Public Sector Laboratories Research Articles

External Quality Assessment Program for SARS-COV-2 Molecular Detection in Pakistan.

Amid coronavirus disease 2019 (COVID-19) pandemic, accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for diagnosis management and breaking down transmission chains. We designed a national external quality assessment panel (EQAP) for SARS-CoV-2 molecular detection comprising working laboratories nationwide. A molecular diagnostic EQA panel that consists of five samples for SARS CoV-2 testing was distributed to 141 public and private sector laboratories across country. These samples contain different concentrations of SARS-CoV-2 to evaluate the sensitivity of commercial kits available. Sensitivity among public and private sector laboratories was variable, particularly lower SARS-CoV-2 concentrations significantly increased the risk of false-negative tests, whereas Ct values of accurately tested SARS-CoV-2 specimens increased as concentration decreased. These findings highlighted that performance of used commercial kits was not significantly correlated to various extraction or PCR methods. This study highlights the need for a national external quality assessment panel (EQAP) in the country to improve the quality of the healthcare system while ensuring the accuracy and reliability of results. Furthermore, EQAPs can help laboratories meet accreditation and regulatory requirements. However, continued participation in EQAP is recommended for quality enhancement of laboratories.

Lessons Leanrt Of The First Public Sector ISO 15189 Accredited Laboratory In Ghana

Background: Accreditation of public sector medical laboratories in developing countries such as Ghana have been described as an almost impossible task despite major efforts to establish and maintain efficient quality laboratory management systems. The Pathology Division of the 37 Military Hospital provides evidence of an efficient approach to accreditation to ISO 15189 in Ghana and the need to make medical laboratory accreditation an integral part of the national healthcare delivery system.Methods: The laboratory adopted the Strengthening Laboratory Management Towards Accreditation (SLMTA) programme. After implementation the laboratory accelerated the process towards accreditation using an approach involving senior management in allaccreditation activities, use of specific teams to focus on key improvement projects coordinated by an efficient mentorship programme. The laboratory was finally assessed by the Southern African Development Community for Accreditation Services to meeting the requirement of ISO 15189.Results: The Pathology Division of the 37 Military Hospital attained accreditation for its Haematology and Chemical Pathology departments making it the first public sector laboratory in Ghana to meet the requirement of ISO 15189. There has been an observedimprovement in confidence of personnel and a culture for quality and meeting standards in support of quality healthcare delivery.Conclusion: ISO 15189 accreditation of medical laboratories is possible for all public sector laboratories in Ghana and the approach is scalable scalable especially for tertiary level laboratories. Accreditation ensures a culture for quality which is critical in supportof quality patient care and must be an important aspect of national healthcare delivery systems.

Open Online Courses for Strengthening Laboratory-Based Detection of Antimicrobial Resistance in Pakistan.

IntroductionQuality-assured antimicrobial susceptibility testing (AST) depends upon the knowledge and skills of laboratory staff. In many low- and middle-income countries (LMICs), including Pakistan, such types of knowledge and skills are limited. Therefore, the objective of this study was to use openaccess online courses to improve the knowledge of laboratory staff involved in the detection and reporting of antimicrobial resistance (AMR).MethodologySeven online modules comprising 22 courses aimed at strengthening the laboratory detection of Antimicrobial resistance (AMR) were developed. The courses were uploaded onto the website www.parn.org.pk. Participants had an option of selecting courses of their interest. Online registration and completion of a pre-course assessment (pre-test) were essential for enrolment. However, participation in post-course assessment (post-test) was optional. The number of registered participants and the proportion of participants who completed each course were computed. A paired t-test was used to assess the increase between mean pre- and post-test scores. The association between the participants working in public vs. private laboratories and course completion rates were determined using the chi-square test.ResultsA total of 227 participants from Pakistan (March 2018 to June 2020) were registered. The largest number of registered participants and the highest completion rate were noted for AST and biosafety courses, while quality-related courses attracted a lower interest. A comparison of pre- and post-test performance using the paired mean score for the individual courses showed a statistically significant (the value of p < 0.05) improvement in 13/20 assessed courses. A higher course completion rate was observed in participants from public vs. private sector laboratories (56.8 vs. 30.8%, the value of p = 0.005).ConclusionsOur study suggests a promising potential for open online courses (OOCs) toward addressing knowledge gaps in laboratory practice in resource limited settings.

Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia.

Early detection of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) variants and use of data for public health action requires a coordinated, rapid, and high throughput approach to whole genome sequencing (WGS). Currently, WGS output from many low- and middle-income countries (LMIC) has lagged. By fostering diverse partnerships and multiple sequencing technologies, Indonesia accelerated SARS-CoV-2 WGS uploads to GISAID from 1,210 in April 2021 to 5,791 in August 2021, an increase from 11 submissions per day between January to May, to 43 per day between June to August. Turn-around-time from specimen collection to submission decreased from 77 to 5 days, allowing for timely public health decisions. These changes were enabled by establishment of the National Genomic Surveillance Consortium, coordination between public and private sector laboratories with WGS capability, and diversification of sequencing platform technologies. Here we present how diversification on multiple levels enabled a rapid and significant increase of national WGS performance, with potentially valuable lessons for other LMICs.

Nationwide external quality assessment of SARS-CoV-2 nucleic acid amplification tests in Japan

ObjectivesWe conducted a nationwide external quality assessment (EQA) study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid amplification testing in Japan. MethodsA total of 563 public health and private sector laboratories participated. The EQA samples comprised 6 RNA and full-process controls. ResultsThe overall agreements were 99.3% and 97.9% for the RNA and full-process controls, respectively. A total of 530/563 (94.1%) laboratories reported correct results; public health laboratories had the highest accuracy. Thirty-three laboratories reported at least one incorrect result (26 laboratories of medical facilities, 5 commercial laboratories, 1 public health laboratory, and 1 other). Sixteen laboratories of medical facilities that used a fully automated assay system failed to detect the presence of the full-process control, due to inherent insufficiency in the limit of detection (LOD). Other causes of incorrect results included failure to ensure the LOD (n = 13), error in result judging or reporting (n = 3), and error in sample handling (n = 1). ConclusionsPerformance was mostly dependent on the laboratory category and assay evaluation, particularly the LOD. Guidance should be developed based on these results, particularly in the phase of new entry into laboratory services for SARS-CoV-2.

Cancer in HIV-positive and HIV-negative adolescents and young adults in South Africa: a cross-sectional study

ObjectiveTo determine the spectrum of cancers in adolescents and young adults (AYAs) living with and without HIV in South Africa.DesignCross-sectional study with cancer records provided by the National Cancer Registry...

Guest Editorial: Papers from the SEE International Conference RADAR 2019

This Editorial introduces a Special Issue of papers from the SEE International Conference RADAR 2019, which took place in Toulon, France, 23–27 September 2019. The papers are expanded versions of ones that were judged in the reviewing process to be of the highest quality and relevance. Benefitting from the unique location of the conference centre on the French Riviera, the conference was given the theme ‘Sensing from sea to space’, attracting nearly 400 attendees from 26 countries from all over the world (Figure 1). Engineers and researchers coming from private or public sector (universities and laboratories) shared their knowledge and experience on radar topics of common interests from physics to signal processing, from sensor validation to system design, and also on emerging technologies based on artificial intelligence; all topics being supported by 200 papers presented either in oral (150 papers in 36 sessions), or poster sessions (50 papers). Figure 2 shows the range of topics of the papers. FIGURE 1Open in figure viewerPowerPoint Conference attendees by country FIGURE 2Open in figure viewerPowerPoint Conference paper topics

Community health workers augment the cascade of TB detection to care in urban slums of two metro cities in India.

