SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis

BACKGROUND

SARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccinescaused by inequitable distribution.

OBJECTIVE

To monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health.

METHODS

Here we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples weresequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed.

RESULTS

The Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acidsubstitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previousinfection or vaccination.

CONCLUSION

There were nine lineages circulating in Zimbabwe during the second wave. The B.1.351 was dominant, accounting for >75%.There were over 3 000 mutations on the diagnostic genes and lineage B.1.351, contributing almost two-thirds of the mutations. The S-genehad the most mutations and the E-gene was the least mutated.

Antigenic distribution of Streptococcus agalactiae isolates from pregnant women at Garankuwa hospital - South Africa

INTRODUCTION

Streptococcus agalactiae (group B streptococcus; GBS) is globally recognised as one of the leading causes of neonatal sepsis and meningitis. It also causes adverse pregnancy outcomes such as stillbirth and miscarriages. Incidence of invasive disease is increasing in non-pregnant adults with underlying medical conditions (e.g., diabetes mellitus). Epidemiological studies of GBS infections are based on capsular serotyping. Genotyping of the surface anchored protein genes is also becoming an important tool for GBS studies. Currently ten different GBS serotypes have been identified. This study was performed to determine the prevalence of GBS capsular types (CTs) and surface anchored protein genes in isolates from colonized pregnant women attending antenatal clinic, at Dr George Mukhari Academic Hospital, Garankuwa, Pretoria, South Africa.

METHODS

The samples were collected over 11 months and cultured on selective media. GBS was identified using different morphological and biochemical tests. Capsular typing was done using latex agglutination test and conventional PCR. Multiplex PCR with specific primers was used to detect the surface anchored protein genes.

RESULTS

Of the 413 pregnant women recruited, 128 (30.9%) were colonized with GBS. The capsular polysaccharide (CPS) typing test showed that CPS type III (29.7%) was the most prevalent capsular type followed by CPS type Ia (25.8%), II (15.6%), IV (8.6%), V (10.9%) and Ib (8.6%); 0.7% of the isolates were nontypeable. Multiplex PCR revealed that the surface proteins genes were possessed by all the capsular types: rib (44.5%), bca (24.7%), alp2/3 (17.9%), epsilon (8.6%) and alp4 (4.7%).

CONCLUSION

The common capsular types found in this study are Ia, III, and II. The most common protein genes identified were rib and bca, and the distribution of the surface protein genes among the isolates of different capsular types showed similar trends to the distribution reported from previous studies.

Streptococcus agalactiae colonization and correlation with HIV-1 and HBV seroprevalence in pregnant women from Zimbabwe

OBJECTIVE

To estimate the frequency of coinfection of Streptococcus agalactiae or Group B streptococcus (GBS), hepatitis B virus (HBV) and HIV-1 in pregnant women and evaluate any association between them.

STUDY DESIGN

Three health centres from rural, rural-urban and urban communities were selected and at least 369 pregnant women had samples available for simultaneous analysis of GBS colonization rates, and HIV and HBV seroprevalence rates. Swabs were collected at two different stages in the course of pregnancy and at delivery to isolate GBS. Serum samples were collected at recruitment for analysis of standard HBV seromarkers and the presence of HIV-1. The odds ratio (95% CI) and chi(2) tests were used for analysis of the results at a level of significance set at <or=0.05.

RESULTS

Single infections with GBS, HBV and HIV-1 were found to be 35.7%, 3.3% and 20.1% respectively. The HIV-1 prevalence rate was 14.1%, 23.1% and 19.5% for the rural, rural-urban and urban communities respectively. The HBV prevalence rates were 3.3%, 3.0% and 3.7% for Chitsungo, Guruve and Harare respectively. There were no significant differences in HBV prevalence rates among the three communities. Simultaneous coinfection with GBS, HBV and HIV-1 was registered in only one (0.3%) of the women. The prevalence of coinfection with GBS/HBV, GBS/HIV-1 and HBV/HIV-1 was 0.5%, 9.2% and 0.8% respectively. The prevalence rate of GBS/HIV-1 coinfection was significantly higher in the rural-urban than the two other communities (p<0.001).

CONCLUSIONS

There was a high prevalence of single infections with GBS and HIV-1 but a lower HBV prevalence among pregnant women studied compared to other studies in Zimbabwe. Coinfection with GBS/HIV-1 was more common than GBS/HBV and HBV/HIV-1. Coinfection with HIV-1 and HBV did not differ between GBS colonized and GBS negative women. There was no difference in GBS colonization rate between HIV-1 positive and HIV-1 negative pregnant women.

Streptococcus agalactiae (group B streptococcus (GBS)) colonisation and persistence, in pregnancy; a comparison of two diverse communities (rural and urban)

OBJECTIVE

To establish the extent of GBS colonisation, persistence of colonisation in pregnancy and influence of obstetric history in two diverse communities (rural and urban) in Zimbabwe.

DESIGN

Cross sectional survey.

SETTING

Rutsanana Clinic in Highfield, Harare (representing the urban area) and Chitsungo Mission Hospital in Lower Guruve, (representing the rural area).

SUBJECTS

300 and 100 pregnant women from the urban and rural areas respectively.

MAIN OUTCOME MEASURES

GBS colonisation and persistence rates for both urban and rural areas were established, together with pregnancy outcome.

RESULTS

Mother colonisation rate was significantly higher in the rural areas (60%) as compared to the urban areas (46%). GBS colonisation persistence was evidently more in rural (48%) that in urban women (12%). Baby colonisation was also more in the rural (23%) that in urban area (5%). In both the rural and urban areas, flu-like illness was a common feature and was equally reported by the subjects. Vaginal discharge requiring treatment, previous stillbirths and previous miscarriages were equally reported in both communities.

Use of culture methods for recovery of atypical mycobacteria from stools of AIDS patients

OBJECTIVE

To establish recovery rates of atypical mycobateria from stools of suspected AIDS patients using culture media.

DESIGN

Laboratory evaluation of recovery rates, contamination rates, optimum exposure time and optimum concentration of alkali used for decontamination.

SETTING

The study was conducted in Harare, Zimbabwe at two medical institutions: Beatrice Road Infectious Diseases Hospital (BRIDH) (a tuberculosis referral hospital) and Mashambanzou Care Unit (MCU) (a home-based care centre).

SUBJECTS

A total of 386 stool specimens from suspected AIDS patients from the two health institutions plus 81 stool specimens from clinically healthy patients were collected. The number of patients from MCU was 144 (49 females, 95 males) and 242 from BRIDH (119 males, 123 females).

MAIN OUTCOME MEASURE

The main goals were to determine optimum exposure time and optimum concentration of alkali used in decontamination and to identify the culture medium with the best recovery rates of atypical mycobacteria.

RESULTS

Optimum recovery of atypical mycobacteria was achieved on Peizer TB medium after treating stool specimens with 4% sodium hydroxide for 35 minutes. In addition, the use of Kirchner's medium improved isolation rates, although with a slight increase in contamination at levels of 2.9%.

CONCLUSION

A stool specimen can be used to recover atypical mycobacteria in suspected AIDS patients. Recovery is achieved using Peizer TB medium at a concentration of 4%. Varying the exposure time of the stool specimen to the decontaminating alkali and incorporating antifungal agents and antibiotics into the medium, improves recovery of atypical mycobacteria.