Mutations on COVID-19 diagnostic targets

Abstract

Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic when there is neither a preventive vaccine nor a specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It will cause a large number of false-positive and false-negative tests if currently used diagnostic reagents are undermined. Based on genotyping of 31,421 SARS-CoV-2 genome samples collected up to July 23, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have undergone mutations. We further show that SARS-CoV-2 has the most mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been widely used around the world to diagnose COVID-19. To understand whether SARS-CoV-2 genes have mutated unevenly, we have computed the mutation rate and mutation h-index of all SARS-CoV-2 genes, indicating that the N gene is one of the most non-conservative genes in the SARS-CoV-2 genome. We show that due to human immune response induced APOBEC mRNA (C > T) editing, diagnostic targets should also be selected to avoid cytidines. Our findings might enable optimally selecting the conservative SARS-CoV-2 genes and proteins for the design and development of COVID-19 diagnostic reagents, prophylactic vaccines, and therapeutic medicines. AVAILABILITY: Interactive real-time online Mutation Tracker.

Fig. 1

The scatter plot of six distinct clusters in the world. The light blue, dark blue, green, red, pink, and yellow represent Cluster I, Cluster II, Cluster III, Cluster IV, Cluster V, and Cluster VI, respectively. The base color of each country is decided by the color of the dominated Cluster. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Illustration of mutation positions and frequencies on the primer and/or probes of RX7038-N1 primer (Fw), RX7038-N1 primer (Rv), RX7038-N2 primer (Fw), RX7038-N2 primer (Rv), RX7038-N3 primer (Fw), RX7038-N3 primer (Rv), N1-U.S.-P, N2-U.S.-P, N3-U.S.-P, N-Sarbeco-F.

Fig. 3

Illustration of mutation positions and frequencies on the primer and/or probes of N-Sarbeco-P, N-Sarbeco-R, N-China-F, N-China-R, N-China-P, N-HK-F, N-HK-R, N-JP-F, N-JP-P, N-TL-F.

Fig. 4

Illustration of mutation positions and frequencies on the primer and/or probes of N-TL-R, N-TL-P, E-Sarbeco-F1, E-Sarbeco-R2, E-Sarbeco-P1, nCoV-IP2-12669Fw, nCoV-IP2-12759Rv, nCoV-IP2-12696bProbe(+), nCoV-IP4-14059Fw, nCoV-IP4-14146Rv.

Fig. 5

Illustration of mutation positions and frequencies on the primer and/or probes of nCoV-IP4-14084Probe(+), RdRP-SARSr-F2, RdRP-SARSr-R1, RdRP-SARSr-P2, ORF1ab-China-F, ORF1ab-China-R, ORF1ab-China-P, ORF1b-nsp14-HK-F, ORF1b-nsp14-HK-R, ORF1b-nsp14-HK-P.

Fig. 6

Illustration of mutation positions and frequencies on the primer and/or probes of SC2-F, SC2-R,NIID_WH-1_F501,NIID_WH-1_R913, NIID_WH-1_F509, NIID_WH-1_R85, NIID_WH-1_Seq F519, NIID_WH-1_Seq R840, WuhanCoV-spk1-f, WuhanCoV-spk1-r, NIID_WH-1_F24381, NIID_WH-1_R24873, NIID_WH-1_Seq F24383, NIID_WH-1_Seq R24865.

Fig. 7

The pie chart of the distribution of 12 different types of mutations.

Fig. 8

Illustration of SARS-CoV-2 mutation ratio and mutation h-index one various genes. For each gene, its length is given in the mutation ratio bar while the number of unique SNPs is given in the h-index bar.