Distribution and molecular diversity of three cucurbit-infecting poleroviruses in China

Cucurbit aphid-borne yellows virus (CABYV) and Melon aphid-borne yellows virus (MABYV) have been found to be associated with cucurbit yellowing disease in China. Our report identifies for the first time a third distinct polerovirus, tentatively named Suakwa aphid-borne yellows virus (SABYV), infecting Suakwa vegetable sponge. To better understand the distribution and molecular diversity of these three poleroviruses infecting cucurbits, a total of 214 cucurbitaceous crop samples were collected from 25 provinces in China, and were investigated by RT-PCR and sequencing. Of these, 108 samples tested positive for CABYV, while 40 samples from five provinces were positive for MABYV, and SABYV was detected in only 4 samples which were collected in the southern part of China. Forty-one PCR-amplified fragments containing a portion of the RdRp gene, intergenic NCR and CP gene were cloned and sequenced. Sequence comparisons showed that CABYV isolates shared 78.0–79.2% nucleotide sequence identity with MABYV isolates, and 69.7–70.8% with SABYV. Sequence identity between MABYV and SABYV was 73.3–76.5%. In contrast, the nucleotide identities within each species were 93.2–98.7% (CABYV), 98.1–99.9% (MABYV), and 96.1–98.6% (SABYV). Phylogenetic analyses revealed that the polerovirus isolates fit into three distinct groups, corresponding to the three species. The CABYV group could be further divided into two subgroups: the Asia subgroup and the Mediterranean subgroup, based on CP gene and partial RdRp gene sequences. Recombination analysis suggested that MABYV may be a recombinant virus.     

Archaeal diversity in acid mine drainage from Dabaoshan Mine, China

Three acid mine drainage (AMD) samples collected from Dabaoshan Mine (Guangdong Province, China) were studied. In addition to physicochemical analyses, the diversity and community structures of the archaeal communities in these samples were described at the genetic level by amplified ribosomal DNA restriction analysis (ARDRA). Nine different ARDRA patterns were obtained from 146 clones and were studied as operational taxonomic units (OTUs), which were re-amplified and sequenced. Sequence data and phylogenetic analysis showed that most of the clones belonged to the Thermoplasmatales, and that archaea belonging to the Sulfolobales were absent. Only 1 OTU attributed to Ferroplasma was found and was observed to be abundant in all 3 samples. Eight OTUs were related to 2 new undefined groups in the Thermoplasmatales. Of the 8 OTUs, the clones in 2 similar units were isolated from samples collected from an abandoned sulfide mine (Huelva, Spain) and those in 5 similar units were isolated from samples collected from a closed copper mine (Tonglushan, China). These diversities were characterized by the reciprocal of Simpson's index (1/D) and correlated with the concentrations of ferrous ions and toxic ions in the AMD samples. The high temperature of the sampling sites was one of the factors that could explain why archaea belonging to the Thermoplasmatales were abundant in the analyzed AMD samples while those belonging to the Sulfolobales were absent.     

Prevalence and genetic diversity of human sapovirus associated with sporadic acute gastroenteritis in South China from 2013 to 2017

Human sapovirus (SaV) is an important viral agent for acute diarrhea worldwide, but timely prevalence data of human SaV in South China are still lacking. In this study, a 4-year surveillance was conducted to characterize the prevalence and genetic characteristics of the circulating SaV associated with sporadic diarrhea in South China. From November 2013 to October 2017, 569 fecal samples from patients with acute diarrhea were collected. SaV was detected in 11 samples with a positive rate of 1.93%. Three human genogroups of GI, GII, and GIV were identified, including five GI.1 strains, three GI.2 strains, one GI.3 strain, one GII.8 strain, and one GIV strain. Furthermore, multiple alignments of complete capsid protein VP1 genes of five local GI.1 strains and other available GI.1 strains in GenBank were performed. Average pairwise identities were calculated at 95.33% and 99.36% at nucleotide and amino acid levels, and only six variable amino acid sites were found during its 36-years’ evolution process. GI.1 strains could be further phylogenetically divided into four clusters with an approximate temporal evolution pattern, and local strains belonged to Cluster-d with other four strains from China and Japan. In summary, SaV was identified as an etiological agent responsible for sporadic gastroenteritis in Guangzhou with a low prevalence rate as in other Chinese cities, but its high genetic diversity suggested the necessity of continuous SaV surveillance in the future.