Oxford Nanopore Sequencing Reveals an Exotic Broad bean mottle virus Genome within Australian Grains Post-Entry Quarantine.

A Broad bean mottle virus (BBMV) isolate (S52) obtained from an infected Vicia faba leaf sample from Syria was sequenced using Oxford Nanopore long-read sequencing at the Australian border. The genome had 95.6%, 98.2%, and 93.4% nucleotide sequence identity to BBMV strains RNA1 (Bawden), RNA2 (Mo), and RNA3 (Bawden).

Transcriptome Sequencing Reveals the Genome Sequence of Pea Early Browning Virus from a 29-Year-Old Faba Bean Sample.

Pea early browning virus (PEBV) is transmitted by soil-inhabiting trichodorid nematodes and via seeds. The transcriptome sequencing method, followed by de novo assembly, revealed the PEBV Libyan isolate LyV66-91 genome. Its RNA1 resembled that of UK isolate SP5 with 93.91% nucleotide identity, and its RNA2 had 63.32% nucleotide identity to that of Dutch isolate E116.

Genome Sequence and Phylogeny of a Bean Yellow Mosaic Virus Isolate Obtained from a 14-Year-Old Australian Lentil Sample.

Using RNA strand-specific sequencing followed by de novo assembly, a Bean yellow mosaic virus (BYMV) genome was obtained from a lentil sample (Aus14BY) collected in Victoria, Australia, in 2005. When compared with 51 BYMV genomes, it closely resembled the Western Australian isolate PN83A (Lupinus angustifolius), with 98.4% nucleotide identity.

Coding-Complete Sequences of Barley Virus G Isolates from Australia, Obtained from a 34-Year-Old and a 1-Year-Old Sample.

Coding-complete sequences of two barley virus G isolates from Australia were obtained from a 34-year-old oat sample (isolate Aus8) and a 1-year-old barley sample (isolate Aus17N). The Aus8 and Aus17N isolates share 96.3% nucleotide identity with each other and 95.7 to 95.8% nucleotide identity with the South Korean isolate Uiseong.

Metagenomic Analysis Reveals a Nearly Complete Genome Sequence of Alfalfa Mosaic Virus from a Field Pea in Australia.

Here, we report the first nearly complete genome sequence of Alfalfa mosaic virus (AMV) obtained from a symptomatic field pea sample (Aus295) in Australia. Its genome RNA1 and RNA2 segments resembled those of the Argentinian isolate Manfredi, with 99.4% and 96.7% nucleotide (nt) identity, respectively; its RNA3 segment resembled that of Chinese isolate AMV-Gyn, with 99.6% nt identity.

Illumina Sequencing Reveals the First Near-Complete Genome Sequence of Ugandan Passiflora Virus.

Here, we present the first near-complete genome of Ugandan Passiflora virus (UPV) sequenced from a symptomatic sample of KH7 passion fruit (Passiflora edulis Sims) variety. UPV had limited amino acid identity with other potyviruses known to cause passion fruit woodiness disease (PWD). The closest relationship (71.2% amino acid similarity) was with Bean common mosaic necrosis virus.

Transcriptome Sequencing Reveals a Complete Genome Sequence of Cowpea Aphid-Borne Mosaic Virus from Passion Fruit in Kenya.

Analysis of transcriptome sequencing (RNA-Seq) data revealed a complete Cowpea aphid-borne mosaic virus (CABMV) genome from virus-infected passion fruit in Kenya. We compared it with six complete CABMV genomes, one each from Zimbabwe and Uganda and two each from Brazil and India. The Zimbabwean isolate CABMV-Z was the closest, with 83.0% nucleotide identity.

Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: predominance of P[8] genotype resembling human strains.

Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1-29.7%). This study revealed that age, management system and pig density significantly (p<0.01) influenced the incidence of RVA infections, with housed_free-range management system and larger herd size showing higher risks for RVA infection. Partial (811-1604nt region) sequence of the VP4 gene of selected positive samples revealed that different genotypes (P[6], P[8] and P[13]) are circulating in the study area with P[8] being predominant. The P[6] strain shared nucleotide (nt) and amino acid (aa) sequence identity of 84.4-91.3% and 95.1-96.9%, respectively, with known porcine and human P[6] strains. The P[8] strains shared high nt and aa sequence identity with known human P[8] strains ranging from 95.6-100% to 92-100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6-91.7% and 89.3-96.4%, respectively, only with known porcine P[13] strains. No P[8] strains yielded RNA of sufficient quality/quantity for full genome sequencing. However analysis of the full genome constellation of the P[6], two P[13] and one untypeable strains revealed that the P[6] strain (Ke-003-5) genome constellation was G26-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, P[13] strains (Ug-049 and Ug-453) had G5-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 while the untypeable strain (Ug-218) had G5-P[?]-I5-R1-C1-M1-A8-N1-T1-E1-H? In conclusion, P[6] and P[8] genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Further studies are required to determine the role of RVA in swine enteric disease burden and to determine the genetic/antigenic heterogeneity of the circulating strains for development of accurate diagnostic tools and to implement appropriate prophylaxis programs.

INTERNAL ROOT MORPHOLOGY IN MANDIBULAR FIRST PERMANENT MOLARS IN A KENYAN POPULATION.

