PANDEMIC DEFENSE COALITION STUDIES

Detection of SARS-CoV-2 antibodies after confirmed Omicron BA.1 and presumed BA.4/5 infections using Abbott ARCHITECT and Panbio assays

As more COVID variants evolve, it is important to determine whether tests can still detect antibody responses after infections with new variants. In this study, we detected an increase in antibody levels after Omicron BA.1/2 or BA.4/5 infection amongst a group of vaccinated healthcare workers in the US with the ARCHITECT AdviseDx SARS-CoV-2 IgG II and ARCHITECT SARS-CoV-2 IgG tests. Antibodies were also detected in these patients with the Panbio COVID-19 IgG Rapid Test Device, indicating that antibodies that develop during BA.1/2 or BA.4/5 infection in vaccinated individuals can readily be detected with all three of these tests.

Read this study in IJID Regions.

Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans

Bunyaviruses are known to cause severe illness in people, so tracking them is important for public health. In this study, a single Bangui bunyavirus infection was found through unbiased sequencing to identify all viruses present (ie ‘virome’) in patients participating in a viral diversity study in the Democratic Republic of Congo (DRC). A prototype molecular test to detect Bangui was developed and used to screen >2500 samples from DRC and neighboring countries. With no other infections found through the screening and the only other documented infection occurring 50 years earlier, this virus remains extremely rare in humans. Interestingly, genetic analysis suggests that Bangui virus remains better suited to bird or insect hosts instead of humans, meaning human infections will likely continue to be very rare.

Read this study in Virus Evolution.

The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic

With thousands of COVID variants recorded to date, we have a wealth of data to learn from about how some variants became global variants of concern (VOC) while others did not. Analysis in this study focused on the competition of two variants in Colombia in early 2021 that had an unexpected outcome – Mu vs Gamma. Although Gamma became a VOC in other Latin American countries, it never fully established itself in Colombia due to the rapid rise in Mu. Later in 2021, VOC Delta began spreading worldwide; our genetic analysis determined that Mu’s established presence in Colombia may have been responsible for keeping Delta at bay and vice versa; in most other countries VOC Delta was well established before Mu could spread, leaving Mu as a regional variant of interest instead of a VOC. These results demonstrate that regional variant trends may not be entirely predictable simply based on the spread of a VOC in other parts of the world.

Read this study in Microbiology Spectrum.

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance

With more viruses on Earth than stars in our night sky, it is critical to monitor which ones have the ability to infect people. By using an unbiased sequencing approach, our study characterized all viruses present (ie ‘virome’) in a panel of >700 people participating in a viral surveillance program. Interestingly, nine highly divergent viruses were identified that, when studied with genetic and machine learning models, were found to be most closely related to viruses found in bird and bat excrement. While there was no indication that these viruses made anyone sick, their presence highlights the importance of monitoring the viromes of many different populations to enable rapid identification of something that is clearly linked to illness.

Read this study in Viruses.

Measuring Hepatitis B pgRNA Stability using an Updated Automated HBV pgRNA Assay with Increased Sensitivity

Approximately 296 million people are living with chronic hepatitis B virus (HBV) infections and are at risk for developing liver disease or cancer. Although there is no cure for HBV, some patients may benefit from treatment and determining the duration of that treatment requires careful monitoring. In this research study, a more sensitive prototype molecular test was developed to monitor HBV RNA levels, which serve as a biomarker for how active the virus is in an infected patient. By accurately detecting lower levels of HBV RNA, the new research use only (RUO) test could be useful in refining predictions on treatment outcomes.

Read this study in Hepatology Communications.

Nationwide hepatitis C serosurvey and progress towards HCV elimination in the country of Georgia, 2021

Hepatitis C virus (HCV) causes a chronic infection that may not have symptoms until later in life when a patient develops liver disease. Fortunately, HCV infection can be cured, but only if people are diagnosed to find their infection. To work towards elimination of HCV in the country of Georgia where an estimated 58 million people are living with the virus, a screening approach has been taken to proactively find HCV patients and cure their infections. To understand how successful the program has been since it started in 2015, a nationwide survey was conducted. The results showed an overall reduction in HCV infections of 67%, indicating the program has made substantial progress. 

Read this study in The Journal of Infectious Diseases

Assessment of SARS-CoV-2 Mu Variant Emergence and Spread in Colombia

The Mu variant prevailed in Colombia in January 2021 and spread to more than 30 countries. Scientists from Abbott and the Colombia-Wisconsin One Health Consortium at the Universidad Nacional de Colombia studied 1,000+ samples to learn more about this COVID-19 variant.

Read this study in JAMA Network Open.

Seroprevalence of SARS-CoV-2 IgG Antibodies in a Healthcare Setting During the First Pandemic Wave in Senegal

Seroprevalence, or the percentage of people in a population who have antibodies, was studied in conjunction with Institut de Recherche en Sante, de Surveillance Epidémiologique et de Formation (IRESSEF) in Senegal. Plasma from healthcare clinic volunteers was tested between June and October 2020.

Read this study in IJID Regions.

A Tale of 3 Pandemics: Severe Acute Respiratory Syndrome Coronavirus 2, Hepatitis C Virus, and Human Immunodeficiency Virus in an Urban Emergency Department in Baltimore, Maryland

Scientists from multiple entities, including Johns Hopkins and Abbott, studied SARS-CoV-2, hepatitis C virus (HCV) and human immunodeficiency virus (HIV) in emergency department patients in Baltimore, Maryland to determine rates of infection and co-infection.  Sociodemographic disparities, such as race, ethnicity and poverty, were also examined.

Read this study in Open Forum Infectious Diseases.

The Early SARS-CoV-2 Epidemic in Senegal was Driven by the Local Emergence of B.1.416 and the Introduction of B.1.1.420 from Europe

The spread of COVID-19 in Senegal during the first year of the pandemic showed that there were two notable lineages of the SARS-CoV-2 virus that dominated the country. In mid-2020, a lineage called B.1.416 started in Senegal and was exported mainly to Europe. Another lineage, B.1.1.420, originated in Italy, gained mutations that made it more capable of reproducing in Senegal in late 2020, and then spread worldwide.

Read this study, conducted with Pandemic Defense Coalition partner Institut de Recherche en Sante, de Surveillance Epidémiologique et de Formation (IRESSEF), in Virus Evolution.