First Complete Genome Sequence of a Subgenotype Vd Newcastle Disease Virus Isolate

Abstract

A Newcastle disease virus was isolated from a chicken from a live bird market in the Mbeya region of Tanzania. Complete genome characterization of the isolate identified it as a member of subgenotype Vd. This is the first complete genome sequence of this subgenotype.

Molecular Characterization of Newcastle Disease Viruses Isolated from Chickens in Tanzania and Ghana

“…However, according to the most recent NDV phylogenetic classification using the full-length F gene, these sequences lack branch support and are no longer classified into a separate subgenotype [5]. Genotype V isolates have been previously reported in Tanzania [11,15,23], but most of the Tanzanian sequences deposited in GenBank were significantly shorter than the sequences from this study and therefore were not used. The single strain from Tanzania used in this study is from Mbeya [23], which is approximately 630 km southwest of Morogoro, near the northeast region of Zambia.…”

“…Four genotype V isolates (MT335735, -36, -38 and -40) originated from chickens experimentally exposed to vNDV and were 100% identical. Altogether, the genotype V isolates from Morogoro were closely related to sequences from Mbeya (Tanzania, MK583011) [23], Kenya (JQ217418 to JQ217420) and Uganda (HG937571 to HG937573 and HG937580) [12]. The identities of these genotype V isolates are displayed in Table S2.…”

“…Genotype V isolates have been previously reported in Tanzania [11,15,23], but most of the Tanzanian sequences deposited in GenBank were significantly shorter than the sequences from this study and therefore were not used. The single strain from Tanzania used in this study is from Mbeya [23], which is approximately 630 km southwest of Morogoro, near the northeast region of Zambia. Sequences from Uganda and Kenya, countries bordering Northern Tanzania, also clustered with the isolates from Morogoro.…”

Surveillance and Genetic Characterization of Virulent Newcastle Disease Virus Subgenotype V.3 in Indigenous Chickens from Backyard Poultry Farms and Live Bird Markets in Kenya

“…The current study has classified the Kenyan vNDVs into a new subgenotype V.3, which, in accordance with the recently revised NDV classification system [ 19 ], is supported by the presence of several independent isolates without a direct epidemiologic link and phylogenetic clustering with bootstrap values of more than 70%. The Kenyan vNDV V.3 isolates are closely related to four other East African isolates identified with complete genome sequences [ 25 , 50 ], and others identified with partial F and HN gene sequences from Uganda in 2011 [ 24 ] and Kenya in 2018 [ 26 ]. So far, no other NDV strains related to subgenotype V.3 viruses have been reported from Northern, Western, and Southern Africa, suggesting that the viruses may be geographically restricted to the East African region.…”

First Complete Genome Sequence of Currently Circulating Infectious Bronchitis Virus Strain DMV/1639 of the GI-17 Lineage

“…Next-generation paired-end sequencing (2 × 150 bp) was performed on a MiSeq instrument using the 300-cycle MiSeq reagent kit version 2 (Illumina, USA). Sequence data were assembled using a de novo approach and utilizing MIRA version 3.4.1 (10) within a customized workflow on the Galaxy platform (11), as described previously (12, 13). Briefly, the following parameters were specified for the assembly step: assembly method, de novo ; assembly quality grade, accurate; use read extension, yes; minimum reads per contig, 100; minimum overlap, 16; mark repeats, yes; maximum megahub ratio, 0.2; and spoiler detection, yes.…”