HIV-1 pretreatment and acquired antiretroviral drug resistance before tenofovir/ /lamivudine /dolutegravir (TLD) roll-out in Mozambique.

BACKGROUND: The World Health Organization (WHO) recommends that HIV treatment scale-up is accompanied by a robust assessment of drug resistance emergence and transmission. The WHO HIV Drug Resistance (HIVDR) monitoring and surveillance strategy includes HIVDR testing in adults both initiating and receiving antiretroviral therapy (ART). Due to limited information about HIVDR in Mozambique, we conducted two nationally representative surveys of adults initiating and receiving first-line ART regimes to better inform the HIV program. METHODS: We carried out a cross-sectional study between March 2017 and December 2019. Adults (older than 15 years) living with HIV (PLHIV) initiating ART or receiving first-line ART for between 9-15 months at 25 health facilities across all eleven provinces in Mozambique were included. Genotypic HIVDR was assessed on dried blood spots (DBS) when viral loads were ≥ 1000 copies/ml. Genotypic resistance for non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) was determined using the Stanford HIV database algorithm 9.5 and calibrated population resistance tool 8.1. RESULTS: Of 828 participants -enrolled, viral load (VL) testing was performed on 408 initiators and 409 ART experienced. Unsuppressed VL was found in 68.1% 419 initiators and 18.8% (77/409) of the ART experienced. Of the 278 initiators and 70 ART experienced who underwent sequencing, 51.7% (144/278) and 75.7% (53/70) were sequenced successfully. Among the new initiators, pretreatment drug resistance (PDR) for NNRTI and PI was found in 16.0% (23/144) and 1.4% (2/144) of the participants, respectively. Acquired drug resistance (ADR) was found in 56.5% (30/53) of the ART-experienced participants of whom 24.5% (13/53) were resistant to both NRTI and NNRTI. CONCLUSION: High rates of PDR and ADR for NNRTI and ADR for NRTI were observed in our study. These findings support the replacement of NNRTIs with dolutegravir (DTG) but high levels of NRTI resistance in highly treatment-experienced individuals still require attention when transitioning to new regimens. Moreover, the study underlines the need for routine VL testing and HIVDR surveillance to improve treatment management strategies.

Performance of two plasma separation devices for HIV-1 viral load measurement in primary healthcare settings.

IMPORTANCE: Burnett and HemaSpot are two novel technologies that allow whole blood collection and plasma separation and stabilization at room temperature without the need of additional equipment. Hence, these devices are potential alternatives to fresh plasma as a suitable specimen for viral load scale-up to monitor antiretroviral therapy in resource-limited settings.

Hepatitis B Virus Genotype E/A Recombinants from Blood Donors in Beira, Mozambique.

Hepatitis B virus (HBV) is endemic in many parts of sub-Saharan Africa. Here, we present 5 full-length HBV recombinant genomes from blood donors in Beira, Mozambique. The genomes are recombinants between genotypes E and A and are distantly related to one another, based on their genetic distances.

Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique.

Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflecting the first 25 months of the epidemic. The epidemic in the country was marked by four waves of infection, the first associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for most infections and deaths during the second, third, and fourth waves. Large-scale viral exchanges occurred during the latter three waves and were largely attributed to southern African origins. Not only did the country remain vulnerable to the introductions of new variants but these variants continued to evolve within the borders of the country. Due to the Mozambican health system already under constraint, and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.

Hepatitis B virus genotypes and drug resistance mutations circulating in blood donors in Beira, Mozambique.

Hepatitis B virus (HBV) infects nearly 300 million people and is the leading cause of hepatitis and hepatocellular carcinoma worldwide. Despite the high burden of HBV in sub-Saharan Africa, countries such as Mozambique have limited data available on circulating HBV genotypes and the presence of drug resistance mutations. Blood donors from Beira, Mozambique were tested for HBV surface antigen (HBsAg) and HBV DNA at the Instituto Nacional de Saúde in Maputo, Mozambique. Regardless of HBsAg status, donors with detectable HBV DNA were evaluated for HBV genotype. PCR was performed with primers amplifying a 2.1-2.2 kilobase fragment of the HBV genome. PCR products were submitted for next generation sequencing (NGS), and consensus sequences were evaluated for HBV genotype, recombination, and the presence or absence of drug resistance mutations. Of the 1281 blood donors tested, 74 had quantifiable HBV DNA. The polymerase gene could be amplified from 45 of 58 (77.6%) individuals with chronic HBV infection and 12 of 16 (75%) with occult HBV infection. Among these 57, 51 (89.5%) sequences belonged to HBV genotype A1, while 6 (10.5%) were HBV genotype E. All genotype E sequences were E/A recombinants, and clustered separately from other genotype E references. Genotype A samples had a median viral load of 637 IU/mL, while genotype E samples had a median viral load of 476,084 IU/mL. No drug resistance mutations were observed in the consensus sequences. The current study demonstrates the genotypic diversity of HBV in blood donors in Mozambique, but the absence of dominant (consensus) drug resistance mutations. Studies in other at-risk populations are essential for understanding the epidemiology, risk of liver disease, and likelihood of treatment resistance in resource-limited settings.

