Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches: 15 isolates from the early epidemic (March 12–April 1 2020) and 31 from later time-points ( 25–27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades: 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5–99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana.     

Experimental manipulation of immune-mediated disease and its fitness costs for rodent malaria parasites

Background  

Explaining parasite virulence (harm to the host) represents a major challenge for evolutionary and biomedical scientists alike. Most theoretical models of virulence evolution assume that virulence arises as a direct consequence of host exploitation, the process whereby parasites convert host resources into transmission opportunities. However, infection-induced disease can be immune-mediated (immunopathology). Little is known about how immunopathology affects parasite fitness, or how it will affect the evolution of parasite virulence. Here we studied the effects of immunopathology on infection-induced host mortality rate and lifetime transmission potential – key components of parasite fitness – using the rodent malaria model, Plasmodium chabaudi chabaudi.     

Inhibitory activity of Indian spice plant Cinnamomum zeylanicum extracts against Alternaria solani and Curvularia lunata, the pathogenic dematiaceous moulds

Background

Enteric fever is an endemic problem in Nepal and Widal agglutination test is widely used for its diagnosis but a normal baseline titer in healthy population and cutoff values have not been established.

Methods

We measured average baseline antibody titers against "O" and "H" antigens of Salmonella enterica serotype Typhi and "H" antigens of serotypes Paratyphi A and Paratyphi B among apparently healthy blood donors in Nepal. The antibody titers were measured using Standard Widal Confirmatory Quantitative Tube test.

Results

Among the 100 blood samples collected from healthy volunteers, 62 individuals had significant antibody titers (≥ 1:20) against one of the four antigens against S. enterica. Among 54 samples with an anti-O titer against serotype Typhi, 15 and 36 samples had titers of ≥ 1:60 and ≥ 1:40, respectively. A significant proportion (12% of all) had anti-O titer of ≥ 1:80. Similarly, among the 59 samples demonstrating anti-H titers of ≥ 1:20 to S. enterica serotype Typhi, 29 had a titer of ≥ 1:80 and 12 had 1:160. For S. enterica serotypes Paratyphi A and B, anti-H titers of ≥ 1:20 were found only in 12% and 3%, respectively, of all samples tested.

Conclusion

When a single Widal agglutination titer is used for the diagnosis of enteric fever, it will be more appropriate to change the currently used cutoff levels against S. enterica serotype Typhi to > 1:80 for anti-O and > 1:160 for anti-H titers for Nepal.     

Molecular characterization of 'Bhut Jolokia' the hottest chilli

The northeast region of India, considered as 'hot spot' of biodiversity, having unique ecological environment with hot and high-humidity conditions, has given rise to the world's hottest chilli, 'Bhut Jolokia', which is at least two times hotter than Red Savina Habanero in terms of Scoville heat units (SHU). This study was undertaken to determine the distinctiveness of 'Bhut Jolokia' from Capsicum frutescens or Capsicum chinense through sequencing of the ribosomal RNA (rRNA) gene-internal transcribed ((ITS) region along with its phylogenetic analysis. Although a compensatory base change (CBC) in the ITS2 region was not observed between the closely related species of C. frutescens and C. chinense when compared with Bhut Jolokia; phylogenetic analysis using ITS1, 5.8S and ITS2 sequences indicated a distinct clade for all the accessions of 'Bhut Joloikia', while C. frutescens and C. chinense occupied discrete lineages. Further, a unique 13-base deletion was observed in all the representative accessions of 'Bhut Jolokia', making it distinct from all other members within the genus and beyond. The degree of genetic variations along with its extreme pungency might be related to ambient environmental factors of northeastern India.     

Pseudomonas aeruginosa corneal infection affects cholinergic enzymes in rat lacrimal gland

Since the increased use of extended-wear contact lenses, Pseudomonas aeruginosa has emerged as a primary etiological agent of ulcerative keratitis. Clinical isolates have been classified into two types: cytotoxic and non-cytotoxic. This study revealed significant immune and neuro-enzymatic changes elicited by the two types of P. aeruginosa in the lacrimal gland of rats. The humoral immune response in the lacrimal gland to the non-cytotoxic strain was significantly lower than to the cytotoxic strain, possibly due to the immunogenicity of the extracellular toxin; however, the same effect was not seen in the serum. Choline acetyltransferase and acetylcholinesterase are known to be responsible for synthesis and degradation of acetylcholine, respectively, binding receptors on acini and plasma cells, modulating their activity, and constituting the principle regulator of tear secretion. Following infection, neuro-enzyme activities were significantly modified to reduce the concentration of acetylcholine and therefore potentially reduce secretion from the glands. The data lead to the hypothesis that P. aeruginosa may have the potential to reduce the protective barrier provided by the lacrimal gland to benefit pathogenicity. It was also observed that the neuro-enzyme response of the lacrimal glands of uninfected eyes of the test animals was the same as that of infected eyes, implying that the signal may be relayed by common lymphoidal tissue or the central nervous system and a measurable response returned to both eyes.     

Comparison of verdeluz orange G and modified Gallego stains

Tumors of the oral cavity include combinations of hard and soft tissues that may be difficult to identify using routine hematoxylin and eosin (H & E) staining. Although combination stains can demonstrate hard and soft tissues, trichrome stains, such as VanGieson and Masson, cannot differentiate dental hard tissues, such as dentin, cementum and osteoid. Modified Gallegos (MGS) and verdeluz orange G-acid fuchsin (VOF) stains can differentiate components of teeth. We used 10 tissue sections of decalcified bone and 10 pathologic tissue sections that contained different calcified tissues including peripheral ossifying fibroma, odontoma, central ossifying fibroma and cemento-ossifying fibroma. Sections were stained with H & E, VOF or MGS. H and E stained both hard tissues pink. VOF stained bone purple-red, cementum red and collagen blue. MGS stained bone green-blue, cementum red and collagen blue. VOF staining intensity and differentiation was better than MGS staining. VOF staining demonstrated hard tissue components distinctly and exhibited good contrast with the surrounding connective tissue. VOF also is a simple, single step, rapid staining procedure.