Detection of a SARS-CoV-2 variant of concern in South Africa.

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.

Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.

The circulation of Omicron BA.1 led to the rapid increase in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases in South Africa in November 2021, which warranted the use of more rapid detection methods. We, therefore, assessed the ability to detect Omicron BA.1 using genotyping assays to identify specific mutations in SARS-CoV-2 positive samples, Gauteng province, South Africa. The TaqPath™ COVID-19 real-time polymerase chain reaction assay was performed on all samples selected to identify spike gene target failure (SGTF). SARS-CoV-2 genotyping assays were used for the detection of del69/70 and K417N mutation. Whole-genome sequencing was performed on a subset of genotyped samples to confirm these findings. Of the positive samples received, 11.0% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. We identified SGTF in 98.9% (173/175) of samples, of which 88.0% (154/175) had both the del69/70 and K417N mutation. The genotyped samples (45.7%; 80/175) that were sequenced confirmed Omicron BA.1 (97.5%; 78/80). Our data show that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, we still require assays for the detection of unique mutations that will allow for the differentiation between other Omicron sublineages. Therefore, the use of genotyping assays to detect new dominant or emerging lineages of SARS-CoV-2 will be beneficial in limited-resource settings.

Genomic analysis of nontypeable pneumococci causing invasive pneumococcal disease in South Africa, 2003-2013.

BACKGROUND: The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as such, limited data exist which describe these organisms. We aimed to describe disease and genotypically characterize NTPn causing invasive pneumococcal disease in South Africa. RESULTS: Isolates were detected through national, laboratory-based surveillance for invasive pneumococcal disease in South Africa and characterized by whole genome analysis. We predicted ancestral serotypes (serotypes from which NTPn may have originated) for Group I NTPn using multilocus sequence typing and capsular region sequence analyses. Antimicrobial resistance patterns and mutations potentially causing nontypeability were identified. From 2003-2013, 39 (0.1 %, 39/32,824) NTPn were reported. Twenty-two (56 %) had partial capsular genes (Group I) and 17 (44 %) had complete capsular deletion of which 15 had replacement by other genes (Group II). Seventy-nine percent (31/39) of our NTPn isolates were derived from encapsulated S. pneumoniae. Ancestral serotypes 1 (27 %, 6/22) and 8 (14 %, 3/22) were most prevalent, and 59 % (13/22) of ancestral serotypes were serotypes included in the 13-valent pneumococcal conjugate vaccine. We identified a variety of mutations within the capsular region of Group I NTPn, some of which may be responsible for the nontypeable phenotype. Nonsusceptibility to tetracycline and erythromycin was higher in NTPn than encapsulated S. pneumoniae. CONCLUSIONS: NTPn are currently a rare cause of invasive pneumococcal disease in South Africa and represent a genetically diverse collection of isolates.

Two cases of serotypeable and non-serotypeable variants of Streptococcus pneumoniae detected simultaneously during invasive disease.

BACKGROUND: More than 94 serotypes of Streptococcus pneumoniae have been described to date, however the majority of disease is caused by approximately 20 serotypes. Some pneumococci do not react with commercially available antisera used for serotyping and are thus regarded as non-serotypeable (NT). These pneumococci are commonly isolated during carriage studies and very rarely cause invasive disease. Colonization may occur with more than one serotype however disease with more than one serotype is rarely detected. Thus there are limited data describing cases of pneumococcal disease caused by more than one isolate. RESULTS: In two cases of invasive pneumococcal disease in South Africa, a non-serotypeable and a serotypeable isolate were co-detected during routine serotyping. A serotype 1 and 18C isolate were each co-detected with a non-serotypeable isolate in 2009 (case A) and 2010 (case B), from cerebrospinal fluid and blood, respectively. Both patients were 10-14 years old. For case A, the serotypeable isolate could not be obtained due to low representation in the mixed culture. Using electron microscopy we confirmed lack of capsule for the non-serotypeable isolates. Comparison of the case A non-serotypeable isolate with a serotype 1 genome revealed only the presence of the rhamnose biosynthesis genes (rmlA, B, C and D) in the capsular locus, all other capsular genes were absent. Nonetheless it had a multilocus sequence type (ST) associated with serotype 1 (ST217 and ribosomal ST3462) and its core genome clustered with other ST217 isolates. The case B non-serotypeable isolate had all serotype 18C capsular genes except for variation in the wchA and wze genes, compared to the 18C isolate. Both case B isolates were ST9817 and their core genomes were identical. CONCLUSIONS: The ability of pneumococci to alter capsule production is a potential vaccine escape mechanism and therefore non-serotypeable pneumococci should be monitored as such organisms may increase under vaccine pressure.

