Physical and chemical aspects at the interface and in the bulk of CuInSe2-based thin-film photovoltaics

Technical issues which remain in CuInSe2-based solar cells are reviewed. A study of single-crystalline Cu(In,Ga)Se2 film devices, carrier recombination analysis, and effects of alkali-metal doping and silver-alloying are particularly focused on.

Novel characteristics of Chinese NADC34-like PRRRSV during 2020-2021

NADC34-like PRRSV strains were first detected in China in 2017, with epidemic potential. In this study, the phylogenetic, epidemic, and recombinant properties of NADC34-like PRRSV in China were evaluated comprehensively. From 2020 to October 2021, 82 NADC34-like PRRSV isolates were obtained from 433 PRRSV-positive clinical samples. These strains accounted for 11.5% and 28.6% of positives in 2020 and 2021, respectively, and have spread to eight provinces. We selected 15 samples for whole-genome sequencing, revealing genome lengths of 15,009 to 15,113 nt. Phylogenetic analysis revealed that Chinese NADC34-like strains cluster with American sublineage 1.5 strains and do not form an independent branch. Recombination analysis revealed that six of fifteen complete genome sequences derived from recombination between NADC34-like and NADC30-like or HP-PRRSV; they all recombined with local strains in China, exhibiting a complex recombination pattern. Partial Nsp2 sequence alignment showed that nine of fifteen isolates have a continuous 100-aa deletion (similar to IA/2014/NADC34); other isolates have a 131-aa discontinuity deletion (similar to NADC30). Five of them also have additional amino acid deletions, all of which are reported for the first time here. In the last two years, NADC34-like PRRSV has become one of the main epidemic strains in some areas of China; it has changed significantly, its homology has decreased significantly, and it has undergone complex recombination with local Chinese strains. These results are of great significance for understanding the current epidemic situation of PRRSV in China.

Isolation and Molecular Charcteristic of a Recombinant Feline Calicivirus from Qingdao, China

Feline calicivirus (FCV) is a highly contagious pathogen that can cause seriously upper respiratory tract and oral disease in feline. Despite widespread vaccination, the prevalence of FCV remains high. In this study, the FCV qd/2019/china was isolated from domestic feline oropharyngeal swab which was collected in qingdao, China. The virus was purified with plaque assay and identified with PCR and IFA method. the capsid amino acid ,VP1, of qd/2019/china [1] showed sequence identity with other isolate ranging from 83.9% (ym3/2001/jp) to 91.1% (CH-JL4) .Sequence analysis of the capsid amino acid revealed that qd/2019/china was closely related to CH-JL4 and clustered with CH-JL4 in the phylogenetic tree. Phylogenetic analysis indicated that complete genome of qd/2019/china and CH-JL4 was also classified into the same cluster. While the recombination analysis with Simplot indicate that the qd/2019/china originated from the recombination of CH-JL4 and HRB-SS, and the region 3821–5301 nt originated from HRB-SS. Further, the region 3821–5301 nt belong to protease -polymerase (PP) of HRB-SS. Here we isolate a new FCV qd/2019/china, which may be a recombinant virus, These results were beneficial for understanding the evolution of FCV.

Horizontal transmission and recombination of Wolbachia in the butterfly tribe Aeromachini Tutt, 1906 (Lepidoptera: Hesperiidae)

Wolbachia is arguably one of the most ubiquitous heritable symbionts among insects and understanding its transmission dynamics is crucial for understanding why it is so common. While previous research has studied the transmission pathways of Wolbachia in several insect lineages including Lepidoptera, this study takes advantage of data collected from the lepidopteran tribe Aeromachini in an effort to assess patterns of transmission. Twenty-one of the 46 species of Aeromachini species were infected with Wolbachia. Overall, 25% (31/125) of Aeromachini specimens tested were Wolbachia positive. All Wolbachia strains were species specific except for the wJho strain which appeared to be shared by three host species with a sympatric distribution based on a co-phylogenetic comparison between Wolbachia and the Aeromachini species. Two tests of phylogenetic congruence did not find any evidence for cospeciation between Wolbachia strains and their butterfly hosts. The co-phylogenetic comparison, divergence time estimation and Wolbachia recombination analysis revealed that Wolbachia acquisition in Aeromachini appears to have mainly occurred mainly through horizontal transmission rather than codivergence.