BackgroundTuberculosis Health Action Learning Initiative (THALI) funded by USAID is a person-centered initiative, supporting vulnerable urban populations to gain access to TB services. THALI trained and placed 112 Community health workers (CHWs) to detect and support individuals with TB symptoms or disease within urban slums in two cities, Hyderabad and Bengaluru, covering a population of about 3 million.MethodsCHWs visited the slums once in a fortnight. They conducted TB awareness activities. They referred individuals with TB symptoms for sputum testing to nearest public sector laboratories. They visited those testing TB positive, once a fortnight in the intensive phase, and once a month thereafter. They supported TB patients and families with counselling, contact screening and social scheme linkages. They complemented the shortfall in urban TB government field staff numbers and their capacity to engage with TB patients. Data on CHWs’ patient referral for TB diagnosis and treatment support activities was entered into a database and analyzed to examine CHWs’ role in the cascade of TB care. We compared achievements of six monthly referral cohorts from September 2016 to February 2019.ResultsOverall, 31 617 (approximately 1%) of slum population were identified as TB symptomatic and referred for diagnosis. Among the referred persons, 23 976 (76%) underwent testing of which 3841 (16%) were TB positive. Overall, 3812 (99%) were initiated on treatment and 2760 (72%) agreed for regular follow up by the CHWs. Fifty-seven percent of 2952 referred were tested in the first cohort, against 86% of 8315 in the last cohort. The annualized case detection rate through CHW referrals in Bengaluru increased from 5.5 to 52.0 per 100 000 during the period, while in Hyderabad it was 35.4 initially and increased up to 118.9 per 100 000 persons. The treatment success rate was 87.1% among 193 in the first cohort vs 91.3% among 677 in the last cohort.ConclusionsCHWs in urban slums augment TB detection to care cascade. Their performance and TB treatment outcomes improve over time. It would be important to examine the cost per TB case detected and successfully treated.

The burden of cancers associated with HIV in the South African public health sector, 2004\u20132014: a record linkage study

IntroductionThe impact of South Africa’s high human immunodeficiency virus (HIV) burden on cancer risk is not fully understood, particularly in the context of antiretroviral treatment (ART) availability. We examined national cancer trends and excess cancer risk in people living with HIV (PLHIV) compared to those who are HIV-negative.MethodsWe used probabilistic record linkage to match cancer records provided by the National Cancer Registry to HIV data provided by the National Health Laboratory Service (NHLS). We also used text search of specific HIV terms from the clinical section of pathology reports to determine HIV status of cancer patients. We used logistic and Joinpoint regression models to evaluate the risk and trends in cancers in PLHIV compared to HIV-negative patients from 2004 to 2014. In sensitivity analysis, we used inverse probability weighting (IPW) to correct for possible selection bias.ResultsA total of 329,208 cancer cases from public sector laboratories were reported to the NCR from 2004 to 2014 with the HIV status known for 95,279 (28.9%) cancer cases. About 50% of all the female cancer cases (n = 30,486) with a known status were HIV-positive. PLHIV were at higher risk of AIDS-defining cancers (Kaposi sarcoma [adjusted OR:134, 95% CI:111–162], non-Hodgkin lymphoma [adjusted OR:2.73, 95% CI:2.56–2.91] and, cervix [adjusted OR:1.70, 95% CI:1.63–1.77], conjunctival cancer [adjusted OR:21.5, 95% CI:16.3–28.4] and human papilloma virus (HPV) related cancers (including; penis [adjusted OR:2.35, 95% CI:1.85–2.99], and vulva [adjusted OR:1.94, 95% CI:1.67–2.25]) compared to HIV-negative patients. Analysis using the IPW population yielded comparable results.ConclusionThere is need for improved awareness and screening of conjunctival cancer and HPV-associated cancers at HIV care centres. Further research and discussion is warranted on inclusive HPV vaccination in PLHIV.

Continental drift? Do European clinical genetic testing laboratories have a patent problem?

Recent US Supreme Court decisions have invalidated patent claims on isolated genomic DNA, and testing methods that applied medical correlations using conventional techniques. As a consequence, US genetic testing laboratories have a relatively low risk of infringing patents on naturally occurring DNA or methods for detecting genomic variants. In Europe, however, such claims remain patentable, and European laboratories risk infringing them. We report the results from a survey that collected data on the impact of patents on European genetic testing laboratories. The results indicate that the proportion of European laboratories that have refrained from providing associated testing services owing to patent protection has increased over the last decade (up from 7% in 2008 to 15% in 2017), and that the non-profit sector was particularly strongly affected (up from 4% in 2008 to 14% in 2017). We renew calls for more readily available legal support to help public sector laboratories deal with patent issues, but we do not recommend aligning European law with US law at present. Watchful monitoring is also recommended to ensure that patents do not become a greater hindrance for clinical genetic testing laboratories.

