus with PHA stimulated PBMCs from HIV negative blood donors resulted in a maximum of virus production at day 12 post infection. Maximum virus titers regularity obtained by growing and titrating the virus on PBMCs, were reproducibly in the range of 1 X 104 TCID50 per ml culture supernatant. Conversely, inoculation of the cell free virus with different T-cell-lines (H9, MT2, MT4) demonstrated only weak and transient replication to low titers, indicating the NSI/macrophage-tropic character of the RL42-isolate (data not shown).In o...

Avian hepatitis E virus (HEV) has been identified in chickens; however, only 4 complete or near-complete genomic sequences have been reported. We found that the near-complete genomic sequence of avian HEV in chickens from China shared the highest identity (98.3%) with avian HEV from Europe and belonged to avian HEV genotype 3.

Abstract. A total of 1,345 Ixodes persulcatus ticks collected from northeastern China were investigated for the presence of Anaplasma phagocytophila and Borrelia burgdorferi by a nested polymerase chain reaction (PCR). Sixty-two (4.6%) ticks were positive for A. phagocytophila and 454 (33.8%) were positive for B. burgdorferi. Seven (0.5%) were coinfected with both agents. Sequence analysis of 919-basepair PCR amplicons revealed three types of A. phagocytophila. Type 1 was identical to the published sequences of A. phagocytophilas responsible for human granulocytic ehrlichiosis (HGE). The other two variants differed from the HGE agent sequence at one and four positions, respectively. These findings imply that infection with A. phagocytophila poses a potential health threat to both humans and animals in northeastern China, and that ehrlichiosis should be considered in the differential diagnosis of febrile patients with a history of tick bite, particularly when clinical manifestations are atypical for Lyme disease.

COVID-19 is a complex disease phenotype where the underlying microbiome could influence morbidity and mortality. Amplicon and metagenomic MinION based sequencing was used to rapidly (within 8 hours) identify SARS-CoV-2 and assess the microbiome in nasopharyngeal swabs obtained from patients with COVID-19 by the ISARIC 4C consortium.

Hepatitis E virus (HEV) is a quasi-enveloped, single-stranded positive-sense RNA virus. HEV belongs to the family Hepeviridae, a family comprised of highly diverse viruses originating from various species. Since confirmation of HEV’s zoonosis, HEV-induced hepatitis has been a public health concern both for developing and developed countries. Meanwhile, the demonstration of a broad host range for zoonotic HEV suggests the existence of a variety of transmission routes that could lead to human infection. Moreover, anti-HEV antibody serosurveillance worldwide demonstrates a higher than expected HEV prevalence rate that conflicts with the rarity and sporadic nature of reported acute hepatitis E cases. In recent years, chronic HEV infection, HEV-related acute hepatic failure, and extrahepatic manifestations caused by HEV infection have been frequently reported. These observations suggest a significant underestimation of the number and complexity of transmission routes previously predicted to cause HEV-related disease, with special emphasis on zoonotic HEV as a public health concern. Significant research has revealed details regarding the virology and infectivity of zoonotic HEV in both humans and animals. In this review, the discovery of HEV zoonosis, recent progress in our understanding of the zoonotic HEV host range, and classification of diverse HEV or HEV-like isolates from various hosts are reviewed in a historic context. Ultimately, this review focuses on current understanding of viral pathogenesis and cross-species transmission of zoonotic HEV. Moreover, host factors and viral determinants influencing HEV host tropism are discussed to provide new insights into HEV transmission and prevalence mechanisms.

By using multilocus sequence analysis, five Borrelia valaisiana-related strains isolated from rodents and ticks in southwestern China were eventually classified as a new genospecies of B. burgdorferi sensu lato rather than B. valaisiana. The finding explained the differences in transmission cycle and phenotype between B. valaisiana strains from Europe and B. valaisiana-related strains from eastern Asia.Strains of Borrelia burgdorferi sensu lato, the causative agent of Lyme borreliosis, have been divided into at least 13 genospecies (7,8,10,15). The bacterium is maintained mainly in natural foci through the transmission cycles of Ixodes ticks and a wide variety of vertebrate hosts (15). Different B. burgdorferi sensu lato genospecies are distributed unevenly throughout the world and are associated with distinct ecologic features (15).To date, five established genospecies and a group of B. valaisiana-related strains have been isolated in mainland China (7,14,16). B. garinii and B. afzelii are major genospecies in natural foci of northern China and are maintained mainly in a tick-rodent cycle (16). Some B. valaisiana-related strains and B. sinica strains were recently isolated in some regions of the Yangtze River valley (7,14). B. valaisiana-related strains were once tentatively classified as B. afzelii based on the phylogenetic analysis of the rrs gene (2) and then considered to be B. valaisiana based on the phylogenetic analysis of the rrf-rrl intergenic spacer, the rrs gene, and the flagellin gene (4). Recently, Masuzawa et al. suggested that these isolates should be classified as a new genospecies based on a similar phylogenetic analysis (5). In order to clarify the exact taxonomy of B. valaisiana-related strains and explain the differences in transmission cycle and phenotype between B. valaisiana-related strains and B. valaisiana strains, we examined five B. valaisiana-related strains isolated from Guizhou Province in southwestern China by multilocus sequence analysis (MLSA), which was confirmed to surpass the discrimination power of whole-genome DNA-DNA hybridization (the "gold standard" in taxonomy) for B. burgdorferi sensu lato genospecies definition (8, 10). Moreover, new species B. spielmanii and B. californiensis were also confirmed and validated by MLSA (8, 10).Borrelia strains and culture conditions. The five strains used in this study were isolated either from ticks or from the urinary bladders of rodents in Guizhou Province in southwestern China in May 2006, as described previously (1). Strain QTMP2 was from Ixodes granulatus fed from Niviventer fulvescens, strains QSYSP3 and QSYSP4 were from Haemaphysalis longicornis fed from Apodemus agrarius, strain QSDS4 was from A. agrarius, and strain QLZSP1 was from I. granulatus fed from A. agrarius. These strains belong to the B. valaisiana-related group rather than the B. sinica and other B. burgdorferi sensu lato genospecies according to the results of restriction fragment length polymorphism analysis and the analysis of rrf-rrl intergenic spacer sequences...