A novel subgenotype C6 Enterovirus A71 originating from the recombination between subgenotypes C4 and C2 strains in mainland China

Recombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.

House sparrows do not exhibit a preference for the scent of potential partners with different MHC-I allele numbers and genetic distances

MHC genes play a fundamental role in immune recognition of pathogens and parasites. Therefore, females may increase offspring heterozygosity and genetic diversity by selecting MHC genetically compatible or heterozygous males. In birds, several studies suggest that MHC genes play a role in mate choice, and recent evidence suggest that olfaction may play a role in such discrimination. Previous studies indicated that house sparrow females with low allelic diversity prefer males with higher diversity in MHC-I alleles. Here, we directly explored whether both house sparrow females and males could estimate by scent the number in MHC amino acid and functional variants as well as the level of MHC-I similarity or dissimilarity of potential partners. Our results show that neither females nor males exhibit a preference related to the number of MHC-I amino acid variants or functional variants or in relation to MHC amino acid or functional similarity of potential partners, suggesting that MHC-I is not detected through olfaction. Further studies are needed to understand the mechanisms responsible for MHC-I based mate discrimination in birds.

On the taxonomy of Negeta semialba Hampson, 1918 with descriptions of two new Leucobaeta László, Ronkay & Witt, 2010 species (Lepidoptera, Nolidae, Nolinae)

The taxonomic position of the West African Negeta semialba Hampson, 1918 is revised and the species is transferred from the genus Negeta Walker, 1862 of Westermanniinae to Leucobaeta László, Ronkay & Witt, 2010 of Nolinae: Leucobaeta semialba (Hampson, 1918) comb. n., based on morphological analysis. The hitherto unknown male adult and genitalia of both sexes are described and illustrated. Leucobaeta semialba is compared to the superficially similar Afrotropical Negeta mesoleuca (Holland, 1894) and N. ruficeps (Hampson, 1902); two sibling species from East Africa and Madagascar are described as new to science: L. smithi and L. malagassa spp. n. Pairwise genetic distances of COI-5P sequences between the taxa are provided.

Molecular assessment of the species of Gracilariaceae (Gracilariales, Rhodophyta) from the Yucatan Peninsula, Mexico, including two new records for the Mexican Atlantic

Background. The Gracilariaceae is one of the most diverse and abundant families of marine red algae. Most species in this family exhibit high morphological variability and overlapping of characters. In the Yucatan Peninsula 30 species have been historically recorded, but the phylogenetic identity for many of them is still unknown. Questions: Is the current diversity of the family in the area overestimated? Studied species: Crassiphycus caudatus, C. corneus, C. usneoides, Gracilaria flabelliformis, G. hayi, G. cf isabellana, G. microcarpa, G. occidentalis, G. suzanneae, Gracilariopsis tenuifrons. Study site and dates: Campeche: km 33 carretera Champotón, Bahía Tortuga, Puente Xen Kan III, Punta Xen, Sabancuy, 2017, 2018; Yucatan: Puerto Sisal, Puerto Progreso, Puerto Chicxulub, Puerto Telchac, 2018; Quintana Roo: Playa 88, Xcalacoco, Punta Esmeralda, 2019. Methods. Phylogenetic analysis (with COI-5P and rbcL sequences), supported by DNA species delimitation methods, genetic distances and morphological comparisons, allowed us to molecularly identify the specimens collected. Results. The phylogenetic identity of 10 species of Gracilariaceae was confirmed, two of which are new records for the Mexican Atlantic: G. hayi and G. suzanneae. Conclusion. The study demonstrated that the molecular assessment has proved to be very useful for the diversity evaluation, thus, the future phylogenetic identifies for the rest of morphospecies recorded in the area will allow a better approximation of Gracilariaceae diversity species.

A genetic history of migration, diversification, and admixture in Asia

L.L. Cavalli-Sforza spearheaded early efforts to study the genetic history of humans, recognizing the importance of sampling diverse populations worldwide. He supported research on human evolutionary genetics in Asia, with research on human dispersal into Asia and genetic distances between present-day East Asians in the late 20th century. Since then, great strides have been made in understanding the genetic history of humans in Asia, through large-scale genomic sequencing of present-day humans and targeted sequencing of DNA from ancient humans. In this review, I survey the genetic prehistory of humans in Asia, based on research using sequence data from humans who lived in Asia as early as 45,000 years ago. Genetic studies comparing present-day Australasians and Asians show that they likely derived from a single dispersal out of Africa, rapidly differentiating into three main lineages: one that persists partially in South Asia, one that is primarily found today in Australasia, and one that is widely represented across Siberia, East Asia, and Southeast Asia. Studies of ancient DNA from human remains in Asia dating from as far back as 45,000 years has greatly increased our understanding of the population dynamics leading to the current Asian populations. Based on "Jin L, Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc Natl Acad Sci U S A. 1999;96(7):3796-3800”.