Triple Helix of University–Industry–Government Relations in Japan: Transitions of Collaborations and Interactions

Japan’s stringent university regulations were considerably relaxed after 1998. This paper’s analysis of Japan clarifies changes in the collaborations and interactions between universities, industries, and governments before and after this deregulation. A historical case study with the triple helix framework is applied; it uses the ‘triple helix’ for modelling the dynamics of university–industry–government relations. Most studies that use the triple helix model focus on university collaborations, while this study examines the whole range of university–industry–government collaborations. The results show that the collaborations which lead the development of university–industry–government relations, as well as the scope of collaborations, change in response to reforms in regulations. Industry–government collaboration led the development of university–industry–government relations before deregulation, and university–industry collaboration did so after deregulation. Though university–industry–government relations continue to develop, the scope of industry–government collaboration decreases because of deregulation. We interpret these factual findings in line with the triple helix model. We discover the characteristic development process of the triple helix model; it has a period wherein the triple helix develops under the prominent role of the government. Two possible reasons could be cited for this process: first, there were stringent regulations on university–industry collaborations; and second, industry–government collaborations were active through public-sector laboratories which were widespread in Japan.

Antimicrobial Resistance Surveillance in Typhoidal Salmonella in Ahmedabad in an Era of Global Antimicrobial Resistance Surveillance Systems.

Introduction:India possibly carries the highest burden of antimicrobial resistant typhoidal salmonellae in the world. We report on the health-care ecosystem that produces data on antimicrobial resistance (AMR) testing and the resistance patterns of typhoidal Salmonella isolates in the city of Ahmedabad.Materials and Methods:Through municipality records and internet searches, we identified 1696 private and 83 public laboratories in the city; 4 medical colleges, 4 health-care institution attached laboratories, and 4 corporate laboratories (CLs) were performing culture and antibiotic sensitivity testing (AST), but only 2 medical colleges and 1 CL shared their data with us. There was considerable variation in culturing and sensitivity testing methodology across laboratories.Results:Out of 51,260 blood cultures, Salmonella isolates were detected in only 146 (0.28%). AST was conducted on 124 isolates, of which 67 (54%) were found resistant. Multidrug resistance was absent. Concurrent resistance to more than one antibiotic was very high, 88%, among the 67 resistant isolates. Ciprofloxacin resistance varied widely between the private and public sector laboratories. Notably, isolates from the private sector laboratory showed complete resistance to azithromycin.Conclusions:High resistance to ciprofloxacin and azithromycin observed in Ahmedabad may be due to the increased use of these two antibiotics in the public and private sectors, respectively. The need of the hour is to identify a representative sample of laboratories from both the public and the private sectors and encourage them to participate in the national AMR surveillance network.

Antimicrobial resistance surveillance in the South African public sector

Electronic surveillance for antimicrobial resistance was established in 2013 for public sector laboratories and released annually. This article reports susceptibility data on ESKAPE pathogens for 2016.

Antimicrobial resistance surveillance in the South African public sector

Electronic surveillance for antimicrobial resistance was established in 2013 for public sector laboratories and released annually. This article reports susceptibility data on ESKAPE pathogens for 2016.

Contamination with HIV antibody may be responsible for false positive results in specimens tested on automated platforms running HIV 4th generation assays in a region of high HIV prevalence.

IntroductionIn South Africa where the prevalence of HIV infection is very high, 4th generation HIV antibody/p24 antigen combo immunoassays are the tests of choice for laboratory based screening. Testing is usually performed in clinical pathology laboratories on automated analysers. To investigate the cause of false positive results on 4th generation HIV testing platforms in public sector laboratories, the performance of two automated platforms was compared in a clinical pathology setting, firstly on routine diagnostic specimens and secondly on known sero-negative samples.MethodsFirstly, 1181 routine diagnostic specimens were sequentially tested on Siemens and Roche automated 4th generation platforms. HIV viral load, western blot and follow up testing were used to determine the true status of inconclusive specimens. Subsequently, known HIV seronegative samples from a single donor were repeatedly tested on both platforms and an analyser was tested for surface contamination with HIV positive serum to identify how suspected specimen contamination could be occurring.ResultsSerial testing of diagnostic specimens yielded 163 weakly positive or discordant results. Only 3 of 163 were conclusively shown to indicate true HIV infection. Specimen contamination with HIV antibody was suspected, based on the following evidence: the proportion of positive specimens increased on repeated passage through the analysers; viral loads were low or undetectable and western blots negative or indeterminate on problem specimens; screen negative, 2nd test positive specimens tested positive when reanalysed on the screening assay; follow up specimens (where available) were negative. Similarly, an increasing number of known negative specimens became (repeatedly) sero-positive on serial passage through one of the analysers. Internal and external analyser surfaces were contaminated with HIV serum, evidence that sample splashes occur during testing.ConclusionsDue to the extreme sensitivity of these assays, contamination with minute amounts of HIV antibody can cause a negative sample to test positive. Better contamination control measures are needed on analysers used in clinical pathology environments, especially in regions where HIV sero-prevalence is high.