Prevalence of hepatitis B virus and immunity status among healthcare workers in Beira City, Mozambique.

BACKGROUND: Hepatitis B virus (HBV) infection can be prevented by vaccination. Exposure to blood or body fluids poses a high risk of transmission of HBV in health care workers (HCWs). This study aimed to determine the prevalence of markers of exposure, susceptibility, and protection to HBV infection in HCWs in Beira, Mozambique. METHODS: A cross-sectional study was conducted between June and August 2020 in Beira City, Mozambique, in HCWs based on self-administered questionnaires and blood samples. Plasma samples were tested for HBV surface antigen (HBsAg), antibodies to HBV core antigen (anti-HBc), antibodies to HBsAg (anti-HBs) and HBV viral load (HBV DNA). RESULTS: Most of the 315 HCWs in the study were nurses (125; 39.7%). Of the HCWs, 5.1% (16; 95% Confidence Interval (CI): 2.9 to 8.1%) were infected by HBV (HBsAg and/or HBV DNA positive). Occult HBV infection (OBI) (HBV DNA positive and HBsAg negative) was found in 0.3% (1; 95% CI: 0.0 to 1.8%) of participants; 27.9% (88; 95% CI: 23.1 to 33.2%) were susceptible (negative for all markers), 6.3% (20; 95% CI: 3.9 to 9.6) were immune due to natural infection (anti-HBs and anti-HBc positive only), while 60% (189; 95% CI: 54.4 to 65.5) were immune due to vaccination (anti-HBs positive only). CONCLUSION: This study showed a high intermediate prevalence of chronic hepatitis B among healthcare workers in Beira City, Central Mozambique, and one-third of healthcare workers were susceptible to HBV infection. There is a need to implement a national hepatitis B screening and vaccination strategy among healthcare workers in Mozambique.

Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibodies in the Mozambican Population: A Cross-Sectional Serologic Study in 3 Cities, July-August 2020

The extent of population exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was uncertain in many African countries during the onset of the pandemic. Methods: We conducted a cross-sectional study and randomly selected and surveyed general population and occupational groups from 6 July to 24 August 2020, in 3 cities in Mozambique. Anti-SARS-CoV-2-specific immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies were measured using a point-of-care rapid test. The prevalence was weighted for population (by age, sex, and city) and adjusted for test sensitivity and specificity. Results: A total of 21 183 participants, including 11 143 from the general population and 10 040 from occupational groups, were included across all 3 cities. General population seropositivity (IgM or IgG) prevalence was 3.0% (95% confidence interval [CI], 1.0%-6.6%) in Pemba, 2.1% (95% CI, 1.2%-3.3%) in Maputo City, and 0.9% (95% CI, .1%-1.9%) in Quelimane. The prevalence in occupational groups ranged from 2.8% (95% CI, 1.3%-5.2%) to 5.9% (95% CI, 4.3%-8.0%) in Pemba, 0.3% (95% CI, .0%-2.2%) to 4.0% (95% CI, 2.6%-5.7%) in Maputo City, and 0.0% (95% CI, .0%-.7%) to 6.6% (95% CI, 3.8%-10.5%) in Quelimane, and showed variations between the groups tested. Conclusions: In the first representative COVID-19 serosurveys in Mozambique, in mid-2020, weighted and assay-adjusted seroprevalence in 3 provincial capitals of anti-SARS-CoV-2 ranged from 0.9% to 3.0%, whereas adjusted prevalence in occupational groups ranged from 0.0% to 6.6% with variation between groups. Exposure to SARS-CoV-2 was extensive during the first pandemic wave, and transmission may have been more intense among occupational groups. These data have been of utmost importance to inform public health intervention to control and respond to the pandemic in Mozambique.