Coding-Complete Genome Sequences for Two Confirmed Monkeypox Cases in South Africa 2022.

The coding-complete genome sequences of monkeypox virus (MPXV) were obtained from skin lesion swabs from two human cases detected in South Africa in June 2022. Sequence analyses indicated that the genetic sequences of the viruses associated with these two cases were related most closely to the genetic sequences of other MPXVs reported during the 2022 multicountry outbreak and belong to the monkeypox hMPXV-1 clade (previously West Africa clade) and B.1 lineage.

Marked Effects of Larval Salt Exposure on the Life History and Gut Microbiota of the Malaria Vector Anopheles merus (Diptera: Culicidae).

Anopheles merus can breed in a range of saltwater concentrations. The consequences of this ability on the life history of adult An. merus are poorly understood. This study examined the effects of exposure to 0, 2.1875, 4.375, 8.75, and 17.5 g/L of sodium chloride on An. merus. The effects on larval development, adult longevity, fertility, and fecundity, as well as deltamethrin tolerance were examined. The effect of larval salt exposure on the expression of defensin-1 in adults was examined by quantitative Real-Time PCR. Finally, the effect of the larval salt concentration on microbial dynamics was assessed by 16S Next Generation Sequencing. High concentrations of saltwater increased larval development time and number of eggs laid, as well as deltamethrin tolerance. Larval exposure to salt also reduced the expression of defensin-1. The exposure also had a significant effect on microbial diversity in larvae and adults. The diversity of larvae decreased once adults emerged. Salt-tolerant bacterial genera predominated in larvae but were absent in adults. High salt concentrations resulted in greater abundance of Plasmodium-protective genera in adults. Although this study was conducted on a laboratory strain of An. merus, these data suggest that osmoregulation has a significant effect on the life history of the species with potential epidemiological consequences.

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.

Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The initial C.1.2 detection is associated with a high substitution rate, and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 variants of concern or variants of interest. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent donors infected with either Beta or Delta show high plasma neutralization against C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection against C.1.2.

Genome Sequencing of a Severe Acute Respiratory Syndrome Coronavirus 2 Isolate Obtained from a South African Patient with Coronavirus Disease 2019.

As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here we present the sequence, phylogenetic analysis, and modeling of nonsynonymous mutations for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome that was detected in a South African patient with coronavirus disease 2019 (COVID-19).

Genomic differences among carriage and invasive nontypeable pneumococci circulating in South Africa.

Most pneumococci express a polysaccharide capsule, a key virulence factor and target for pneumococcal vaccines. However, pneumococci showing no serological evidence of capsule expression [nontypeable pneumococci (NTPn)] are more frequently isolated from carriage studies than in invasive disease. Limited data exist about the population structure of carriage NTPn from the African continent. We aimed to characterize carriage NTPn and compare them to previously described invasive NTPn. Carriage and invasive NTPn isolates were obtained from South African cross-sectional studies (2009 and 2012) and laboratory-based surveillance for invasive pneumococcal disease (2003-2013), respectively. Isolates were characterized by capsular locus sequence analysis, multilocus sequence typing, antimicrobial non-susceptibility patterns and phylogenetic analysis. NTPn represented 3.7 % (137/3721) of carriage isolates compared to 0.1 % (39/32 824) of invasive isolates (P<0.001), and 24 % (33/137) of individuals were co-colonized with encapsulated pneumococci. Non-susceptibility to cotrimoxazole [84 % (112/133) vs 44 % (17/39)], penicillin [77 % (102/133) vs 36 % (14/39)], erythromycin [53 % (70/133) vs 31 % (12/39)] and clindamycin [36 % (48/133) vs 18 % (7/39)] was higher (P=0.03) among carriage than invasive NTPn. Ninety-one per cent (124/137) of carriage NTPn had complete deletion of the capsular locus and 9 % (13/137) had capsule genes, compared to 44 % (17/39) and 56 % (22/39) of invasive NTPn, respectively. Carriage NTPn were slightly less diverse [Simpson's diversity index (D)=0.92] compared to invasive NTPn [D=0.97]. Sixty-seven per cent (92/137) of carriage NTPn belonged to a lineage exclusive to NTPn strains compared to 23 % (9/39) of invasive NTPn. We identified 293 and 275 genes that were significantly associated with carriage and invasive NTPn, respectively. NTPn isolates detected in carriage differed from those causing invasive disease, which may explain their success in colonisation or in causing invasive disease.