Cross reaction and forensic comparison of blood testing done by private and public sector laboratories

Blood evidence consists of one of the most important forensic pieces. However, it is not always easy to identify a stain as blood. The best and fastest way of doing so, is by using rapid screening derived from immunochromatographic tests to spot hemoglobin. However, cross reaction between species might be an issue since hemoglobin of other animals could be present, especially considering crimes against fauna, outdoor crime scenes with an easy access for animals, and human and domestic animal trauma cases. According to the particular structure in each country there are private and/or public laboratories working in this field. Methods and resources from private and public sectors are different, and procedures also differ from country to country. The main objective of our work was to validate the presence of human blood using interspecific samples and the criteria defined by each lab using rapid blood detection test kits from the public sector related to forensic analysis in Brazil and from the private sector in Germany. As a secondary goal, we have evaluated sensibility, the Hook Effect and pH effect in some commercially available kits. Our results showed that the tests carried out are suitable for the detection of human blood in forensic samples using methods commonly employed in the public and private sectors.

The Epidemiology of Meningitis among Adults in a South African Province with a High HIV Prevalence, 2009-2012.

IntroductionMeningitis is a major cause of mortality in southern Africa. We aimed to describe the aetiologies and frequencies of laboratory-confirmed fungal and bacterial meningitis among adults in a South African province with an 11% HIV prevalence, over 4 years.MethodsWe conducted a retrospective, observational study of secondary laboratory data, extracted on all cerebrospinal fluid (CSF) specimens submitted to public-sector laboratories in Gauteng province from 2009 through 2012. We calculated cause-specific incidence rates in the general and HIV-infected populations and used Poisson regression to determine if trends were significant.ResultsWe identified 11,891 (10.7%) incident cases of meningitis from 110,885 CSF specimens. Cryptococcal meningitis, tuberculous meningitis and pneumococcal meningitis accounted for 62.3% (n = 7,406), 24.6% (n = 2,928) and 10.1% (n = 1,197) of cases over the four-year period. The overall incidence (cases per 100,000 persons) of cryptococcal meningitis declined by 23% from 24.4 in 2009 to 18.7 in 2012 (p <0.001) and decreased by 19% among HIV-infected persons from 178.2 to 144.7 (p <0.001). Tuberculous meningitis decreased by 40% from 11.3 in 2009 to 6.8 in 2012 (p <0.001) and decreased by 36% among HIV-infected persons from 54.4 to 34.9 (p <0.001). Pneumococcal meningitis decreased by 41% from 4.2 in 2009 to 2.5 in 2012 (p <0.001) and decreased by 38% among HIV-infected persons from 28.0 to 17.5 (p <0.001). Among cases of other bacterial meningitis (248/11,891, 2.1%), Neisseria meningitidis (n = 93), Escherichia coli (n = 72) and Haemophilus influenzae (n = 20) were the most common organisms identified.ConclusionsIn this high HIV-prevalence province, cryptococcal meningitis was the leading cause of laboratory-confirmed meningitis among adults. Over a 4-year period, there was a significant decrease in incidence of cryptococcal, tuberculous and pneumococcal meningitis. This coincided with expansion of the national antiretroviral treatment programme, enhanced tuberculosis control programme and routine childhood immunisation with pneumococcal conjugate vaccines.

Using standard and institutional mentorship models to implement SLMTA in Kenya.

