Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests

AbstractRoutine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.

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Norovirus diversity in children with gastroenteritis in South Africa from 2009 to 2013: GII.4 variants and recombinant strains predominate

Epidemiology and Infection ◽

10.1017/s0950268815002150 ◽

2015 ◽

Vol 144 (5) ◽

pp. 907-916 ◽

Cited By ~ 21

Author(s):

J. MANS ◽

T. Y. MURRAY ◽

S. NADAN ◽

R. NETSHIKWETA ◽

N. A. PAGE ◽

...

Keyword(s):

South Africa ◽

Nucleotide Sequence ◽

Rna Polymerase ◽

New Orleans ◽

Sequence Analyses ◽

Rna Dependent Rna Polymerase ◽

Recombinant Strains

SUMMARYFrom 2009 to 2013 the diversity of noroviruses (NoVs) in children (⩽5 years) hospitalized with gastroenteritis in South Africa was investigated. NoVs were genotyped based on nucleotide sequence analyses of partial RNA-dependent RNA polymerase (RdRp) and capsid genes. Seventeen RdRp genotypes (GI.P2, GI.P3, GI.P6, GI.P7, GI.P not assigned (NA), GI.Pb, GI.Pf, GII.P2, GII.P4, GII.P7, GII.P13, GII.P16, GII.P21, GII.Pc, GII.Pe, GII.Pg, GII.PNA) and 20 capsid genotypes (GI.1, GI.2, GI.3, GI.5, GI.6, GI.7, GI.NA, GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.10, GII.12, GII.13, GII.14, GII.16, GII.17, GII.21) were identified. The combined RdRp/capsid genotype was determined for 275 GII strains. Fifteen confirmed recombinant NoV strains circulated during the study period. NoV GII.P4/GII.4 (47%) and GII.Pe/GII.4 (18%) predominated, followed by GII.PNA/GII.3 (10%) and GII.P21/GII.3 (7%). Other prevalent strains included GII.Pg/GII.12 (6%) and GII.Pg/GII.1 (3%). Two novel recombinants, GII.Pg/GII.2 and GII.Pg/GII.10 were identified. In 2013 the replacement of GII.4 New Orleans 2009 and GII.P21/GII.3, which predominated during the early part of the study, with GII.4 Sydney 2012 and GII.PNA/GII.3 was observed. This study presents the most comprehensive recent data on NoV diversity in Africa.

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First Report of a Peronospora Species on Sweet Basil in South Africa

Plant Disease ◽

10.1094/pd-90-1115a ◽

2006 ◽

Vol 90 (8) ◽

pp. 1115-1115 ◽

Cited By ~ 18

Author(s):

A. McLeod ◽

S. Coertze ◽

L. Mostert

Keyword(s):

South Africa ◽

Downy Mildew ◽

Sequence Data ◽

Pcr Amplification ◽

Its Sequence ◽

Western Cape ◽

Crop Failure ◽

First Report ◽

Sweet Basil ◽

Initial Symptoms

Sweet basil (Ocimum basilicum) is an herbaceous aromatic annual plant of the family Lamiaceae grown for its flavoring and fragrances that can be used fresh or dried. In South Africa, sweet basil is grown on a commercial scale. Downy mildew has recently been reported as one of the most destructive diseases of sweet basil in Switzerland, France, and Italy (1–3). The identity of the downy mildew species infecting sweet basil has been controversial and has been indicated as Peronospora lamii, a presumably undescribed (unnamed) Peronospora species, as well as a few species of which the status as distinct species is mostly unclear or doubtful (1). The distinction between P. lamii and the unnamed Peronospora species has been based on their sporangial dimensions, with P. lamii having sporangial dimensions with a length and width range of 16 to 26 × 15 to 23 μm (average 21 × 18 μm) and the unnamed Peronospora species having sporangial dimensions of 20 to 35 × 15 to 25 μm (average 28 × 22 μm) (1) or 23 to 36 × 18 to 29 μm (average 29 × 23 μm) (2). Additionally, internal transcribed spacer (ITS) sequence data has also been used to show that P. lamii and the unnamed Peronospora species on basil are not similar (1). In the Western Cape Province of South Africa, a sweet basil sample was received at the Stellenbosch University Plant Disease Clinic in 2005 from a grower in the region who experienced almost 50% crop failure under greenhouse-grown conditions. Initial symptoms were chlorotic leaves that subsequently developed a brown sporulation on the abaxial side. Microscopic observations of the brown sporulation were consistent with a Peronospora species. The sporangiophores branched two to five times with lengths ranging from 130 to 290 μm (average 194 μm). Sporangiophores terminated with dichotomously branched denticels bearing single detachable sporangia. Sporangia measured 26 to 34 × 20 to 28 μm (average 30 × 24 μm) and were elliptical and brown. The sporangia were similar in shape, color, and size range as that previously reported for a unnamed Peronospora species on sweet basil (1,2). Sequence analyses were also conducted on two isolates by first extracting DNA from spores that were washed from leaves using the Wizard SV genomic DNA purification system (Promega, Madison, WI), followed by polymerase chain reaction (PCR) amplification and sequencing of the ITS1, 5.8S, and ITS2 regions using primers ITS6 and ITS4 (4). The sequences of the two isolates were identical (GenBank Accession No. DQ479408). BLAST analyses of the sequences revealed a 99% similarity to the unnamed Peronospora species that was isolated from sweet basil in Switzerland and Italy (1). The sequences of the South African isolates only had low homology to P. lamii. To our knowledge, this is the first report of a Peronospora species on sweet basil in South Africa that on the basis of morphology and ITS sequence data is similar to the unnamed Peronospora species recently described in Switzerland and Italy on sweet basil (1). References: (1) L. Belbahri et al. Mycol. Res. 109:1276, 2005. (2) A. Garibaldi et al. Plant Dis. 88:312, 2004. (3) A. Garibaldi et al. Plant Dis. 89:683, 2005. (4) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds., Academic Press, San Diego, 1990.

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