Temporal Patterns in the Evolutionary Genetic Distance of SARS-CoV-2 during the COVID-19 Pandemic

During coronavirus disease 2019 (COVID-19) pandemic, the genetic mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred frequently. Some mutations in the spike protein are considered to promote transmissibility of the virus, while the mutation patterns in other proteins are less studied and may also be important in understanding the characteristics of SARS-CoV-2. We used the sequencing data of SARS-CoV-2 strains in California to investigate the time-varying patterns of the evolutionary genetic distance. The accumulative genetic distances were quantified across different time periods and in different viral proteins. The increasing trends of genetic distance were observed in spike protein (S protein), the RNA-dependent RNA polymerase (RdRp) region and nonstructural protein 3 (nsp3) of open reading frame 1 (ORF1), and nucleocapsid protein (N protein). The genetic distances in ORF3a, ORF8, and nsp2 of ORF1 started to diverge from their original variants after September 2020. By contrast, mutations in other proteins appeared transiently, and no evident increasing trend was observed in the genetic distance to the original variants. This study presents distinct patterns of the SARS-CoV-2 mutations across multiple proteins from the aspect of genetic distance. Future investigation shall be conducted to study the effects of accumulative mutations on epidemics characteristics.

Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan

In the initial phase of the novel coronavirus disease (COVID-19) pandemic, a large-scale cluster on the cruise ship Diamond Princess (DP) emerged in Japan. Genetic analysis of the DP strains has provided important information for elucidating the possible transmission process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on a cruise ship. However, genome-based analyses of SARS-CoV-2 detected in large-scale cruise ship clusters other than the DP cluster have rarely been reported. In the present study, whole-genome sequences of 94 SARS-CoV-2 strains detected in the second large cruise ship cluster, which emerged on the Costa Atlantica (CA) in Japan, were characterized to understand the evolution of the virus in a crowded and confined place. Phylogenetic and haplotype network analysis indicated that the CA strains were derived from a common ancestral strain introduced on the CA cruise ship and spread in a superspreading event-like manner, resulting in several mutations that might have affected viral characteristics, including the P681H substitution in the spike protein. Moreover, there were significant genetic distances between CA strains and other strains isolated in different environments, such as cities under lockdown. These results provide new insights into the unique evolution patterns of SARS-CoV-2 in the CA cruise ship cluster.

Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia

Mammal-associated coronaviruses have a long evolutionary history across global bat populations, which makes them prone to be the most likely ancestral origins of coronavirus-associated epidemics and pandemics globally. Limited coronavirus research has occurred at the junction of Europe and Asia, thereby investigations in Georgia are critical to complete the coronavirus diversity map in the region. We conducted a cross-sectional coronavirus survey in bat populations at eight locations of Georgia, from July to October of 2014. We tested 188 anal swab samples, remains of previous pathogen discovery studies, for the presence of coronaviruses using end-point pan-coronavirus RT-PCR assays. Samples positive for a 440 bp amplicon were Sanger sequenced to infer coronavirus subgenus or species through phylogenetic reconstructions. Overall, we found a 24.5% positive rate, with 10.1% for Alphacoronavirus and 14.4% for Betacoronavirus. Albeit R. euryale, R. ferrumequinum, M. blythii and M. emarginatus were found infected with both CoV genera, we could not rule out CoV co-infection due to limitation of the sequencing method used and sample availability. Based on phylogenetic inferences and genetic distances at nucleotide and amino acid levels, we found one putative new subgenus and three new species of Alphacoronavirus, and two new species of Betacoronavirus.

Species Relationship and Population Differentiation In Stellaria L. (Caryophyllaceae) Of Iran Using Scot Molecular Marker and Morphological Data

Recognition of species is essential in a variety of domains, most remarkably biology, biogeography, ecology, as well as conservation. The genus Stellaria L. (Caryophyllaceae) has over 120 species spread across Europe and Asia's temperate zones. According to the most remarkable current treatments, nine species recognize Stellaria in Iran. These species are categorized into two types. Despite the broad distribution of several Stellaria species in Iran, no research on their genetic variability, method of divergence, or dispersion trends is accessible. As a result, we conducted genetic and morphological research on six Stellaria species and two of their closest relatives gathered from various habitats in Iran. This research aims to 1) Can SCoT markers be utilized to recognize Stellaria species? 2) What are the genetic characteristics of the mentioned taxa in Iran? and 3) To examine the interrelation of the species. In this research, ten SCoT markers were employed for molecular analysis, and 112 accessions were utilized for morphological study. The genetic distances were calculated using the Jaccard similarity coefficient, and descriptive data on the populations were used to estimate genetic parameters. There were 98 polymorphic bands all over. The integration of morphological and SCoT data demonstrated that the Stellaria species of Iran could be delimited and recognized. The Stellaria species are genetically unique; however, they share some similar alleles, according to AMOVA and STRUCTURE analyses. Bangladesh J. Plant Taxon. 28(2): 317-328, 2021 (December)