OBJECTIVE: To determine the internal root morphology and gender variations in mandibular first permanent molars in a Kenyan population. DESIGN: In vitro descriptive cross sectional study. SETTING: School of Dental Sciences, University of Nairobi RESULTS: The mesial root of mandibular first molars had two canals in 96.3% of the teeth in both males and females and-type IV canal configuration was most prevalent in the mesial root. The distal root of the mandibular first molar had one canal in 57.7% of the teeth in males and females. There were significant gender variations in the number of canals and canal configurations in the distal root. Two canals were more prevalent in females (53.6%) compared to males (30.4%) and a single canal was more frequent in males (69.6%) compared to females (46.4%) (P=0.001). Canal types 1, 11 and IV were the most frequent in the mandibular distal root. The gender variation in the frequency of canal types I, II and IV in the distal root was statistically significant (P=0.001). CONCLUSION: Most of the mandibular first molars have three canals (56%). Two canals in the distal root are more frequent among females (53.6%) compared to males (30.4%).

Internal root morphology of the maxillary first premolars in Kenyans of African descent.

OBJECTIVE: To determine the internal root morphology of the maxillary first premolar in Kenyans of African descent. DESIGN: In vitro descriptive cross-sectional study. SETTING: School of Dental Sciences, University of Nairobi. SUBJECTS: One hundred and fifty five extracted maxillary first premolars obtained from patients aged between 13-30 years attending dental clinics within Nairobi. RESULTS: There were 77 premolars from males and 78 from females. Majority (87.1%) of the teeth had two canals. Males presented with three canals more commonly than females. This difference was statistically significant. According to Vertucci's classification, male specimens demonstrated five of the canals types while female specimens demonstrated all the eight canal types. These differences were not statistically significant. CONCLUSIONS: Kenyan maxillary first premolar was mostly found to have two canals. There were eight canal types, with type IV being the commonest.

Maternal morbidity and mortality in peri-urban Kenya--assessing progress in improving maternal healthcare.

OBJECTIVE: Improving quality of maternal healthcare delivery is pivotal to reversing the trend of maternal health in developing countries and consequently, achieving the 5th millennium goal of reducing maternal mortality and improving universal access to reproductive health. Periodic facility-based reviews of maternal morbidity and mortality are crucial to improving quality of care delivered. METHODS: This retrospective study was conducted in PCEA Kikuyu Hospital, Kenya. Data on sociodemographics, recorded antenatal care activities, maternal morbidities and deaths were elicited from case notes of all pregnancies and births over a 2 year period and subsequently analyzed. RESULTS: There were 1716 deliveries during the period. 1405 (91%) of the women booked for antenatal care; 1068 (57.3%) had at least 3 visits before delivery. 842 (45.9%) were either untested for Human Immunodeficiency Virus or their results were not documented; 55 (3%) tested positive. The caesarean section rate was 27.4% (n=470); PMTCT (Prevention of Mother to Child Transmission) constituted 1.6% (10) of the indications. Urinary tract infection was the commonest maternal illness in pregnancy (14.5%, n=270), however, it was not found to be associated with any adverse outcome. Genital tract trauma was the commonest morbidity suffered by the women during delivery (90.6%, n=800). Psychological disorders constituted 5.3% (7) of reported postpartum complications. There were 2 maternal deaths out of 1673 live births, giving a maternal mortality ratio of 119.55 per 100,000 live births. The deaths resulted from septic abortion and eclampsia. CONCLUSION: Urinary tract infection is an important cause of maternal illness during pregnancy. Routine screening is recommended. PMTCT needs further consolidation to increase the number of screened women and ensure those who need interventions like caesarean sections get access to them. Diagnosis and management of psychological disorders in pregnancy remain unsatisfactory. Further studies to identify the true burden of these conditions are needed.

Oral hygiene habits and dental health awareness of Kenyan children aged 9-15 years in a peri-urban and urban school.

The oral hygiene habits and dental health awareness of 541 Kenyan children from a peri-urban and urban school and aged 9-15 years, were investigated. 80.2% of the urban children and 43.1% of the peri-urban children had visited a dentist before. 12.4% of the urban children and 9.2% of the peri-urban children knew that bacteria cause dental caries. Over 87% of the children from either school knew that dental caries and periodontitis can be prevented. The main reason for visiting a dentist was to have tooth extraction. Failure to brush teeth was believed to be the cause of gingival bleeding by 38.9% of the peri-urban children and 37.6% of the urban children. 67.2% of the peri-urban children and 39.5% of the urban children brushed their teeth thrice daily. 21.1% of the peri-urban children and 2% of the urban children used a chewing stick to brush their teeth. More urban children (96.5%) used a toothbrush than peri-urban children (64.8%). None of the children from either school admitted using traditional cleaning aids such as the finger and charcoal. It is concluded that there were no consistent differences in oral hygiene habits and dental health awareness between peri-urban and urban children.

Root canal treatment and pulpotomy in Kenya.

This study was carried out to evaluate the practice and depth of knowledge of root canal treatment and pulpotomy by dentists in Kenya. Questionnaires were prepared and mailed to 114 dentists whose addresses were available. Sixty seven (58.8%) dentists responded. Of these, 67.2% carried out root canal treatment (RCT) and 43.3% carried out pulpotomy. The main reasons given by most dentists in the public hospitals for not carrying out these procedures routinely were lack of facilities and materials. Furthermore, it was found that amongst those who carried out these procedures, some used outdated techniques and materials. In order to reduce the large number of teeth lost through extraction, materials and equipment should be made available to enable dentists carry out root canal treatment and pulpotomies routinely. It is also necessary to have continuing dental education amongst dentists to update their knowledge of these procedures.

The average human tooth lengths for black Kenyan population.

Measurement of tooth lengths was carried out on 537 extracted human teeth. The teeth were collected from adults aged 17 years and above and preserved in formalin. The tooth lengths were obtained by taking measurements off calibrated graph paper. The lengths obtained in this study were comparable to previous data reported in the literature. However, this new data will provide useful guidelines in Kenya for the management of endodontic patients especially in the purchase and stocking of the most appropriate endodontic instruments.