BackgroundKenya is home to several high-performing internationally-accredited research laboratories, whilst most public sector laboratories have historically lacked functioning quality management systems. In 2010, Kenya enrolled an initial eight regional and four national laboratories into the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme. To address the challenge of a lack of mentors for the regional laboratories, three were paired, or ‘twinned’, with nearby accredited research laboratories to provide institutional mentorship, whilst the other five received standard mentorship.ObjectivesThis study examines results from the eight regional laboratories in the initial SLMTA group, with a focus on mentorship models.MethodsThree SLMTA workshops were interspersed with three-month periods of improvement project implementation and mentorship. Progress was evaluated at baseline, mid-term, and exit using the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) audit checklist and scores were converted into a zero- to five-star scale.ResultsAt baseline, the mean score for the eight laboratories was 32%; all laboratories were below the one-star level. At mid-term, all laboratories had measured improvements. However, the three twinned laboratories had increased an average of 32 percentage points and reached one to three stars; whilst the five non-twinned laboratories increased an average of 10 percentage points and remained at zero stars. At exit, twinned laboratories had increased an average 12 additional percentage points (44 total), reaching two to four stars; non-twinned laboratories increased an average of 28 additional percentage points (38 total), reaching one to three stars.ConclusionThe partnership used by the twinning model holds promise for future collaborations between ministries of health and state-of-the-art research laboratories in their regions for laboratory quality improvement. Where they exist, such laboratories may be valuable resources to be used judiciously so as to accelerate sustainable quality improvement initiated through SLMTA.

Testing-adjusted chlamydia notification trends in New South Wales, Australia, 2000 to 2010.

Between 2005 and 2010, Australian notification rates for chlamydia infection increased by 64% from 203 to 333 per 100 000 population. Interpreting this trend is difficult without examining rates and local patterns of testing. We examined the effect of adjusting for local testing rates on chlamydia notification trends in New South Wales (NSW), Australia from 2000 to 2010. We used testing data for NSW residents for Medicare Benefits Schedule items for chlamydia from 1 July 1999 to 30 June 2005 and 1 July 2007 to 30 June 2010. This data set excluded testing by public sector laboratories. We also obtained laboratory-confirmed genital chlamydia notifications in NSW residents for 1 July 1999 to 30 June 2010 and excluded notifications from public laboratories. We used negative binomial regression to assess trends in chlamydia notification rates by age and sex after adjusting for local government area (LGA)-level Medicare-funded testing rates, socioeconomic disadvantage, remoteness and Medicare provider density. Testing-adjusted rates of chlamydia notifications declined by 5.2% per annum (rate ratio [RR] = 0.95, 95% confidence interval (CI) = 0.93-0.96) for women overall, and 2.3% (RR = 0.98, 95% CI = 0.96-1.00) and 5.0% per annum (RR = 0.95, 95% CI = 0.93-0.98) for men in LGAs with moderate and high densities of Medicare providers, respectively. Notification rates remained stable for men in low Medicare provider density LGAs (RR = 1.01, 95% CI = 0.96-1.07). It is likely that increased testing for chlamydia has driven increases in chlamydia notification in NSW over the last decade. Notification data provide no evidence for a general increase in the prevalence of chlamydia in the NSW community for this period. Notification-based chlamydia surveillance should be routinely adjusted for local testing rates.

Evolutionary Dynamics of 2009 Pandemic Influenza A Virus Subtype H1N1 in South Africa During 2009–2010

The 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09) was first detected in June 2009 in South Africa and later resulted in extensive transmission throughout Africa. Established routine surveillance programs and collaboration between private and public sector laboratories allowed for comprehensive molecular epidemiological and antigenic investigation of the first and second waves of 2009-2010 pandemic influenza in South Africa. We used reverse-transcription polymerase chain reaction to screen for influenza virus in 9792 specimens recovered during 2009 and 6915 specimens recovered during 2010 from inpatients and outpatients with influenza-like illness or severe acute respiratory illness symptoms identified by surveillance programs. Influenza-positive specimens were subjected to genetic and antigenic characterization. Bayesian and maximum likelihood analyses of the hemagglutinin genes of 96 A(H1N1)pdm09 strains were used for molecular epidemiological investigations. Hemagglutination inhibition assays and sequencing of the PB2 and neuraminidase genes were used to investigate pathogenicity and resistance mutations. The A(H1N1)pdm09 epidemic occurred as a second epidemic peak following seasonal influenza A virus subtype H3N2 cases in 2009 and in 2010. Progressive drift away from the A/California/7/2009 vaccine strain was observed at both the nucleotide and amino acid level, with 2010 strains clustering separate to 2009 strains. A few unique clusters of amino acid changes in severe cases were identified, but most strains were antigenically similar to the vaccine strain, and no resistance or known pathogenicity mutations were detected. Despite limited drift observed over the 2 seasons in South Africa, circulating A(H1N1)pdm09 strains remained antigenically similar to strains identified in other northern and southern hemisphere countries from 2010 and 2011.