Prevalence of hepatitis B virus and immunity status among healthcare workers in Beira City, Mozambique

Background: Hepatitis B virus (HBV) infection can be prevented by vaccination. Exposure to blood or body fluids poses a high risk of transmission of HBV in health care workers (HCWs). This study aimed to determine the prevalence of markers of exposure, susceptibility, and protection to HBV infection in HCWs in Beira, Mozambique. Methods: A cross-sectional study was conducted between June and August 2020 in Beira City, Mozambique, in HCWs based on self-administered questionnaires and blood samples. Plasma samples were tested for HBV surface antigen (HBsAg), antibodies to HBV core antigen (anti-HBc), antibodies to HBsAg (anti-HBs) and HBV viral load (HBV DNA). Results: Most of the 315 HCWs in the study were nurses (125; 39.7%). Of the HCWs, 5.1% (16; 95% Confidence Interval (CI): 2.9 to 8.1%) were infected by HBV (HBsAg and/or HBV DNA positive). Occult HBV infection (OBI) (HBV DNA positive and HBsAg negative) was found in 0.3% (1; 95% CI: 0.0 to 1.8%) of participants; 27.9% (88; 95% CI: 23.1 to 33.2%) were susceptible (negative for all markers), 6.3% (20; 95% CI: 3.9 to 9.6) were immune due to natural infection (anti-HBs and anti-HBc positive only), while 60% (189; 95% CI: 54.4 to 65.5) were immune due to vaccination (anti-HBs positive only). Conclusion: This study showed a high intermediate prevalence of chronic hepatitis B among healthcare workers in Beira City, Central Mozambique, and one-third of healthcare workers were susceptible to HBV infection. There is a need to implement a national hepatitis B screening and vaccination strategy among healthcare workers in Mozambique

Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999-2018.

HIV drug resistance (HIVDR) can become a public health concern, especially in low- and middle-income countries where genotypic testing for people initiating antiretroviral therapy (ART) is not available. For first-line regimens to remain effective, levels of transmitted drug resistance (TDR) need to be monitored over time. To determine the temporal trends of TDR in Mozambique, a search for studies in PubMed and sequences in GenBank was performed. Only studies covering the pol region that described HIVDR and genetic diversity from treatment naïve patients were included. A dataset from seven published studies and one novel unpublished study conducted between 1999 and 2018 were included. The Calibrated Population Resistance tool (CPR) and REGA HIV-1 Subtyping Tool version 3 for sequences pooled by sampling year were used to determine resistance mutations and subtypes, respectively. The prevalence of HIVDR amongst treatment-naïve individuals increased over time, reaching 14.4% in 2018. The increase was most prominent for non-nucleoside reverse transcriptase inhibitors (NNRTIs), reaching 12.7% in 2018. Subtype C was predominant in all regions, but a higher genetic variability (19% non-subtype C) was observed in the north region of Mozambique. These findings confirm a higher diversity of HIV in the north of the country and an increased prevalence of NNRTI resistance among treatment naïve individuals over time.

Clinical Performance of Self-Collected Nasal Swabs and Antigen Rapid Tests for SARS-CoV-2 Detection in Resource-Poor Settings.

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3−85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3−85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2−63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5−82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings.

Clinical Performance of Self-Collected Nasal Swabs and Antigen Rapid Tests for SARS-CoV-2 Detection in Resource-Poor Settings

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3−85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3−85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2−63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5−82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings

Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibodies in the Mozambican Population: A Cross-Sectional Serologic Study in 3 Cities, July-August 2020.

