Rapid Genomic Surveillance Detects P.1 Variant In Japan

As the SARS-CoV-2 virus continues to replicate globally, mutations within the virus’s genome continue to emerge and spread within populations. Though many of these mutations may not impact pathogenicity, virulence, or transmissibility, a small number of these alterations in the genetic code have raised concerns with global public health experts.

In particular, mutations introduced within the s-gene, encoding the spike protein of the virus, have been monitored closely. A region at the “crown” of the spike protein (etymology for the name “coronavirus”) referred to as the receptor binding domain plays a critical role in infecting host cells; changes to this region increasing binding affinity to host cells are likely to out-compete other variants and spread more rapidly within and between individuals. The D614G mutation, referring to a change of the 614th amino acid of the spike protein from the wild type aspartic acid (D) to glycine (G), has been reporting to result in higher viral titers in the upper respiratory track, leading to increased transmissibility¹. According to Nextstrain the B.1 lineage possessing this mutation now accounts for over 99% of all circulating variants in the global population, providing convincing data that a single mutation can have profound impact on the epidemiology of this virus.

Though increased transmissibility can result in more cases and, by way of numbers, a rise in hospitalization rates, the more pressing concern is the ability to identify, monitor, and reduce the spread of those variants that have acquired novel mutations that can evade antibodies developed from prior infection or via vaccination. Characterized as “immune escape” mutations, these alterations in the protein could result in a structural change in an antibody recognition site, or epitope, on the surface of the pathogen. If enough of these mutations are introduced intro a single viral variant, this could prevent an immune system to effectively neutralize the virus.

To date, a handful of suspected “escape” mutations have been identified and, although no single one has shown an ability to evade natural or vaccine-mediated immunity, a small number of evolutionary lineages of SARS-CoV-2 have amassed several of these mutations and could accumulated even more if allowed to replicate at high rates. For this reason, several governing health agencies have classified these as variants of concern, and many countries have established a robust genomic surveillance network to identify, track, and reduce the rate of evolution through effective public health measures. Japan, for one, has shown vigilance amidst reduced travel restrictions and increased risk of global spread. Findings recently published by Hirotsu et. al. in The Journal of Infection², Yamanashi Central Hospital identified of the first P.1 lineage variant in a city of Japan.

The P.1 lineage (officially a sub-lineage of the designated B.1.1.28 Pango lineage), often referred to as the “Brazil” variant due to its presumed introduced in or around the city of Manaus has now been reported in at least 36 other countries. Concerns were raised in January when the first positive case of reinfection by P.1 was identified in Brazil³; although there have been a small number of additional reinfection cases noted in other countries, wide-spread reinfection has not been observed to date.

Similar to the first case of P.1 identified in the United States, international travel has allowed these variants to spread rapidly from continent to continent, exponentially increasing the likelihood of further evolution of the spike protein with an already notable 12 mutations. Japan has established a robust testing and surveillance system for incoming travelers, resulting in early identification of variants of concern introduced to the island nation. In fact, the P.1 sub-lineage was first identified in 4 travelers entering Japan from Manaus⁴ and immediate quarantine efforts were imposed at Tokyo airport in an effort to prevent spread to the local population.

Screening at ports of entry is an important step in surveying and catching new variants, but as the team in Yamanashi Central Hospital found, implementation of rapid genomic sequencing in the community setting is also a critical component to early identification and containment. An individual returning from travel to Brazil had tested negative for the SARS-CoV-2 virus through airport screening. However, he was later admitted to the regional hospital with a high fever and subsequently tested positive. The Genome Analysis Center at the hospital had incorporated the Ion Genexus™ Integrated Sequencer with the Ion AmpliSeq™ SARS-CoV-2 research panel to enable rapid viral sequencing. Within approximately 24 hours, the sample was identified as containing the 12 hallmark spike mutations consistent with the P.1 variant and public health measures were immediately implemented. “As the mutation detection was brief, it was possible to detect the (variant) by the next day if the test was confirmed positive. For example, samples collected (from the individual in the morning) and tested positive in the afternoon were analyzed by [the] Genexus™ system in the evening, which confirmed the Brazilian variant in the following morning” states Dr. Yosuke Hirotsu, chief investigator of the Genome Analysis Center. Dr Yosuke also notes the unique advantage of enabling complete automation of library prep, sequencing, and data analysis on a single instrument in a time where lab resources are constrained.

“By using diverse assays panels and leveraging automation of next-generation sequencing on the Genexus systems, we believe this is an era in which we can engage a number of research (labs) with limited staff”

 

To date, Japan has identified only the 5 cases mentioned of the P.1 variant, as rapid identification combined with robust public health measures continue to limit exposure of this variant to the Japanese population. Through the use of the Genexus™ System, with its automation and single-day turn around time to results, laboratories are now empowered to exploit the previously complex and time-consuming application of NGS with the simplicity and speed needed to address the rapid evolution of this virus and future pathogens.

 

 

 

1. Plante, J.A., Liu, Y., Liu, J. et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature 592, 116–121 (2021)
2. Hirotsu Y, Omata M. Discovery of a SARS-CoV-2 variant 1 from the P.1 lineage harboring K417T/E484K/N501Y mutations in Kofu, Japan. J Infect. 2021 Mar 23:S0163-4453(21)00130-4
3. Naveca, F., da Costa, C., Nascimento, V., Souza, V., Corado, A., Nascimento, F., Costa, A´ ., Duarte, D., Silva, G., Mejı´a, M., et al. (2021). SARS-CoV-2 Reinfection by the New Variant of Concern (VOC) P.1 in Amazonas, Brazil. Published online January 18, 2021.
4. “Japan finds new coronavirus variant in travelers from Brazil” Reuters, January 10, 2021