COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 19 (COVID-19), is a single-stranded positive-sense ribonucleic acid (RNA) virus that typically undergoes one to two single nucleotide mutations per month. COVID-19 continues to spread globally, with case fatality and test positivity rates often linked to locally circulating strains of SARS-CoV-2. Furthermore, mutations in this virus, in particular those occurring in the spike protein (involved in the virus binding to the host epithelial cells) have potential implications in current vaccination efforts. In Rwanda, more than twenty thousand cases have been confirmed as of March 14th 2021, with a case fatality rate of 1.4% and test positivity rate of 2.3% while the recovery rate is at 91.9%. Rwanda started its genomic surveillance efforts, taking advantage of pre-existing research projects and partnerships, to ensure early detection of SARS-CoV-2 variants and to potentially contain the spread of variants of concern (VOC). As a result of this initiative, we here present 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in the country from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the newly emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the VOCs, B.1.1.7 and B.1.351, among incoming travelers tested at Kigali International Airport. We also discuss the potential impact of COVID-19 control measures established in the country to control the spread of the virus. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations during the time frame of interest. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences are currently available or that no longer report positive cases. Our results point to the importance of systematically screening all incoming travelers, regardless of the origin of their travels as well as regional considerations for durable response to COVID-19.

Background: Globally, over 325 and 170 million people are infected with hepatitis B virus (HBV) and hepatitis C virus (HCV), respectively. If untreated, these infections can progress to cirrhosis or hepatocellular carcinoma. The primary aim of this study was to determine the prevalence, genetic diversity, and factors associated with HBV and HCV among couples attending antenatal care in rural Rwanda. Methods: This was a cross-sectional survey of HBV and HCV seroprevalence. Study participants were administered a brief structured questionnaire to obtain information on sociodemographic and behavioural risk factors for HBV and HCV. Participant blood samples were screened for hepatitis B surface antigen (HBsAg) and anti-HCV antibodies (anti-HCV) using rapid diagnostic kits; confirmatory testing was done by enzyme immunoassay and nucleic acid tests. HBV genotypes were determined using nested polymerase chain reaction; HCV genotypes were determined by reverse transcriptase PCR followed by hybridisation with sequence-specific oligonucleotides. Statistical associations between risk factors and infection status were determined using Chi-square tests and bivariate logistic regression. Results: In total, 220 individuals participated in the study. This includes 110 pregnant women and 110 male partners who were attending antenatal care at Gitare and Cyanika health centres. Two participants (0.9%) had serological evidence of HBV infection, and 4 participants (1.8%) were infected with HCV. HBV genotype A accounted for all HBV infections; HCV genotype 4 accounted for all HCV infections. None of the assessed factors were associated with HBV infection while occupation type and scarification were significantly associated with HCV infection (P values were .03 and <.01 respectively). All cases of infection were discordant with their respective partners. Conclusion: Prevalence rates of HBsAg and anti-HCV are low in couples attending antenatal clinics in rural Rwanda. Consideration should be given to interventions aimed at reducing the risk of transmission in discordant couples and infants of infected mothers.

Background: Globally, over 325 and 170 million people are infected with hepatitis B virus (HBV) and hepatitis C virus (HCV), respectively. If untreated, these infections can progress to cirrhosis or hepatocellular carcinoma. The primary aim of this study was to determine the prevalence, genetic diversity, and factors associated with HBV and HCV among couples attending antenatal care in rural Rwanda. Methods: This was a cross-sectional survey of HBV and HCV seroprevalence. Study participants were administered a brief structured questionnaire to obtain information on sociodemographic and behavioural risk factors for HBV and HCV. Participant blood samples were screened for hepatitis B surface antigen (HBsAg) and anti-HCV antibodies (anti-HCV) using rapid diagnostic kits; confirmatory testing was done by enzyme immunoassay and nucleic acid tests. HBV genotypes were determined using nested polymerase chain reaction; HCV genotypes were determined by reverse transcriptase PCR followed by hybridisation with sequence-specific oligonucleotides. Statistical associations between risk factors and infection status were determined using Chi-square tests and bivariate logistic regression. Results: In total, 220 individuals participated in the study. This includes 110 pregnant women and 110 male partners who were attending antenatal care at Gitare and Cyanika health centres. Two participants (0.9%) had serological evidence of HBV infection, and 4 participants (1.8%) were infected with HCV. HBV genotype A accounted for all HBV infections; HCV genotype 4 accounted for all HCV infections. None of the assessed factors were associated with HBV infection while occupation type and scarification were significantly associated with HCV infection (P values were .03 and <.01 respectively). All cases of infection were discordant with their respective partners. Conclusion: Prevalence rates of HBsAg and anti-HCV are low in couples attending antenatal clinics in rural Rwanda. Consideration should be given to interventions aimed at reducing the risk of transmission in discordant couples and infants of infected mothers.