BACKGROUND: The extent of population exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was uncertain in many African countries during the onset of the pandemic. METHODS: We conducted a cross-sectional study and randomly selected and surveyed general population and occupational groups from 6 July to 24 August 2020, in 3 cities in Mozambique. Anti-SARS-CoV-2-specific immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies were measured using a point-of-care rapid test. The prevalence was weighted for population (by age, sex, and city) and adjusted for test sensitivity and specificity. RESULTS: A total of 21 183 participants, including 11 143 from the general population and 10 040 from occupational groups, were included across all 3 cities. General population seropositivity (IgM or IgG) prevalence was 3.0% (95% confidence interval [CI], 1.0%-6.6%) in Pemba, 2.1% (95% CI, 1.2%-3.3%) in Maputo City, and 0.9% (95% CI, .1%-1.9%) in Quelimane. The prevalence in occupational groups ranged from 2.8% (95% CI, 1.3%-5.2%) to 5.9% (95% CI, 4.3%-8.0%) in Pemba, 0.3% (95% CI, .0%-2.2%) to 4.0% (95% CI, 2.6%-5.7%) in Maputo City, and 0.0% (95% CI, .0%-.7%) to 6.6% (95% CI, 3.8%-10.5%) in Quelimane, and showed variations between the groups tested. CONCLUSIONS: In the first representative COVID-19 serosurveys in Mozambique, in mid-2020, weighted and assay-adjusted seroprevalence in 3 provincial capitals of anti-SARS-CoV-2 ranged from 0.9% to 3.0%, whereas adjusted prevalence in occupational groups ranged from 0.0% to 6.6% with variation between groups. Exposure to SARS-CoV-2 was extensive during the first pandemic wave, and transmission may have been more intense among occupational groups. These data have been of utmost importance to inform public health intervention to control and respond to the pandemic in Mozambique.

Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibodies in the Mozambican Population: A Cross-Sectional Serologic Study in 3 Cities, July­August 2020

Background The extent of population exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was uncertain in many African countries during the onset of the pandemic. Methods We conducted a cross-sectional study and randomly selected and surveyed general population and occupational groups from 6 July to 24 August 2020, in 3 cities in Mozambique. Anti­SARS-CoV-2­specific immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies were measured using a point-of-care rapid test. The prevalence was weighted for population (by age, sex, and city) and adjusted for test sensitivity and specificity. Results A total of 21 183 participants, including 11 143 from the general population and 10 040 from occupational groups, were included across all 3 cities. General population seropositivity (IgM or IgG) prevalence was 3.0% (95% confidence interval [CI], 1.0%­6.6%) in Pemba, 2.1% (95% CI, 1.2%­3.3%) in Maputo City, and 0.9% (95% CI, .1%­1.9%) in Quelimane. The prevalence in occupational groups ranged from 2.8% (95% CI, 1.3%­5.2%) to 5.9% (95% CI, 4.3%­8.0%) in Pemba, 0.3% (95% CI, .0%­2.2%) to 4.0% (95% CI, 2.6%­5.7%) in Maputo City, and 0.0% (95% CI, .0%­.7%) to 6.6% (95% CI, 3.8%­10.5%) in Quelimane, and showed variations between the groups tested. Conclusions In the first representative COVID-19 serosurveys in Mozambique, in mid-2020, weighted and assay-adjusted seroprevalence in 3 provincial capitals of anti­SARS-CoV-2 ranged from 0.9% to 3.0%, whereas adjusted prevalence in occupational groups ranged from 0.0% to 6.6% with variation between groups. Exposure to SARS-CoV-2 was extensive during the first pandemic wave, and transmission may have been more intense among occupational groups. These data have been of utmost importance to inform public health intervention to control and respond to the pandemic in Mozambique.

Nucleic acid testing identifies high prevalence of blood borne viruses among approved blood donors in Mozambique.

BACKGROUND: Although blood transfusion is an intervention that saves lives, it poses significant risks to the blood receivers, including the transmission of bloodborne pathogens. We aimed at determining the prevalence of Human Immunodeficiency Virus (HIV), Hepatitis B virus (HBV), and Hepatitis C virus (HCV) in candidates approved for blood donation, and in samples considered to be negative in reference blood banks in Mozambique. METHODS: A cross-sectional study was performed between November 2014 and October 2015 in Maputo and Beira cities. Demographic information was obtained from all consenting blood donors using a structured questionnaire. Plasma samples were screened for HIVAb/Ag combinations, HBsAg and Anti-HCV. Blood donors considered to be negative by serological testing were re-tested in pools of six plasma samples using nucleic acid testing (NAT). RESULTS: Most blood donors were male 2,320 (83.4%) with an age range of 18 to 34 years. The overall seroprevalence of HIV, HBV and HCV infections among blood donors approved for donation was 4.6% (127; 95% CI 3.8-5.4), 4.5% (124; 95% CI 3.7-5.3) and 0.4% (11; 95% CI 0.2-0.7), respectively. The overall frequency by NAT of HIV RNA, HBV DNA, and HCV RNA in serologically negative blood donor samples was 2.6 per 1000 blood donors (7; 95% CI 1.1-5.4); 12.5 per 1000 blood donors (33; 95% CI 8.6-17.5) and 2.6 per 1000 blood donors (6; 95% CI 1.0-5.7), respectively. CONCLUSION: Our results show high seroprevalence of HIV and HBV infections in blood donors approved for donation, and high frequency of molecular biomarkers of HIV, HBV, and HCV in blood considered to be safe. These results suggest the need for a new blood screening policy in Mozambique, including the use of NAT to detect infectious blood donations during the immunologically negative window.

