Confirmation of pygmy sperm whale, Kogia breviceps from Palk Bay, India through Cytochrome Oxidase1 (COI) sequence

The identity of a stranded cetacean from the Palk Bay has been confirmed as a pygmy sperm whale (Kogia breviceps) by the partial sequencing of mitochondrial gene cytochrome oxidase subunit-I (COI). The specimen was unambiguously discriminated from the COI sequence of Kogia sima by matching exactly with the sequence of K. breviceps. Stranding events of the pygmy whales are considered to be uncommon. The sequence developed for K. breviceps is the first of its kind attempt from Indian waters.

Sclerotinia Rot of Peucedanum japonicum Thunb. Caused by Sclerotinia sclerotiorum

Sclerotinia rot was occurred on the leaf and stem of Peucedanum japonicum Thunb. in greenhouse field of Pohang city of Gyeongbuk province in Korea. The typical symptom of the disease was light brown spot and tipburn on infected leaves. The colony of the isolated fungus was white to light gray in color. Asci were cylindrical shape and 75‒240×5.9‒17.3 μm in size. Apothecia were cup-shaped with numerous asci and 0.5‒0.9 cm in size. Ascospores were aseptate and ellipsoid in shape, and 8.4‒10.7×4.8‒5.8 μm in size. Sclerotia formed on the plants and potato dextrose agar medium were globose to irregular in shape and black in color. Partial sequencing of rDNA of this isolate showed that it was 100% consistent with that of Sclerotinia sclerotiorum. It was confirmed that the same lesion was formed by reinoculating this pathogen on a healthy P. japonicum Thunb. and the same strain was isolated. This is the first report on the Sclerotinia rot of P. japonicum Thunb. caused by S. sclerotiorum in Korea.

Molecular Epidemiology of Sapovirus in Children Living in the Northwest Amazon Region

Sapovirus is an important etiological agent of acute gastroenteritis (AGE), mainly in children under 5 years old living in lower-income communities. Eighteen identified sapovirus genotypes have been observed to infect humans. The aim of this study was to identify sapovirus genotypes circulating in the Amazon region. Twenty-eight samples were successfully genotyped using partial sequencing of the capsid gene. The genotypes identified were GI.1 (n = 3), GI.2 (n = 7), GII.1 (n = 1), GII.2 (n = 1), GII.3 (n = 5), GII.5 (n = 1), and GIV.1 (n = 10). The GIV genotype was the most detected genotype (35.7%, 10/28). The phylogenetic analysis identified sapovirus genotypes that had no similarity with other strains reported from Brazil, indicating that these genotypes may have entered the Amazon region via intense tourism in the Amazon rainforest. No association between histo-blood group antigen expression and sapovirus infection was observed.

Molecular analysis of G3P[6] rotavirus in the Amazon region of Brazil: evidence of reassortment with equine-like strains

Aim: To perform a molecular analysis of rotavirus A (RVA) G3P[6] strains detected in 2012 and 2017 in the Amazon region of Brazil. Materials & methods: Eighteen RVA G3P[6] strains were collected from children aged under 10 years hospitalized with acute gastroenteritis, and partial sequencing of each segment genome was performed using Sanger sequencing. Results: Phylogenetic analysis showed that all G3P[6] strains had a DS-1-like genotype constellation. Two strains had the highest nucleotide identities with equine-like G3P[6]/G3P[8] genotypes. Several amino acid alterations in VP4 and VP7 neutralizing epitopes of equine-like RVA G3P[6] strains were observed in comparison with vaccine strains. Conclusion: These findings suggest that equine-like RVA G3P[6] strains have been circulating in the Amazon region of Brazil as a result of direct importation, and support natural RVA evolutionary mechanisms.

First-Time Presence of African Swine Fever Virus Genotype II in Nigeria

A confirmed African swine fever (ASF) outbreak in Nigeria was further investigated by partial sequencing of B464L and E183L genes of the ASF virus (ASFV). Results revealed the first-time presence of ASFV genotype II in Nigeria and West Africa. This finding has serious implications for control measures and food security.

Bacteria associated with the intestinal tract of three predators of Dactylopius opuntiae (Hemiptera: Dactylopiidae)

Insects depend on gut bacteria for many metabolic functions including detoxification. Dactylopius (Hemiptera: Dactylopiidae) species (e.g. D. opuntiae and D. coccus) produce carminic acid possibly acting as part of their immune response to predation; thus predators of Dactylopius species may require intestinal symbionts to metabolize carminic acid acquired from their prey. The average content of carminic acid in D. opuntiae and D. coccus is 3–5% and 19–25% respectively; the predators Leucopina bellula and Hyperaspis trifurcata are specialists on D. opuntiae while Laetilia coccidivora feeds on both D. opuntiae and D. coccus. We determined the diversity of bacteria associated with the gut of these predators to test the hypothesis that it would vary significantly depending on the level of prey specialism. Bacteria were isolated from the intestine of Le. bellula, L. coccidivora and H. trifurcata larvae and also adults of H. trifurcata. Bacteria were identified morphologically and by partial sequencing of the 16S rRNA gene. The greatest bacterial diversity was found in L. coccidivora and H. trifurcata adults, followed by H. trifurcata larvae. The lowest diversity was found in Le. bellula. Sequencing revealed the presence of Bacillus cereus, Enterococcus gallinarum and E. casseliflavus in L. coccidivora larvae; Enterobacter sp. in larvae of H. trifurcata; Lactococcus lactis in adults of H. trifurcate; and Staphylococcus sp. in larvae and adults of H. trifurcate. Bacillus pumilus was only found in Le. bellula. The possible role of these bacteria in the ability of predators to feed on D. opuntiae and D. coccus is discussed.

An upsurge of SARS CoV-2 B.1.1.7 Variant in Pakistan

The emergence of a more transmissible variant of SARS-CoV-2 (B1.1.7) in the United Kingdom (UK) during late 2020 has raised major public health concerns. Several mutations have been reported in the genome of the B.1.1.7 variant including the N501Y and 69-70deletion in the Spike that has implications on virus transmissibility and diagnostics. Although the B.1.1.7 variant has been reported from several countries, only two cases have been identified through whole-genome sequencing from Pakistan. We used a two-step strategy for the detection of B.1.1.7 with initial screening through ThermoFisher TaqPathTM SARS-CoV-2 kit followed by partial sequencing of Spike (S) gene of samples having spike gene target failure (SGTF) on real-time PCR. From January 01, 2021, to February 21, 2021, a total of 2,650 samples were tested for the presence of SARS-CoV-2 using TaqPathTM kit and 70.4% (n=1,867) showed amplification of all the 3 genes (S, N, and ORF). Notably, 29.6% (n=783) samples had the spike gene target failure (SGTF). The SGTF cases were detected at a low frequency during the first three weeks of January (n=10, n=13, and n=1 respectively) however, the cases started to increase in the last week. During February, 726 (93%) cases of SGTF was reported with a peak (n=345) found during the 3rd week. Based on the partial sequencing of spike gene of SGTF samples (n=15), 93% (n=14) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1.1.7 variant. Our findings highlight the high prevalence of B.1.1.7 in Pakistan and warrant large scale genomic surveillance and strengthening of laboratory network in the country.