Early Detection and Surveillance of the SARS-CoV-2 Variant BA.2.86 — Worldwide, July–October 2023

Discussion

Despite decreased SARS-CoV-2 sequencing resulting from changing COVID-19 testing practices, U.S. genomic surveillance systems detected BA.2.86, a novel SARS-CoV-2 lineage circulating at very low levels. Using multiple surveillance systems enhanced early detection, tracking, and characterization of emerging SARS-CoV-2 variants. The first U.S. detection of BA.2.86 was identified through a health care facility specimen that was sent to CDC by the state laboratory for isolation and further characterization. Successful virus isolation at CDC allowed for the sharing of BA.2.86 isolates with other laboratories. TGS detected BA.2.86 in a sample from a traveler returning to the United States who was likely infected while abroad (5). NWSS facilitated BA.2.86 early warning in additional areas, and wastewater surveillance was a leading indicator in Ohio where BA.2.86 was identified 9 days before a respiratory sequence was reported in the same area.

Specimen collection dates support that BA.2.86 was likely beginning to circulate in the United States before the end of July 2023. Currently, BA.2.86 has not become predominant but is likely circulating across the United States at low levels. Preliminary laboratory research findings indicate that existing antibodies from previous SARS-CoV-2 infection or vaccination are effective in neutralizing BA.2.86 but real-world human outcome data are also needed to better understand the impacts of preexisting immunity^¶¶¶,**** (6).

Early warning of SARS-CoV-2 variant detection enables timely assessments of risk, mobilization of resources, clear and timely communication, and coordinated public health action (7). The complementary surveillance systems provided critical data and specimens for culture, treatment effectiveness evaluation, and will facilitate the development of other treatments, as needed. Integrating pathogen genomic sequencing throughout the different surveillance system components added important molecular resolution for tracking variant emergence and transmission dynamics. Digital public health surveillance can provide a signal to enhance and focus other surveillance systems toward detection of new variants. Global information-sharing and partnerships for early warning also played an important role; these systems and partnerships are crucial in light of the decrease in specimen sequencing.

Other existing surveillance systems^†††† might become critical to monitoring the impacts of BA.2.86. If circulation increases, epidemiologic data related to relative transmissibility, disease severity, and vaccine and therapeutic effectiveness will be important to understanding this variant’s impact on human health. If BA.2.86 exceeds 1% of circulating variants within the United States, it will be reported through CDC’s Nowcast estimates over time and by region. If BA.2.86 circulation expands to represent a significant proportion of circulating variants in the United States, other complementary COVID-19 surveillance systems that capture detailed laboratory- and patient-level data can be tracked in parallel to understand epidemiologic impacts. If new data become available that result in heightened concern, CDC can launch epidemiologic field studies on transmissibility and severity.

Limitations

The findings of this report are subject to at least five limitations. First, data analyzed from complementary surveillance systems included varying levels of geographic, epidemiologic, clinical, and demographic information. Links between surveillance data and epidemiologic and clinical data necessary to guide action are often missing, limiting the level of analysis performed. In addition, unequal levels of global sequencing capacity and funding also limit understanding of geographic spread. Second, digital public health surveillance methods employed both informal and formal manual data gathering, which was resource-intensive. Third, global genomic surveillance is limited by the variable lag times between specimen collection and reporting, which can impact real-time actionability. Fourth, standardized national methods for genomic sequence (or partial sequence) data reporting into different public repositories are lacking; this limitation is especially apparent for wastewater sequences. Finally, data quality, reporting, and aggregation standards are needed for multicomponent pathogen genomic surveillance.

Implications for Public Health and Preparedness

The emergence of BA.2.86 has highlighted the importance of early detection through multiple, complementary surveillance systems involving diverse approaches, populations, and specimen types. These systems can be further improved by addressing timeliness, improving understanding of both the strengths and limitations of each system, and increasing cross-public health coordination and action. Leveraging, maintaining, and prioritizing these robust, multipurpose public health surveillance systems require sustained financial resources.

Early detection data are more actionable as the lag time between specimen collection and reporting of results decreases, and when more clinical and epidemiologic data are available. Innovations in pathogen testing and genomic sequencing, capacity building, and reporting systems can support earlier public health action. New technology is also needed from the private sector to offer less expensive, targeted, and more sustainable products (e.g., cheaper, faster diagnostic tests) to support the future of public health surveillance. Continuous, automated data scraping^§§§§ for early warning signs (e.g., robust event-based surveillance) can more efficiently alert health authorities of global events to guide preparation measures. Complementary surveillance systems in place for early warning can be used for other known and novel public health threats. As public health and surveillance advancements continue, the deployment of multiple innovations to strengthen early warning, preparedness, and response will be critical.