Nucleic acid testing identifies high prevalence of blood borne viruses among approved blood donors in Mozambique

Background: Although blood transfusion is an intervention that saves lives, it poses significant risks to the blood receivers, including the transmission of bloodborne pathogens. We aimed at determining the prevalence of Human Immunodeficiency Virus (HIV), Hepatitis B virus (HBV), and Hepatitis C virus (HCV) in candidates approved for blood donation, and in samples considered to be negative in reference blood banks in Mozambique. Methods: A cross-sectional study was performed between November 2014 and October 2015 in Maputo and Beira cities. Demographic information was obtained from all consenting blood donors using a structured questionnaire. Plasma samples were screened for HIVAb/Ag combinations, HBsAg and Anti-HCV. Blood donors considered to be negative by serological testing were re-tested in pools of six plasma samples using nucleic acid testing (NAT). Results: Most blood donors were male 2,320 (83.4%) with an age range of 18 to 34 years. The overall seroprevalence of HIV, HBV and HCV infections among blood donors approved for donation was 4.6% (127; 95% CI 3.8-5.4), 4.5% (124; 95% CI 3.7-5.3) and 0.4% (11; 95% CI 0.2-0.7), respectively. The overall frequency by NAT of HIV RNA, HBV DNA, and HCV RNA in serologically negative blood donor samples was 2.6 per 1000 blood donors (7; 95% CI 1.1-5.4); 12.5 per 1000 blood donors (33; 95% CI 8.6-17.5) and 2.6 per 1000 blood donors (6; 95% CI 1.0-5.7), respectively. Conclusion: Our results show high seroprevalence of HIV and HBV infections in blood donors approved for donation, and high frequency of molecular biomarkers of HIV, HBV, and HCV in blood considered to be safe. These results suggest the need for a new blood screening policy in Mozambique, including the use of NAT to detect infectious blood donations during the immunologically negative window.

Stability of HIV-1 Nucleic Acids in cobas Plasma Separation Card for Viral Load Measurement.

OBJECTIVES: Our study aimed to evaluate the stability of human immunodeficiency virus 1 (HIV-1) RNA on cobas plasma separation card (PSC) specimens for viral load (VL) testing after being exposed to varied temperatures and storage times. METHODS: For this purpose, venous PSC specimens were collected and stored at 25ºC to 42ºC for a period of up to 28 days. Plasma VL at baseline was used as reference, against which PSC VL was compared at different time points. RESULTS: From the 30 patients included in the study, 600 PSC and 30 fresh plasma specimens were obtained. Plasma VL at baseline was fewer than 1,000 copies/mL in 16 patients, and 99.4% of PSCs from these patients yielded nonquantifiable VL at all temperature ranges and time points. During the study period, minor variation of VL was observed in PSCs obtained from 13 patients with plasma VL fewer than 1,000 copies/mL at baseline. For the patient with plasma VL at 1,000 copies/mL, the PSC VL varied from undetectable to 1,670 copies/mL. CONCLUSIONS: Our results show minor variation of VL in PSC specimens in the study conditions. HIV RNA is stable in PSCs exposed to high temperatures for up to 28 days.

Stability of HIV-1 Nucleic Acids in cobas Plasma Separation Card for Viral Load Measurement

Objectives: Our study aimed to evaluate the stability of human immunodeficiency virus 1 (HIV-1) RNA on cobas plasma separation card (PSC) specimens for viral load (VL) testing after being exposed to varied temperatures and storage times. Methods: For this purpose, venous PSC specimens were collected and stored at 25ºC to 42ºC for a period of up to 28 days. Plasma VL at baseline was used as reference, against which PSC VL was compared at different time points. Results: From the 30 patients included in the study, 600 PSC and 30 fresh plasma specimens were obtained. Plasma VL at baseline was fewer than 1,000 copies/mL in 16 patients, and 99.4% of PSCs from these patients yielded nonquantifiable VL at all temperature ranges and time points. During the study period, minor variation of VL was observed in PSCs obtained from 13 patients with plasma VL fewer than 1,000 copies/mL at baseline. For the patient with plasma VL at 1,000 copies/mL, the PSC VL varied from undetectable to 1,670 copies/mL. Conclusions: Our results show minor variation of VL in PSC specimens in the study conditions. HIV RNA is stable in PSCs exposed to high temperatures for up to 28 days.