A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China

A novel beta-coronavirus, SARS-CoV-2, emerged in late 2019 and rapidly spread throughout the world, causing the COVID-19 pandemic. However, the origin and direct viral ancestors of SARS-CoV-2 remain elusive. Here, we discovered a new SARS-CoV-2-related virus in Yunnan province, in 2018, provisionally named PrC31, which shares 90.7% and 92.0% nucleotide identities with SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment revealed that several genomic regions shared strong identity with SARS-CoV-2, phylogenetic analysis supported that PrC31 shares a common ancestor with SARS-CoV-2. The receptor binding domain of PrC31 showed only 64.2% amino acid identity with SARS-CoV-2. Recombination analysis revealed that PrC31 underwent multiple complex recombination events within the SARS-CoV and SARS-CoV-2 sub-lineages, indicating the evolution of PrC31 from yet-to-be-identified intermediate recombination strains. Combination with previous studies revealed that the beta-CoVs may possess more complicated recombination mechanism. The discovery of PrC31 supports that bats are the natural hosts of SARS-CoV-2.

Molecular Characterization of the Nsp2 and ORF5 (ORF5a) Genes of PRRSV Strains in Nine Provinces of China During 2016–2018

Porcine reproductive and respiratory syndrome virus (PRRSV) causes a highly contagious disease and brings huge economic losses to commercial pork production worldwide. PRRSV causes severe reproductive failure in sows and respiratory distress in piglets. To trace the evolution of PRRSV in pigs with respiratory diseases in some regions of China, 112 samples were collected from nine provinces in China during 2016–2018. All samples were detected by RT-PCR and analyzed by the Nsp2/ORF5 (ORF5a)-genes-phylogeny. Sequence analysis and recombination analysis were conducted on the Nsp2/ORF5 (ORF5a) genes of the identified strain in the study. The RT-PCR result shown that the positive rate of PRRSV was 50.89% (57/112). Phylogenetic analysis showed that the identified PRRSV strains were all NA genotype and belonged to lineage 1, 3, and 8. The Nsp2 gene of identified PRRSV strains exhibited nucleotide homologies of 53.0 ~ 99.8%, and amino acid homologies of 46.8 ~ 99.7%. The ORF5 gene of identified PRRSV strains exhibited nucleotide homologies of 82.4 ~ 100%, and amino acid homologies of 79.6 ~ 100%. Sequence analysis revealed that a discontinuous 30-amino-acid deletion (positions 481 and 533–561) and a 131-amino-acid discontinuity deletion (positions 323–433, 481, and 533–551) in Nsp2 of PPRSV isolates; all identified strains in this study may be wild strains, and most identified strains may be highly virulent strains. Sequence analysis of ORF5 and ORF5a revealed that the mutation sites of GP5 were mainly concentrated in the signal peptide and epitopes region, while the mutation sites of ORF5a were mainly concentrated in the transmembrane and the intramembrane region. The recombination analysis indicated that there may be multiple recombination regions in identified strains, and the recombination pattern was more complex. This study showed that the prevalent PRRSV strain in some regions of China was still HP-PRRSV, while NADC30 strain also occupied a certain proportion; different types of PRRSV strains showed different patterns and variation in China. This study suggested that the monitoring of PRRSV prevalence and genetic variation should be further strengthened.

Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

Background The SARS-CoV-2 pandemic is one of the greatest global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. Results We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215–1425] of gene S and region [534–727] of gene N. Moreover, some statistically significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. Conclusions The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of this dangerous virus.