Evaluating the Impact of Sex-Biased Genetic Admixture in the Americas through the Analysis of Haplotype Data.

A general imbalance in the proportion of disembarked males and females in the Americas has been documented during the Trans-Atlantic Slave Trade and the Colonial Era and, although less prominent, more recently. This imbalance may have left a signature on the genomes of modern-day populations characterised by high levels of admixture. The analysis of the uniparental systems and the evaluation of continental proportion ratio of autosomal and X chromosomes revealed a general sex imbalance towards males for European and females for African and Indigenous American ancestries. However, the consistency and degree of this imbalance are variable, suggesting that other factors, such as cultural and social practices, may have played a role in shaping it. Moreover, very few investigations have evaluated the sex imbalance using haplotype data, containing more critical information than genotypes. Here, we analysed genome-wide data for more than 5000 admixed American individuals to assess the presence, direction and magnitude of sex-biased admixture in the Americas. For this purpose, we applied two haplotype-based approaches, ELAI and NNLS, and we compared them with a genotype-based method, ADMIXTURE. In doing so, besides a general agreement between methods, we unravelled that the post-colonial admixture dynamics show higher complexity than previously described.

Putative pathogen-selected polymorphisms in the PKLR gene are associated with mycobacterial susceptibility in Brazilian and African populations.

Pyruvate kinase (PK), encoded by the PKLR gene, is a key player in glycolysis controlling the integrity of erythrocytes. Due to Plasmodium selection, mutations for PK deficiency, which leads to hemolytic anemia, are associated with resistance to malaria in sub-Saharan Africa and with susceptibility to intracellular pathogens in experimental models. In this case-control study, we enrolled 4,555 individuals and investigated whether PKLR single nucleotide polymorphisms (SNPs) putatively selected for malaria resistance are associated with susceptibility to leprosy across Brazil (Manaus-North; Salvador-Northeast; Rondonópolis-Midwest and Rio de Janeiro-Southeast) and with tuberculosis in Mozambique. Haplotype T/G/G (rs1052176/rs4971072/rs11264359) was associated with leprosy susceptibility in Rio de Janeiro (OR = 2.46, p = 0.00001) and Salvador (OR = 1.57, p = 0.04), and with tuberculosis in Mozambique (OR = 1.52, p = 0.07). This haplotype downregulates PKLR expression in nerve and skin, accordingly to GTEx, and might subtly modulate ferritin and haptoglobin levels in serum. Furthermore, we observed genetic signatures of positive selection in the HCN3 gene (xpEHH>2 -recent selection) in Europe but not in Africa, involving 6 SNPs which are PKLR/HCN3 eQTLs. However, this evidence was not corroborated by the other tests (FST, Tajima's D and iHS). Altogether, we provide evidence that a common PKLR locus in Africans contribute to mycobacterial susceptibility in African descent populations and also highlight, for first, PKLR as a susceptibility gene for leprosy and TB.

Putative pathogen-selected polymorphisms in the PKLR gene are associated with mycobacterial susceptibility in Brazilian and African populations

Investigation of human genes under pathogen-driven selection as Plasmodium sp. has pinpointed genetic variants that participate in the adaptation to the environment and/or are related to severities of human diseases. The current study examined an example of an evolutionary trade-off in which genetic variants in the PKLR gene putatively selected for malaria resistance influence the susceptibility to mycobacterial diseases (leprosy and tuberculosis) in Brazilian population and Mozambique. A complete characterization of the biological effect of those risk variants may clarify the role of the PKLR gene in leprosy and tuberculosis. Deciphering the genetic basis of mycobacterial diseases has implications for the identification of true high-risk individuals in order to optimize screening strategies. Furthermore, the trade-off mechanism discussed in this work might occur in other central genes of immune response and biochemical pathways, controlling the susceptibility to other infectious diseases.